1
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Popelka H, Klionsky DJ. When an underdog becomes a major player: the role of protein structural disorder in the Atg8 conjugation system. Autophagy 2024; 20:2338-2345. [PMID: 38808635 PMCID: PMC11423692 DOI: 10.1080/15548627.2024.2357496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
The noncanonical ubiquitin-like conjugation cascade involving the E1 (Atg7), E2 (Atg3, Atg10), and E3 (Atg12-Atg5-Atg16 complex) enzymes is essential for incorporation of Atg8 into the growing phagophore via covalent linkage to PE. This process is an indispensable step in autophagy. Atg8 and E1-E3 enzymes are the first subset from the core autophagy protein machinery structures that were investigated in earlier studies by crystallographic analyses of globular domains. However, research over the past decade shows that many important functions in the conjugation machinery are mediated by intrinsically disordered protein regions (IDPRs) - parts of the protein that do not adopt a stable secondary or tertiary structure, which are inherently dynamic and well suited for protein-membrane interactions but are invisible in protein crystals. Here, we summarize earlier and recent findings on the autophagy conjugation machinery by focusing on the IDPRs. This summary reveals that IDPRs, originally considered dispensable, are in fact major players and a driving force in the function of the autophagy conjugation system. Abbreviation: AD, activation domain of Atg7; AH, amphipathic helix; AIM, Atg8-family interacting motif; CL, catalytic loop (of Atg7); CTD, C-terminal domain; FR, flexible region (of Atg3 or Atg10); GUV, giant unilammelar vesicles; HR, handle region (of Atg3); IDPR, intrinsically disordered protein region; IDPs: intrinsically disordered proteins; LIR, LC3-interacting region; NHD: N-terminal helical domain; NMR, nuclear magnetic resonance; PE, phosphatidylethanolamine; UBL, ubiquitin like.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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2
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Jin C, Zhu M, Ye J, Song Z, Zheng C, Chen W. Autophagy: Are Amino Acid Signals Dependent on the mTORC1 Pathway or Independent? Curr Issues Mol Biol 2024; 46:8780-8793. [PMID: 39194736 DOI: 10.3390/cimb46080519] [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: 06/26/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024] Open
Abstract
Autophagy is a kind of "self-eating" phenomenon that is ubiquitous in eukaryotic cells. It mainly manifests in the damaged proteins or organelles in the cell being wrapped and transported by the autophagosome to the lysosome for degradation. Many factors cause autophagy in cells, and the mechanism of nutrient-deficiency-induced autophagy has been a research focus. It has been reported that amino-acid-deficiency-induced cellular autophagy is mainly mediated through the mammalian rapamycin target protein complex 1 (mTORC1) signaling pathway. In addition, some researchers also found that non-mTORC1 signaling pathways also regulate autophagy, and the mechanism of autophagy occurrence induced by the deficiency of different amino acids is not precisely the same. Therefore, this review aims to summarize the process of various amino acids regulating cell autophagy and provide a narrative review on the molecular mechanism of amino acids regulating autophagy.
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Affiliation(s)
- Chenglong Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510640, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - Min Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jinling Ye
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510640, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - Zhiwen Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Chuntian Zheng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510640, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - Wei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510640, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
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3
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Lan HJ, Ran J, Wang WX, Zhang L, Wu NN, Zhao YT, Huang MJ, Ni M, Liu F, Cheng N, Nakata PA, Pan J, Whitham SA, Baker BJ, Liu JZ. Clathrin light chains negatively regulate plant immunity by hijacking the autophagy pathway. PLANT COMMUNICATIONS 2024; 5:100937. [PMID: 38693694 PMCID: PMC11369776 DOI: 10.1016/j.xplc.2024.100937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/02/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
The crosstalk between clathrin-mediated endocytosis (CME) and the autophagy pathway has been reported in mammals; however, the interconnection of CME with autophagy has not been established in plants. Here, we report that the Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopies Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants in both autoimmunity and nutrient sensitivity. Accordingly, the autophagy pathway is significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation, and degradation of GFP-ATG8h is significantly reduced in the clc2-1 clc3-1 mutant. Notably, simultaneous knockout of ATG8h and ATG8i by CRISPR-Cas9 results in enhanced resistance against Golovinomyces cichoracearum, supporting the functional relevance of the CLC2-ATG8h/8i interactions. In conclusion, our results reveal a link between the function of CLCs and the autophagy pathway in Arabidopsis.
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Affiliation(s)
- Hu-Jiao Lan
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Jie Ran
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Wen-Xu Wang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Lei Zhang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Ni-Ni Wu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Ting Zhao
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Min-Jun Huang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Min Ni
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
| | - Fen Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332000, China
| | - Ninghui Cheng
- U.S. Department of Agriculture-Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul A Nakata
- U.S. Department of Agriculture-Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianwei Pan
- College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Barbara J Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, CA 94706, USA
| | - Jian-Zhong Liu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China; Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China.
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4
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Alam JM, Maruyama T, Noshiro D, Kakuta C, Kotani T, Nakatogawa H, Noda NN. Complete set of the Atg8-E1-E2-E3 conjugation machinery forms an interaction web that mediates membrane shaping. Nat Struct Mol Biol 2024; 31:170-178. [PMID: 38057553 DOI: 10.1038/s41594-023-01132-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 09/20/2023] [Indexed: 12/08/2023]
Abstract
Atg8, a ubiquitin-like protein, is conjugated with phosphatidylethanolamine (PE) via Atg7 (E1), Atg3 (E2) and Atg12-Atg5-Atg16 (E3) enzymatic cascade and mediates autophagy. However, its molecular roles in autophagosome formation are still unclear. Here we show that Saccharomyces cerevisiae Atg8-PE and E1-E2-E3 enzymes together construct a stable, mobile membrane scaffold. The complete scaffold formation induces an in-bud in prolate-shaped giant liposomes, transforming their morphology into one reminiscent of isolation membranes before sealing. In addition to their enzymatic roles in Atg8 lipidation, all three proteins contribute nonenzymatically to membrane scaffolding and shaping. Nuclear magnetic resonance analyses revealed that Atg8, E1, E2 and E3 together form an interaction web through multivalent weak interactions, where the intrinsically disordered regions in Atg3 play a central role. These data suggest that all six Atg proteins in the Atg8 conjugation machinery control membrane shaping during autophagosome formation.
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Affiliation(s)
| | | | - Daisuke Noshiro
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Chika Kakuta
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
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5
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Farnung J, Muhar M, Liang JR, Tolmachova KA, Benoit RM, Corn JE, Bode JW. Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3. ACS CENTRAL SCIENCE 2023; 9:1025-1034. [PMID: 37252361 PMCID: PMC10214526 DOI: 10.1021/acscentsci.3c00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 05/31/2023]
Abstract
Macroautophagy is one of two major degradation systems in eukaryotic cells. Regulation and control of autophagy are often achieved through the presence of short peptide sequences called LC3 interacting regions (LIR) in autophagy-involved proteins. Using a combination of new protein-derived activity-based probes prepared from recombinant LC3 proteins, along with protein modeling and X-ray crystallography of the ATG3-LIR peptide complex, we identified a noncanonical LIR motif in the human E2 enzyme responsible for LC3 lipidation, ATG3. The LIR motif is present in the flexible region of ATG3 and adopts an uncommon β-sheet structure binding to the backside of LC3. We show that the β-sheet conformation is crucial for its interaction with LC3 and used this insight to design synthetic macrocyclic peptide-binders to ATG3. CRISPR-enabled in cellulo studies provide evidence that LIRATG3 is required for LC3 lipidation and ATG3∼LC3 thioester formation. Removal of LIRATG3 negatively impacts the rate of thioester transfer from ATG7 to ATG3.
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Affiliation(s)
- Jakob Farnung
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Matthias Muhar
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jin Rui Liang
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Kateryna A. Tolmachova
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Roger M. Benoit
- Laboratory
of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jacob E. Corn
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
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6
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Liu L, Tang Y, Zhou Z, Huang Y, Zhang R, Lyu H, Xiao S, Guo D, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Membrane Curvature: The Inseparable Companion of Autophagy. Cells 2023; 12:1132. [PMID: 37190041 PMCID: PMC10136490 DOI: 10.3390/cells12081132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Autophagy is a highly conserved recycling process of eukaryotic cells that degrades protein aggregates or damaged organelles with the participation of autophagy-related proteins. Membrane bending is a key step in autophagosome membrane formation and nucleation. A variety of autophagy-related proteins (ATGs) are needed to sense and generate membrane curvature, which then complete the membrane remodeling process. The Atg1 complex, Atg2-Atg18 complex, Vps34 complex, Atg12-Atg5 conjugation system, Atg8-phosphatidylethanolamine conjugation system, and transmembrane protein Atg9 promote the production of autophagosomal membranes directly or indirectly through their specific structures to alter membrane curvature. There are three common mechanisms to explain the change in membrane curvature. For example, the BAR domain of Bif-1 senses and tethers Atg9 vesicles to change the membrane curvature of the isolation membrane (IM), and the Atg9 vesicles are reported as a source of the IM in the autophagy process. The amphiphilic helix of Bif-1 inserts directly into the phospholipid bilayer, causing membrane asymmetry, and thus changing the membrane curvature of the IM. Atg2 forms a pathway for lipid transport from the endoplasmic reticulum to the IM, and this pathway also contributes to the formation of the IM. In this review, we introduce the phenomena and causes of membrane curvature changes in the process of macroautophagy, and the mechanisms of ATGs in membrane curvature and autophagosome membrane formation.
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Affiliation(s)
- Lei Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yu Tang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Zijuan Zhou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yuan Huang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Rui Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Hao Lyu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Shuai Xiao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Dong Guo
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Cefan Zhou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Jingfeng Tang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
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7
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Mallén-Ponce MJ, Gámez-Arcas S, Pérez-Pérez ME. Redox partner interactions in the ATG8 lipidation system in microalgae. Free Radic Biol Med 2023; 203:58-68. [PMID: 37028463 DOI: 10.1016/j.freeradbiomed.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/09/2023]
Abstract
Autophagy is a catabolic pathway that functions as a degradative and recycling process to maintain cellular homeostasis in most eukaryotic cells, including photosynthetic organisms such as microalgae. This process involves the formation of double-membrane vesicles called autophagosomes, which engulf the material to be degraded and recycled in lytic compartments. Autophagy is mediated by a set of highly conserved autophagy-related (ATG) proteins that play a fundamental role in the formation of the autophagosome. The ATG8 ubiquitin-like system catalyzes the conjugation of ATG8 to the lipid phosphatidylethanolamine, an essential reaction in the autophagy process. Several studies identified the ATG8 system and other core ATG proteins in photosynthetic eukaryotes. However, how ATG8 lipidation is driven and regulated in these organisms is not fully understood yet. A detailed analysis of representative genomes from the entire microalgal lineage revealed a high conservation of ATG proteins in these organisms with the remarkable exception of red algae, which likely lost ATG genes before diversification. Here, we examine in silico the mechanisms and dynamic interactions between different components of the ATG8 lipidation system in plants and algae. Moreover, we also discuss the role of redox post-translational modifications in the regulation of ATG proteins and the activation of autophagy in these organisms by reactive oxygen species.
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Affiliation(s)
- Manuel J Mallén-Ponce
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005, Paris, France
| | - Samuel Gámez-Arcas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092, Sevilla, Spain
| | - María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092, Sevilla, Spain.
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8
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Zhang S, Yazaki E, Sakamoto H, Yamamoto H, Mizushima N. Evolutionary diversification of the autophagy-related ubiquitin-like conjugation systems. Autophagy 2022; 18:2969-2984. [PMID: 35427200 PMCID: PMC9673942 DOI: 10.1080/15548627.2022.2059168] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two autophagy-related (ATG) ubiquitin-like conjugation systems, the ATG12 and ATG8 systems, play important roles in macroautophagy. While multiple duplications and losses of the ATG conjugation system proteins are found in different lineages, the extent to which the underlying systems diversified across eukaryotes is not fully understood. Here, in order to understand the evolution of the ATG conjugation systems, we constructed a transcriptome database consisting of 94 eukaryotic species covering major eukaryotic clades and systematically identified ATG conjugation system components. Both ATG10 and the C-terminal glycine of ATG12 are essential for the canonical ubiquitin-like conjugation of ATG12 and ATG5. However, loss of ATG10 or the C-terminal glycine of ATG12 occurred at least 16 times in a wide range of lineages, suggesting that possible covalent-to-non-covalent transition is not limited to the species that we previously reported such as Alveolata and some yeast species. Some species have only the ATG8 system (with conjugation enzymes) or only ATG8 (without conjugation enzymes). More than 10 species have ATG8 homologs without the conserved C-terminal glycine, and Tetrahymena has an ATG8 homolog with a predicted transmembrane domain, which may be able to anchor to the membrane independent of the ATG conjugation systems. We discuss the possibility that the ancestor of the ATG12 and ATG8 systems is more similar to ATG8. Overall, our study offers a whole picture of the evolution and diversity of the ATG conjugation systems among eukaryotes, and provides evidence that functional diversifications of the systems are more common than previously thought.Abbreviations: APEAR: ATG8-PE association region; ATG: autophagy-related; LIR: LC3-interacting region; NEDD8: neural precursor cell expressed, developmentally down-regulated gene 8; PE: phosphatidylethanolamine; SAMP: small archaeal modifier protein; SAR: Stramenopiles, Alveolata, and Rhizaria; SMC: structural maintenance of chromosomes; SUMO: small ubiquitin like modifier; TACK: Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota; UBA: ubiquitin like modifier activating enzyme; UFM: ubiquitin fold modifier; URM: ubiquitin related modifier.
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Affiliation(s)
- Sidi Zhang
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Euki Yazaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Saitama, Japan
| | - Hirokazu Sakamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,CONTACT Noboru Mizushima Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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9
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Song I, Hong S, Huh SU. Identification and Expression Analysis of the Solanum tuberosum StATG8 Family Associated with the WRKY Transcription Factor. PLANTS (BASEL, SWITZERLAND) 2022; 11:2858. [PMID: 36365311 PMCID: PMC9659186 DOI: 10.3390/plants11212858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Autophagy is an evolutionarily well-conserved cellular catabolic pathway in eukaryotic cells and plays an important role in cellular processes. Autophagy is regulated by autophagy-associated (ATG) proteins. Among these ATG proteins, the ubiquitin-like protein ATG8/LC3 is essential for autophagosome formation and function. In this study, the potato StATG8 family showed clade I and clade II with significantly different sequences. Expression of the StATG8 family was also increased in senescence. Interestingly, the expression of the StATG8 and other core StATG genes decreased in potato tubers as the tubers matured. The StATG8 family also responded to a variety of stresses such as heat, wounding, salicylic acid, and salt stress. We also found that some Arabidopsis WRKY transcription factors interacted with the StATG8 protein in planta. Based on group II-a WRKY, StATG8-WRKY interaction is independent of the ATG8 interacting motif (AIM) or LC3 interacting region (LIR) motif. This study showed that the StATG8 family had diverse functions in tuber maturation and multiple stress responses in potatoes. Additionally, StATG8 may have an unrelated autophagy function in the nucleus with the WRKY transcription factor.
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Affiliation(s)
| | | | - Sung Un Huh
- Department of Biological Science, Kunsan National University, Gunsan 54150, Korea
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10
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Toxoplasma TgAtg8-TgAtg3 Interaction Primarily Contributes to Apicoplast Inheritance and Parasite Growth in Tachyzoite. Microbiol Spectr 2022; 10:e0149521. [PMID: 35196797 PMCID: PMC8865545 DOI: 10.1128/spectrum.01495-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The apicoplast, which harbors key pathways involved in biosynthesis of vital metabolites, is a unique and essential nonphotosynthetic plastid organelle in apicomplexan parasites. Intriguingly, autophagy-related protein 8 (Atg8), a highly conserved eukaryotic protein, can localize to the outermost membrane of the apicoplast and modulate its inheritance in both Toxoplasma and Plasmodium parasites. The Atg8-Atg3 interaction plays a key role in Atg8 lipidation and localization, and our previously work in Toxoplasma has suggested that the core Atg8-family interacting motif (AIM) in TgAtg3, 239FADI242, and the R27 residue of TgAtg8 contribute to TgAtg8-TgAtg3 interaction in vitro. However, little is known about the function of this interaction or its importance in tachyzoite growth in Toxoplasma gondii. Here, we generated two complemented cell lines, TgAtg3F239A/I242A and TgAtg8R27E, based on the TgAtg3 and TgAtg8 conditional knockdown cell lines, respectively. We found that both mutant complemented cell lines were severely affected in terms of tachyzoite growth and displayed delayed death upon conditional knockdown of endogenous TgAtg3 or TgAtg8. Intriguingly, both complemented lines appeared to be defective in TgAtg8 lipidation and apicoplast inheritance. Moreover, we showed that the interaction of TgAtg8 and TgAtg3 is critical for TgAtg8 apicoplast localization. In addition, we found that the TgAtg3F239A/I242A complemented line exhibits an integral mitochondrial network upon ablation of endogenous TgAtg3, which is distinct from TgAtg3-depleted parasites with a fragmented mitochondrial network. Taken together, this work solidifies the contribution of the TgAtg8-TgAtg3 interaction to apicoplast inheritance and the growth of T. gondii tachyzoites. IMPORTANCEToxoplasma gondiiis a widespread intracellular parasite infecting a variety of warm-blooded animals, including humans. Current frontline treatment of toxoplasmosis suffers many drawbacks, including toxicity, drug resistance, and failure to eradicate tissue cysts, underscoring the need to identify novel drug targets for suppression or treatment of toxoplasmosis. TgAtg8 is thought to serve multiple functions in lipidation and is considered essential to the growth and development of both tachyzoites and bradyzoites. Here, we show that Toxoplasma gondii has adapted a conserved Atg8-Atg3 interaction, required for canonical autophagy in other eukaryotes, to function specifically in apicoplast inheritance. Our finding not only highlights the importance of TgAtg8-TgAtg3 interaction in tachyzoite growth but also suggests that this interaction is a promising drug target for the therapy of toxoplasmosis.
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Brennan A, Layfield R, Long J, Williams HEL, Oldham NJ, Scott D, Searle MS. An ALS-associated variant of the autophagy receptor SQSTM1/p62 reprograms binding selectivity toward the autophagy-related hATG8 proteins. J Biol Chem 2022; 298:101514. [PMID: 34929165 PMCID: PMC8762078 DOI: 10.1016/j.jbc.2021.101514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/29/2022] Open
Abstract
Recognition of human autophagy-related 8 (hATG8) proteins by autophagy receptors represents a critical step within this cellular quality control system. Autophagy impairment is known to be a pathogenic mechanism in the motor neuron disorder amyotrophic lateral sclerosis (ALS). Overlapping but specific roles of hATG8 proteins belonging to the LC3 and GABARAP subfamilies are incompletely understood, and binding selectivity is typically overlooked. We previously showed that an ALS-associated variant of the SQSTM1/p62 (p62) autophagy receptor bearing an L341V mutation within its ATG8-interacting motif (AIM) impairs recognition of LC3B in vitro, yielding an autophagy-deficient phenotype. Improvements in understanding of hATG8 recognition by AIMs now distinguish LC3-interaction and GABARAP-interaction motifs and predict the effects of L341V substitution may extend beyond loss of function to biasing AIM binding preference. Through biophysical analyses, we confirm impaired binding of the L341V-AIM mutant to LC3A, LC3B, GABARAP, and GABARAPL1. In contrast, p62 AIM interactions with LC3C and GABARAPL2 are unaffected by this mutation. Isothermal titration calorimetry and NMR investigations provided insights into the entropy-driven GABARAPL2/p62 interaction and how the L341V mutation may be tolerated. Competition binding demonstrated reduced association of the L341V-AIM with one hATG8 manifests as a relative increase in association with alternate hATG8s, indicating effective reprogramming of hATG8 selectivity. These data highlight how a single AIM peptide might compete for binding with different hATG8s and suggest that the L341V-AIM mutation may be neomorphic, representative of a disease mechanism that likely extends into other human disorders.
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Affiliation(s)
- Andrew Brennan
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Robert Layfield
- School of Life Sciences, University of Nottingham Medical School, Nottingham, UK.
| | - Jed Long
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Huw E L Williams
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Neil J Oldham
- School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Daniel Scott
- School of Life Sciences, University of Nottingham Medical School, Nottingham, UK.
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK.
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12
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Schreiber A, Collins BC, Davis C, Enchev RI, Sedra A, D'Antuono R, Aebersold R, Peter M. Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation. Mol Cell 2021; 81:5066-5081.e10. [PMID: 34798055 PMCID: PMC8693860 DOI: 10.1016/j.molcel.2021.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/23/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022]
Abstract
Autophagy is a conserved intracellular degradation pathway exerting various cytoprotective and homeostatic functions by using de novo double-membrane vesicle (autophagosome) formation to target a wide range of cytoplasmic material for vacuolar/lysosomal degradation. The Atg1 kinase is one of its key regulators, coordinating a complex signaling program to orchestrate autophagosome formation. Combining in vitro reconstitution and cell-based approaches, we demonstrate that Atg1 is activated by lipidated Atg8 (Atg8-PE), stimulating substrate phosphorylation along the growing autophagosomal membrane. Atg1-dependent phosphorylation of Atg13 triggers Atg1 complex dissociation, enabling rapid turnover of Atg1 complex subunits at the pre-autophagosomal structure (PAS). Moreover, Atg1 recruitment by Atg8-PE self-regulates Atg8-PE levels in the growing autophagosomal membrane by phosphorylating and thus inhibiting the Atg8-specific E2 and E3. Our work uncovers the molecular basis for positive and negative feedback imposed by Atg1 and how opposing phosphorylation and dephosphorylation events underlie the spatiotemporal regulation of autophagy.
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Affiliation(s)
- Anne Schreiber
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
| | - Ben C Collins
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; School of Biological Sciences, Queen's University of Belfast, 19 Chlorine Gardens, BT9 5DL Belfast, UK
| | - Colin Davis
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Radoslav I Enchev
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Angie Sedra
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy (CALM) STP, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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13
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Zhou S, Wang X, Ding J, Yang H, Xie Y. Increased ATG5 Expression Predicts Poor Prognosis and Promotes EMT in Cervical Carcinoma. Front Cell Dev Biol 2021; 9:757184. [PMID: 34901004 PMCID: PMC8655861 DOI: 10.3389/fcell.2021.757184] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/22/2021] [Indexed: 01/06/2023] Open
Abstract
Cervical cancer has the second-highest incidence and mortality of female malignancy. The major causes of mortality in patients with cervical cancer are invasion and metastasis. The epithelial–mesenchymal transition (EMT) process plays a major role in the acquisition of metastatic potential and motility. Autophagy-related genes (ARGs) are implicated in the EMT process, and autophagy exerts a dual function in EMT management at different phases of tumor progression. However, the role of specific ARGs during the EMT process has not yet been reported in cervical cancer. Based on the data from the Cancer Genome Atlas (TCGA) cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) sequencing database, we performed the prognosis analysis for those ARGs obtained from the Human Autophagy database. ATG5 was identified as the only important harmful marker influencing survival of cervical cancer patients by univariate Cox regression (HR 1.7; 95% CI: 1.0–2.8, p = 0.047), and the 5-years survival rate for the high- and low-ATG5 expression groups was 0.486 (0.375–0.631) and 0.782 (0.708–0.863), respectively. TCGA CESC methylation data showed that eight methylation sites of ATG5 could also be significantly associated with the overall survival (OS) of cervical cancer patients. Single-sample gene-set enrichment and gene functional enrichment results showed that ATG5 was correlated with some cancer-related pathways, such as phagocytosis-related genes, endocytosis-related genes, immune-related genes, EMT score, and some EMT signature-related genes. Next, cell migration and invasion assay and Western blot were applied to detect the function of ATG5 in EMT of cervical cancer. In cervical cancer cells, ATG5 knockdown resulted in attenuation of migration and invasion. The functional study showed that knockdown of ATG5 could reverse EMT process by P-ERK, P-NFκBp65, P-mTOR pathways, and so on. In conclusion, the present study implies that ATG5 was a major contributor to EMT regulation and poor prognosis in cervical cancer.
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Affiliation(s)
- Suna Zhou
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Xuequan Wang
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Jiapei Ding
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Haihua Yang
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Youyou Xie
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
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14
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Fang D, Xie H, Hu T, Shan H, Li M. Binding Features and Functions of ATG3. Front Cell Dev Biol 2021; 9:685625. [PMID: 34235149 PMCID: PMC8255673 DOI: 10.3389/fcell.2021.685625] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/24/2021] [Indexed: 12/31/2022] Open
Abstract
Autophagy is an evolutionarily conserved catabolic process that is essential for maintaining cellular, tissue, and organismal homeostasis. Autophagy-related (ATG) genes are indispensable for autophagosome formation. ATG3 is one of the key genes involved in autophagy, and its homologs are common in eukaryotes. During autophagy, ATG3 acts as an E2 ubiquitin-like conjugating enzyme in the ATG8 conjugation system, contributing to phagophore elongation. ATG3 has also been found to participate in many physiological and pathological processes in an autophagy-dependent manner, such as tumor occurrence and progression, ischemia-reperfusion injury, clearance of pathogens, and maintenance of organelle homeostasis. Intriguingly, a few studies have recently discovered the autophagy-independent functions of ATG3, including cell differentiation and mitosis. Here, we summarize the current knowledge of ATG3 in autophagosome formation, highlight its binding partners and binding sites, review its autophagy-dependent functions, and provide a brief introduction into its autophagy-independent functions.
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Affiliation(s)
- Dongmei Fang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huazhong Xie
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Shan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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15
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Li B, Song S, Wei X, Tang G, Wang C. Activation of microlipophagy during early infection of insect hosts by Metarhizium robertsii. Autophagy 2021; 18:608-623. [PMID: 34130590 DOI: 10.1080/15548627.2021.1943179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The requirement of macroautophagic/autophagic machinery for filamentous fungal development and pathogenicity has been recognized, but the underlying effects and mechanisms remain elusive. The insect pathogenic fungus Metarhizium robertsii infects hosts by cuticular penetration through the formation of the infection structure appressoria. Here, we show that autophagic fluxes were highly activated during the appressorial formation of M. robertsii. Genome-wide deletion of the autophagy-related genes and insect bioassays identified 10 of 23 encoded MrATG genes with requirements for topical fungal infection of insect hosts. Besides the defect in forming appressoria on insects (two null mutants), these virulence-reduced mutants were largely impaired in penetrating cellophane membrane and insect cuticles, suggesting their failures in generating proper appressorium turgor. We found that the conidial storage of lipid droplets (LDs) had no obvious difference between strains, but autophagic LD degradation was impaired in different mutants. After induction of cell autophagy by nitrogen starvation, we found that LD entry into vacuoles was unaffected in the selected mutant cells with potential failures in forming autophagosomes. The finding therefore reveals a microlipophagy machinery employed in this fungus and that the direct engulfment of LDs occurs without inhibition by the downstream defective lipolysis. Our data first unveil the activation and contribution of microlipophagy to fungal infection biology. The obtained technique may benefit future detection of microlipophagy in different organisms by examining vacuolar or lysosomal engulfment of LDs in core autophagic gene deletion mutants.
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Affiliation(s)
- Bing Li
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangxiu Song
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuefei Wei
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guirong Tang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengshu Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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16
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Kang SM, Kim DH. A Structural Approach into Drug Discovery Based on Autophagy. Life (Basel) 2021; 11:life11060526. [PMID: 34199860 PMCID: PMC8226661 DOI: 10.3390/life11060526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Autophagy is a lysosome-dependent intracellular degradation machinery that plays an essential role in the regulation of cellular homeostasis. As many studies have revealed that autophagy is related to cancer, neurodegenerative diseases, metabolic diseases, and so on, and it is considered as a promising drug target. Recent advances in structural determination and computational technologies provide important structural information on essential autophagy-related proteins. Combined with high-throughput screening methods, structure-activity relationship studies have led to the discovery of molecules that modulate autophagy. In this review, we summarize the recent structural studies on autophagy-related proteins and the discovery of modulators, indicating that targeting autophagy can be utilized as an effective strategy for novel drug development.
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Affiliation(s)
- Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul 01369, Korea;
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
- Correspondence: ; Tel.: +82-64-754-8195
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17
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Qi N, Liao S, Li J, Wu C, Lv M, Liu Y, Mohiuddin M, Lin X, Hu J, Cai H, Yu L, Xiao W, Sun M, Li G. Identification and Characterization of the ATG8, a Marker of Eimeria tenella Autophagy. ACTA ACUST UNITED AC 2021; 30:e017020. [PMID: 33729312 DOI: 10.1590/s1984-29612021002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022]
Abstract
Autophagy plays an important role in maintaining cell homeostasis through degradation of denatured proteins and other biological macromolecules. In recent years, many researchers focus on mechanism of autophagy in apicomplexan parasites, but little was known about this process in avian coccidia. In our present study. The cloning, sequencing and characterization of autophagy-related gene (Etatg8) were investigated by quantitative real-time PCR (RT-qPCR), western blotting (WB), indirect immunofluorescence assays (IFAs) and transmission electron microscopy (TEM), respectively. The results have shown 375-bp ORF of Etatg8, encoding a protein of 124 amino acids in E. tenella, the protein structure and properties are similar to other apicomplexan parasites. RT-qPCR revealed Etatg8 gene expression during four developmental stages in E. tenella, but their transcriptional levels were significantly higher at the unsporulated oocysts stage. WB and IFA showed that EtATG8 was lipidated to bind the autophagosome membrane under starvation or rapamycin conditions, and aggregated in the cytoplasm of sporozoites and merozoites, however, the process of autophagosome membrane production can be inhibited by 3-methyladenine. In conclusion, we found that E. tenella has a conserved autophagy mechanism like other apicomplexan parasites, and EtATG8 can be used as a marker for future research on autophagy targeting avian coccidia.
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Affiliation(s)
- Nanshan Qi
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Shenquan Liao
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Juan Li
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Caiyan Wu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Minna Lv
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Yunqiu Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P R China
| | - Mudassar Mohiuddin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Xuhui Lin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Junjing Hu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Haiming Cai
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Linzeng Yu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Wenwan Xiao
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Mingfei Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, P. R. China
| | - Guoqing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, P R China
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Li W, He P, Huang Y, Li YF, Lu J, Li M, Kurihara H, Luo Z, Meng T, Onishi M, Ma C, Jiang L, Hu Y, Gong Q, Zhu D, Xu Y, Liu R, Liu L, Yi C, Zhu Y, Ma N, Okamoto K, Xie Z, Liu J, He RR, Feng D. Selective autophagy of intracellular organelles: recent research advances. Theranostics 2021; 11:222-256. [PMID: 33391472 PMCID: PMC7681076 DOI: 10.7150/thno.49860] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Macroautophagy (hereafter called autophagy) is a highly conserved physiological process that degrades over-abundant or damaged organelles, large protein aggregates and invading pathogens via the lysosomal system (the vacuole in plants and yeast). Autophagy is generally induced by stress, such as oxygen-, energy- or amino acid-deprivation, irradiation, drugs, etc. In addition to non-selective bulk degradation, autophagy also occurs in a selective manner, recycling specific organelles, such as mitochondria, peroxisomes, ribosomes, endoplasmic reticulum (ER), lysosomes, nuclei, proteasomes and lipid droplets (LDs). This capability makes selective autophagy a major process in maintaining cellular homeostasis. The dysfunction of selective autophagy is implicated in neurodegenerative diseases (NDDs), tumorigenesis, metabolic disorders, heart failure, etc. Considering the importance of selective autophagy in cell biology, we systemically review the recent advances in our understanding of this process and its regulatory mechanisms. We emphasize the 'cargo-ligand-receptor' model in selective autophagy for specific organelles or cellular components in yeast and mammals, with a focus on mitophagy and ER-phagy, which are finely described as types of selective autophagy. Additionally, we highlight unanswered questions in the field, helping readers focus on the research blind spots that need to be broken.
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Song Q, Liu H, Zhen H, Zhao B. Autophagy and its role in regeneration and remodeling within invertebrate. Cell Biosci 2020; 10:111. [PMID: 32974004 PMCID: PMC7507827 DOI: 10.1186/s13578-020-00467-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Acting as a cellular cleaner by packaging and transporting defective proteins and organelles to lysosomes for breakdown, autophagic process is involved in the regulation of cell remodeling after cell damage or cell death in both vertebrate and invertebrate. In human, limitations on the regenerative capacity of specific tissues and organs make it difficult to recover from diseases. Comprehensive understanding on its mechanism within invertebrate have strong potential provide helpful information for challenging these diseases. Method In this study, recent findings on the autophagy function in three invertebrates including planarian, hydra and leech with remarkable regenerative ability were summarized. Furthermore, molecular phylogenetic analyses of DjATGs and HvATGs were performed on these three invertebrates compared to that of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens. Results In comparison with Scerevisiae, C elegans, D melanogaster, M musculus and human, our analysis exhibits the following characteristics of autophagy and its function in regeneration within invertebrate. Phylogenetical analysis of ATGs revealed that most autophagy-related genes (ATGs) were highly similar to their homologs in other species, which indicates that autophagy is a highly conservative biological function in both vertebrate and invertebrate. Structurally, almost all the core amino acids necessary for the function of ATG8 in mammal were observed in invertebrate HvATG8s and DjATG8s. For instance, ubiquitin-like domain as a signature structure in each ATG8, was observed in all ATG8s in three invertebrates. Basically, autophagy plays a key role in the regulation of regeneration in planarian. DjATG8-2 and DjATG8-3 associated with mTOR signaling pathway are sophisticated in the invertebrate tissue/organ regeneration. Furthermore, autophagy is involved in the pathway of neutralization of toxic molecules input from blood digestion in the leech. Conclusions The recent investigations on autophagy in invertebrate including planarian, hydra and leech suggest that autophagy is evolutionally conserved from yeast to mammals. The fundamental role of its biological function in the invertebrate contributing to the regeneration and maintenance of cellular homeostasis in these three organisms could make tremendous information to confront life threatening diseases in human including cancers and cardiac disorders.
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Affiliation(s)
- Qian Song
- Laboratory of Developmental and Evolutionary Biology, Shandong University of Technology, Zibo, 255049 Shandong China
| | - Hongjin Liu
- Laboratory of Developmental and Evolutionary Biology, Shandong University of Technology, Zibo, 255049 Shandong China
| | - Hui Zhen
- Laboratory of Developmental and Evolutionary Biology, Shandong University of Technology, Zibo, 255049 Shandong China
| | - Bosheng Zhao
- Laboratory of Developmental and Evolutionary Biology, Shandong University of Technology, Zibo, 255049 Shandong China
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20
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Yamamuro T, Kawabata T, Fukuhara A, Saita S, Nakamura S, Takeshita H, Fujiwara M, Enokidani Y, Yoshida G, Tabata K, Hamasaki M, Kuma A, Yamamoto K, Shimomura I, Yoshimori T. Age-dependent loss of adipose Rubicon promotes metabolic disorders via excess autophagy. Nat Commun 2020; 11:4150. [PMID: 32811819 PMCID: PMC7434891 DOI: 10.1038/s41467-020-17985-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 07/28/2020] [Indexed: 12/31/2022] Open
Abstract
The systemic decline in autophagic activity with age impairs homeostasis in several tissues, leading to age-related diseases. A mechanistic understanding of adipocyte dysfunction with age could help to prevent age-related metabolic disorders, but the role of autophagy in aged adipocytes remains unclear. Here we show that, in contrast to other tissues, aged adipocytes upregulate autophagy due to a decline in the levels of Rubicon, a negative regulator of autophagy. Rubicon knockout in adipocytes causes fat atrophy and hepatic lipid accumulation due to reductions in the expression of adipogenic genes, which can be recovered by activation of PPARγ. SRC-1 and TIF2, coactivators of PPARγ, are degraded by autophagy in a manner that depends on their binding to GABARAP family proteins, and are significantly downregulated in Rubicon-ablated or aged adipocytes. Hence, we propose that age-dependent decline in adipose Rubicon exacerbates metabolic disorders by promoting excess autophagic degradation of SRC-1 and TIF2.
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Affiliation(s)
- Tadashi Yamamuro
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tsuyoshi Kawabata
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Atsunori Fukuhara
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Adipose Management, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shotaro Saita
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Hikari Takeshita
- Department of Geriatric and General Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mari Fujiwara
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yusuke Enokidani
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Gota Yoshida
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Keisuke Tabata
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Akiko Kuma
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Koichi Yamamoto
- Department of Geriatric and General Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Laboratory of Intracellular Membrane Dynamics, Graduate school of Frontier Biosciences, Osaka University, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan.
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21
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Pourhanifeh MH, Mahjoubin-Tehran M, Karimzadeh MR, Mirzaei HR, Razavi ZS, Sahebkar A, Hosseini N, Mirzaei H, Hamblin MR. Autophagy in cancers including brain tumors: role of MicroRNAs. Cell Commun Signal 2020; 18:88. [PMID: 32517694 PMCID: PMC7285723 DOI: 10.1186/s12964-020-00587-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Autophagy has a crucial role in many cancers, including brain tumors. Several types of endogenous molecules (e.g. microRNAs, AKT, PTEN, p53, EGFR, and NF1) can modulate the process of autophagy. Recently miRNAs (small non-coding RNAs) have been found to play a vital role in the regulation of different cellular and molecular processes, such as autophagy. Deregulation of these molecules is associated with the development and progression of different pathological conditions, including brain tumors. It was found that miRNAs are epigenetic regulators, which influence the level of proteins coded by the targeted mRNAs with any modification of the genetic sequences. It has been revealed that various miRNAs (e.g., miR-7-1-3p, miR-340, miR-17, miR-30a, miR-224-3p, and miR-93), as epigenetic regulators, can modulate autophagy pathways within brain tumors. A deeper understanding of the underlying molecular targets of miRNAs, and their function in autophagy pathways could contribute to the development of new treatment methods for patients with brain tumors. In this review, we summarize the various miRNAs, which are involved in regulating autophagy in brain tumors. Moreover, we highlight the role of miRNAs in autophagy-related pathways in different cancers. Video abstract
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Affiliation(s)
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Karimzadeh
- Department of Medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Sadat Razavi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran.,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Amirhossein Sahebkar
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nayyerehsadat Hosseini
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA, 02114, USA.
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22
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Wang S, Li Y, Ma C. Atg3 promotes Atg8 lipidation via altering lipid diffusion and rearrangement. Protein Sci 2020; 29:1511-1523. [PMID: 32277540 DOI: 10.1002/pro.3866] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022]
Abstract
Atg3-catalyzed transferring of Atg8 to phosphatidylethanolamine (PE) in the phagophore membrane is essential for autophagy. Previous studies have demonstrated that this process requires Atg3 to interact with the phagophore membrane via its N-terminal amphipathic helix. In this study, by using combined biochemical and biophysical approaches, our data showed that in addition to binding to the membranes, Atg3 attenuates lipid diffusion and enriches lipid molecules with smaller headgroup. Our data suggest that Atg3 promotes Atg8 lipidation via altering lipid diffusion and rearrangement.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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23
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Roberto TN, Lima RF, Pascon RC, Idnurm A, Vallim MA. Biological functions of the autophagy-related proteins Atg4 and Atg8 in Cryptococcus neoformans. PLoS One 2020; 15:e0230981. [PMID: 32251488 PMCID: PMC7135279 DOI: 10.1371/journal.pone.0230981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/12/2020] [Indexed: 11/28/2022] Open
Abstract
Autophagy is a mechanism responsible for intracellular degradation and recycling of macromolecules and organelles, essential for cell survival in adverse conditions. More than 40 autophagy-related (ATG) genes have been identified and characterized in fungi, among them ATG4 and ATG8. ATG4 encodes a cysteine protease (Atg4) that plays an important role in autophagy by initially processing Atg8 at its C-terminus region. Atg8 is a ubiquitin-like protein essential for the synthesis of the double-layer membrane that constitutes the autophagosome vesicle, responsible for delivering the cargo from the cytoplasm to the vacuole lumen. The contributions of Atg-related proteins in the pathogenic yeast in the genus Cryptococcus remain to be explored, to elucidate the molecular basis of the autophagy pathway. In this context, we aimed to investigate the role of autophagy-related proteins 4 and 8 (Atg4 and Atg8) during autophagy induction and their contribution with non-autophagic events in C. neoformans. We found that Atg4 and Atg8 are conserved proteins and that they interact physically with each other. ATG gene deletions resulted in cells sensitive to nitrogen starvation. ATG4 gene disruption affects Atg8 degradation and its translocation to the vacuole lumen, after autophagy induction. Both atg4 and atg8 mutants are more resistant to oxidative stress, have an impaired growth in the presence of the cell wall-perturbing agent Congo Red, and are sensitive to the proteasome inhibitor bortezomib (BTZ). By that, we conclude that in C. neoformans the autophagy-related proteins Atg4 and Atg8 play an important role in the autophagy pathway; which are required for autophagy regulation, maintenance of amino acid levels and cell adaptation to stressful conditions.
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Affiliation(s)
- Thiago Nunes Roberto
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Ricardo Ferreira Lima
- Departamento de Infectologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Marcelo Afonso Vallim
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
- * E-mail:
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24
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Popelka H. Dancing while self-eating: Protein intrinsic disorder in autophagy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:263-305. [PMID: 32828468 DOI: 10.1016/bs.pmbts.2020.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy is a major catabolic pathway that must be tightly regulated to maintain cellular homeostasis. Protein intrinsic disorder provides a very suitable conformation for regulation; accordingly, the molecular machinery of autophagy is significantly enriched in intrinsically disordered proteins and protein regions (IDPs/IDPRs). Despite experimental challenges that the characterization of IDPRs encounters, remarkable progress has been made in recent years in revealing various roles of IDPs/IDPRs in autophagy. This chapter describes the autophagy pathway from a specific point of view, that of IDPRs. It focuses in detail on structural and mechanistic functions in autophagy that are executed by disordered regions. Via a description of autophagosome biogenesis, linking the cargo to the autophagy machinery, as well as a discussion of certain post-translational regulations, this review reveals many indispensable roles of IDPRs in the functional autophagy pathway. Devastating pathologies such as neurodegeneration, cancer, or diabetes have been linked to a malfunction in IDPs/IDPRs. The same pathologies are associated with dysfunctional autophagy, indicating that autophagic IDPRs may be a paramount causative factor. Several disease-related mechanisms of the autophagy pathway involving protein intrinsic disorder are reported in this chapter, to illustrate a wide-ranging potential of IDPRs in the therapeutic modulation of autophagy.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States.
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25
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Yu ZQ, Sun LL, Jiang ZD, Liu XM, Zhao D, Wang HT, He WZ, Dong MQ, Du LL. Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop to promote autophagy. Autophagy 2020; 16:2036-2051. [PMID: 31941401 PMCID: PMC7595586 DOI: 10.1080/15548627.2020.1713644] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroautophagy (autophagy) is driven by the coordinated actions of core autophagy-related (Atg) proteins. Atg8, the core Atg protein generally considered acting most downstream, has recently been shown to interact with other core Atg proteins via their Atg8-family-interacting motifs (AIMs). However, the extent, functional consequence, and evolutionary conservation of such interactions remain inadequately understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg38, a subunit of the phosphatidylinositol 3-kinase (PtdIns3K) complex I, interacts with Atg8 via an AIM, which is highly conserved in Atg38 proteins of fission yeast species, but not conserved in Atg38 proteins of other species. This interaction recruits Atg38 to Atg8 on the phagophore assembly site (PAS) and consequently enhances PAS accumulation of the PtdIns3K complex I and Atg proteins acting downstream of the PtdIns3K complex I, including Atg8. The disruption of the Atg38-Atg8 interaction leads to the reduction of autophagosome size and autophagic flux. Remarkably, the loss of this interaction can be compensated by an artificial Atg14-Atg8 interaction. Our findings demonstrate that the Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop between Atg8 and the PtdIns3K complex I to promote efficient autophagosome formation, underscore the prevalence and diversity of AIM-mediated connections within the autophagic machinery, and reveal unforeseen flexibility of such connections. Abbreviations: AIM: Atg8-family-interacting motif; AP-MS: affinity purification coupled with mass spectrometry; Atg: autophagy-related; FLIP: fluorescence loss in photobleaching; PAS: phagophore assembly site; PB: piggyBac; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol 3-phosphate.
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Affiliation(s)
- Zhong-Qiu Yu
- National Institute of Biological Sciences , Beijing, China.,PTN Graduate Program, School of Life Sciences, Peking University , Beijing, China
| | - Ling-Ling Sun
- National Institute of Biological Sciences , Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences , Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences , Beijing, China
| | - Dan Zhao
- National Institute of Biological Sciences , Beijing, China
| | - Hai-Tao Wang
- National Institute of Biological Sciences , Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences , Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
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26
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Fan T, Yang W, Zeng X, Xu X, Xu Y, Fan X, Luo M, Tian C, Xia K, Zhang M. A Rice Autophagy Gene OsATG8b Is Involved in Nitrogen Remobilization and Control of Grain Quality. FRONTIERS IN PLANT SCIENCE 2020; 11:588. [PMID: 32582228 PMCID: PMC7287119 DOI: 10.3389/fpls.2020.00588] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/20/2020] [Indexed: 05/03/2023]
Abstract
Enhancing nitrogen (N) use efficiency is a potential way to reduce excessive nitrogen application and increase yield. Autophagy is a conserved degradation system in the evolution of eukaryotic cells and plays an important role in plant development and stress response. Autophagic cores have two conjugation pathways that attach the product of autophagy-related gene 8 (ATG8) to phosphatidylethanolamine (PE) and ATG5 to ATG12, respectively, which then help with vesicle elongation and enclosure. Rice has six ATG8 genes, which have not been functionally confirmed so far. We identified the rice gene OsATG8b and characterized its role in N remobilization to affect grain quality by generating transgenic plants with its over-expression and knockdown. Our study confirmed the autophagy activity of OsATG8b through the complementation of the yeast autophagy-defective mutant scatg8 and by observation of autophagosome formation in rice. The autophagy activity is higher in OsATG8b-OE lines and lower in OsATG8b-RNAi than that in wild type (ZH11). 15N pulse-chase analysis revealed that OsATG8b-OE plants conferred higher N recycling efficiency to grains, while OsATG8b-RNAi transgenic plants exhibited lower N recycling efficiency and poorer grain quality. The autophagic role of OsATG8b was experimentally confirmed, and it was concluded that OsATG8b-mediated autophagy is involved in N recycling to grains and contributes to the grain quality, indicating that OsATG8b may be a potential gene for molecular breeding and cultivation of rice.
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Affiliation(s)
- Tian Fan
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Wu Yang
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xuan Zeng
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xinlan Xu
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yanling Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Ming Luo
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Changen Tian
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Kuaifei Xia
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Mingyong Zhang
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Mingyong Zhang,
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27
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Zheng Y, Qiu Y, Grace CRR, Liu X, Klionsky DJ, Schulman BA. A switch element in the autophagy E2 Atg3 mediates allosteric regulation across the lipidation cascade. Nat Commun 2019; 10:3600. [PMID: 31399562 PMCID: PMC6689050 DOI: 10.1038/s41467-019-11435-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/14/2019] [Indexed: 12/28/2022] Open
Abstract
Autophagy depends on the E2 enzyme, Atg3, functioning in a conserved E1-E2-E3 trienzyme cascade that catalyzes lipidation of Atg8-family ubiquitin-like proteins (UBLs). Molecular mechanisms underlying Atg8 lipidation remain poorly understood despite association of Atg3, the E1 Atg7, and the composite E3 Atg12–Atg5-Atg16 with pathologies including cancers, infections and neurodegeneration. Here, studying yeast enzymes, we report that an Atg3 element we term E123IR (E1, E2, and E3-interacting region) is an allosteric switch. NMR, biochemical, crystallographic and genetic data collectively indicate that in the absence of the enzymatic cascade, the Atg3E123IR makes intramolecular interactions restraining Atg3′s catalytic loop, while E1 and E3 enzymes directly remove this brace to conformationally activate Atg3 and elicit Atg8 lipidation in vitro and in vivo. We propose that Atg3′s E123IR protects the E2~UBL thioester bond from wayward reactivity toward errant nucleophiles, while Atg8 lipidation cascade enzymes induce E2 active site remodeling through an unprecedented mechanism to drive autophagy. Autophagy mediated by the conjugation pathway for ubiquitin-like proteins plays a key role in controlling homeostasis in eukaryotic cells. Here the authors provide a molecular basis for allosteric activation of the E2 ligase Atg3, uncovering the mechanism underlying Atg8 lipidation and a novel mechanism regulating E1-E2-E3-mediated ubiquitin-like protein conjugation.
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Affiliation(s)
- Yumei Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yu Qiu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Biologics Research, Sanofi, Framingham, MA, USA
| | - Christy R R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xu Liu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | | | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA. .,Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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28
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Birgisdottir ÅB, Mouilleron S, Bhujabal Z, Wirth M, Sjøttem E, Evjen G, Zhang W, Lee R, O’Reilly N, Tooze SA, Lamark T, Johansen T. Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs. Autophagy 2019; 15:1333-1355. [PMID: 30767700 PMCID: PMC6613885 DOI: 10.1080/15548627.2019.1581009] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/04/2019] [Accepted: 01/28/2019] [Indexed: 12/24/2022] Open
Abstract
Autophagosome formation depends on a carefully orchestrated interplay between membrane-associated protein complexes. Initiation of macroautophagy/autophagy is mediated by the ULK1 (unc-51 like autophagy activating kinase 1) protein kinase complex and the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1). The latter contains PIK3C3/VPS34, PIK3R4/VPS15, BECN1/Beclin 1 and ATG14 and phosphorylates phosphatidylinositol to generate phosphatidylinositol 3-phosphate (PtdIns3P). Here, we show that PIK3C3, BECN1 and ATG14 contain functional LIR motifs and interact with the Atg8-family proteins with a preference for GABARAP and GABARAPL1. High resolution crystal structures of the functional LIR motifs of these core components of PtdIns3K-C1were obtained. Variation in hydrophobic pocket 2 (HP2) may explain the specificity for the GABARAP family. Mutation of the LIR motif in ATG14 did not prevent formation of the PtdIns3K-C1 complex, but blocked colocalization with MAP1LC3B/LC3B and impaired mitophagy. The ULK-mediated phosphorylation of S29 in ATG14 was strongly dependent on a functional LIR motif in ATG14. GABARAP-preferring LIR motifs in PIK3C3, BECN1 and ATG14 may, via coincidence detection, contribute to scaffolding of PtdIns3K-C1 on membranes for efficient autophagosome formation. Abbreviations: ATG: autophagy-related; BafA1: bafilomycin A1; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor associated protein like 1; GFP: enhanced green fluorescent protein; KO: knockout; LDS: LIR docking site; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; SQSTM1/p62: sequestosome 1; VPS: Vacuolar protein sorting; ULK: unc-51 like autophagy activating kinase.
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Affiliation(s)
- Åsa Birna Birgisdottir
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | | | - Zambarlal Bhujabal
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Martina Wirth
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Eva Sjøttem
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Gry Evjen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Wenxin Zhang
- Structural Biology, The Francis Crick Institute, London, UK
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Rebecca Lee
- Structural Biology, The Francis Crick Institute, London, UK
| | - Nicola O’Reilly
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, London, UK
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Trond Lamark
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
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29
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Macharia MW, Tan WYZ, Das PP, Naqvi NI, Wong SM. Proximity-dependent biotinylation screening identifies NbHYPK as a novel interacting partner of ATG8 in plants. BMC PLANT BIOLOGY 2019; 19:326. [PMID: 31324141 PMCID: PMC6642529 DOI: 10.1186/s12870-019-1930-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/09/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Autophagy is a conserved, highly-regulated catabolic process that plays important roles in growth, development and innate immunity in plants. In this study, we compared the rate of autophagy induction in Nicotiana benthamiana plants infected with Tobacco mosaic virus or the TMV 24A + UPD mutant variant, which replicates at a faster rate and induces more severe symptoms. Using a BirA* tag and proximity-dependent biotin identification (BioID) analysis, we identified host proteins that interact with the core autophagy protein, ATG8 in TMV 24A + UPD infected plants. By combining the use of a fast replicating TMV mutant and an in vivo protein-protein screening technique, we were able to gain functional insight into the role of autophagy in a compatible virus-host interaction. RESULTS Our study revealed an increased autophagic flux induced by TMV 24A + UPD, as compared to TMV in N. benthamiana. Analysis of the functional proteome associated with ATG8 revealed a total of 67 proteins, 16 of which are known to interact with ATG8 or its orthologs in mammalian and yeast systems. The interacting proteins were categorized into four functional groups: immune system process, response to ROS, sulphur amino acid metabolism and calcium signalling. Due to the presence of an ubiquitin-associated (UBA) domain, which is demonstrated to interact with ATG8, the Huntingtin-interacting protein K-like (HYPK) was selected for validation of the physical interaction and function. We used yeast two hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and subcellular localization to validate the ATG8-HYPK interaction. Subsequent down-regulation of ATG8 by virus-induced gene silencing (VIGS) showed enhanced TMV symptoms, suggesting a protective role for autophagy during TMV 24A + UPD infection. CONCLUSION This study presents the use of BioID as a suitable method for screening ATG8 interacting proteins in planta. We have identified many putative binding partners of ATG8 during TMV 24A + UPD infection in N. benthamiana plants. In addition, we have verified that NbHYPK is an interacting partner of ATG8. We infer that autophagy plays a protective role in TMV 24A + UPD infected plants.
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Affiliation(s)
- Mercy W Macharia
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore
| | - Wilfred Y Z Tan
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore
| | - Prem P Das
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore
| | - Naweed I Naqvi
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Singapore, 119543, Singapore.
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore.
- National University of Singapore Research Institute, Suzhou, Jiangsu, 215123, People's Republic of China.
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de la Ballina LR, Munson MJ, Simonsen A. Lipids and Lipid-Binding Proteins in Selective Autophagy. J Mol Biol 2019; 432:135-159. [PMID: 31202884 DOI: 10.1016/j.jmb.2019.05.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells have the capacity to degrade intracellular components through a lysosomal degradation pathway called macroautophagy (henceforth referred to as autophagy) in which superfluous or damaged cytosolic entities are engulfed and separated from the rest of the cell constituents into double membraned vesicles known as autophagosomes. Autophagosomes then fuse with endosomes and lysosomes, where cargo is broken down into basic building blocks that are released to the cytoplasm for the cell to reuse. Autophagic degradation can target either cytoplasmic material in bulk (non-selective autophagy) or particular cargo in what is called selective autophagy. Proper autophagic turnover requires the orchestrated participation of several players that need to be tightly and temporally coordinated. Whereas a large number of autophagy-related (ATG) proteins have been identified and their functions and regulation are starting to be understood, there is substantially less knowledge regarding the specific lipids constituting the autophagic membranes as well as their role in initiating, enabling or regulating the autophagic process. This review focuses on lipids and their corresponding binding proteins that are crucial in the process of selective autophagy.
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Affiliation(s)
- Laura R de la Ballina
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Michael J Munson
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; 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, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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Yin Z, Chen C, Yang J, Feng W, Liu X, Zuo R, Wang J, Yang L, Zhong K, Gao C, Zhang H, Zheng X, Wang P, Zhang Z. Histone acetyltransferase MoHat1 acetylates autophagy-related proteins MoAtg3 and MoAtg9 to orchestrate functional appressorium formation and pathogenicity in Magnaporthe oryzae. Autophagy 2019; 15:1234-1257. [PMID: 30776962 DOI: 10.1080/15548627.2019.1580104] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macroautophagy/autophagy is critical for normal appressorium formation and pathogenicity of the rice blast fungus Magnaporthe oryzae, but the molecular base of autophagy linked to pathogenicity remains elusive in this or other pathogenic fungi. We found that MoHat1, a histone acetyltransferase (HAT) homolog, had a role in the regulation of autophagy through the acetylation of autophagy related proteins MoAtg3 and MoAtg9. We also found that MoHat1 was subject to regulation by the protein kinase MoGsk1 that modulated the translocation of MoHat1 from the nucleus to the cytoplasm with the assistance of MoSsb1, a protein chaperone. The alternation of intracellular location affected MoHat1 in the modification of cytosolic autophagy proteins that maintained normal autophagy. Furthermore, we provided evidence linking acetylation of MoAtg3 and MoAtg9 by MoHat1 to functional appressorium development and pathogenicity. Together with the first report of MoAtg9 being subject to acetylation regulation by MoHat1, our studies depicted how MoHat1 regulated autophagy in conjunction with MoGsk1 and how normal autophagy was linked to appressorium formation and function and pathogenicity of M. oryzae. Abbreviations: A/Ala: alanine; AP: autophagosome; Atg genes/proteins: autophagy-related genes/proteins; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; DAPI: 4', 6-diamidino-2-phenylindole; D/Asp: aspartic acid; GFP: green fluorescent protein; GSK3: glycogen synthase kinase 3; HAT: histone acetyltransferase; Hsp70: heat-shock protein 70; IH: invasive hyphae; K/Lys: lysine; MMS: methyl methanesulfonate; Mo: Magnaporthe oryzae; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; R/Arg: arginine; S/Ser: serine; T/Thr: threonine; TOR: target of rapamycin; WT: wild type; YFP: yellow fluorescent protein.
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Affiliation(s)
- Ziyi Yin
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Chen Chen
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Jie Yang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Wanzhen Feng
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Xinyu Liu
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Rongfang Zuo
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Jingzhen Wang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Lina Yang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Kaili Zhong
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Chuyun Gao
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Haifeng Zhang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Xiaobo Zheng
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
| | - Ping Wang
- c Departments of Pediatrics, and Microbiology, Immunology, and Parasitology , Louisiana State University Health Sciences Center , New Orleans , LA , USA
| | - Zhengguang Zhang
- a Department of Plant Pathology, College of Plant Protection , Nanjing Agricultural University , Nanjing , China.,b Key Laboratory of Integrated Management of Crop Diseases and Pests , Ministry of Education , Nanjing , China
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Yoshitake Y, Ohta H, Shimojima M. Autophagy-Mediated Regulation of Lipid Metabolism and Its Impact on the Growth in Algae and Seed Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:709. [PMID: 31214225 PMCID: PMC6558177 DOI: 10.3389/fpls.2019.00709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/13/2019] [Indexed: 05/08/2023]
Abstract
Under nutrient starvation conditions, algae and seed-plant cells accumulate carbon metabolites such as storage lipids, triacylglycerols (TAGs), and starches. Recent research has suggested the involvement of autophagy in the regulation of carbon metabolites under nutrient starvation. When algae are grown under carbon starvation conditions, such as growth in darkness or in the presence of a photosynthesis inhibitor, lipid droplets are surrounded by phagophores. Indeed, the amount of TAGs in an autophagy-deficient mutant has been found to be greater than that in wild type under nitrogen starvation, and cerulenin, which is one of the inhibitors of fatty acid synthesis, induces autophagy. In land plants, TAGs accumulate predominantly in seeds and etiolated seedlings. These TAGs are degraded in peroxisomes via β-oxidation during germination as a source of carbon for growth without photosynthesis. A global analysis of the role of autophagy in Arabidopsis seedlings under carbon starvation revealed that a lack of autophagy enhances the accumulation of TAGs and fatty acids. In Oryza sativa, autophagy-mediated degradation of TAGs and diacylglycerols has been suggested to be important for pollen development. In this review, we introduce and summarize research findings demonstrating that autophagy affects lipid metabolism and discuss the role of autophagy in membrane and storage-lipid homeostasis, each of which affects the growth and development of seed plants and algae.
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Affiliation(s)
- Yushi Yoshitake
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Open Innovation Platform with Enterprises, Research Institute and Academia (OPERA), Japan Science and Technology Agency, Chiyoda, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- *Correspondence: Mie Shimojima,
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Osawa T, Alam JM, Noda NN. Membrane-binding domains in autophagy. Chem Phys Lipids 2019; 218:1-9. [DOI: 10.1016/j.chemphyslip.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
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Liu S, Zhang F, Wang Y, Wang H, Chen X, Hu Y, Chen M, Lan S, Wang C, Cao J, Hu X, Tan F. Characterization of the molecular mechanism of the autophagy-related Atg8-Atg3 protein interaction in Toxoplasma gondii. J Biol Chem 2018; 293:14545-14556. [PMID: 30026233 DOI: 10.1074/jbc.ra118.002614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Toxoplasmosis is caused by an obligate intracellular parasite, the protozoan Toxoplasma gondii Discovery of novel drugs against T. gondii infection could circumvent the toxicity of existing drugs and T. gondii resistance to current treatments. The autophagy-related protein 8 (Atg8)-Atg3 interaction in T. gondii is a promising drug target because of its importance for regulating Atg8 lipidation. We reported previously that TgAtg8 and TgAtg3 interact directly. Here we validated that substitutions of conserved residues of TgAtg8 interacting with the Atg8 family-interacting motif (AIM) in Atg3 disrupt the TgAtg8-TgAtg3 interaction and reduce TgAtg8 lipidation and autophagosome formation. These findings were consistent with results reported previously for Plasmodium Atg8, suggesting functional conservation of Atg8 in Toxoplasma and Plasmodium. Moreover, using peptide and AlphaScreen assays, we identified the AIM sequence in TgAtg3 that binds TgAtg8. We determined that the core TgAtg3 AIM contains a Phe239-Ala240-Asp241-Ile242 (239FADI242) signature distinct from the 105WLLP108 signature in the AIM of Plasmodium Atg3. Furthermore, an alanine-scanning assay revealed that the TgAtg8-TgAtg3 interaction in T. gondii also depends strongly on several residues surrounding the core TgAtg3 AIM, such as Asn238, Asp243, and Cys244 These results indicate that distinct AIMs in Atg3 contribute to differences between Toxoplasma and Plasmodium Atg8-Atg3 interactions. By elucidating critical residues involved in the TgAtg8-TgAtg3 interaction, our work paves the way for the discovery of potential anti-toxoplasmosis drugs. The quantitative and straightforward AlphaScreen assay developed here may enable high-throughput screening for small molecules disrupting the TgAtg8-TgAtg3 interaction.
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Affiliation(s)
- Shuxian Liu
- From the Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fangfei Zhang
- Renji College, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yan Wang
- From the Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Han Wang
- From the Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xiaojian Chen
- the Department of Clinical Laboratory, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yue Hu
- From the Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Ming Chen
- the Chemical Biology Core Facility, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shujue Lan
- the Chemical Biology Core Facility, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chenhong Wang
- the School of the Second Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jiaxin Cao
- From the Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xin Hu
- the School of Medical Laboratory Science and School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Feng Tan
- From the Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
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Gao Y, Ge W. The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis. Cell Death Dis 2018; 9:33. [PMID: 29348610 PMCID: PMC5833786 DOI: 10.1038/s41419-017-0040-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/14/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
Abstract
Osteoclasts are absorptive cells that play a critical role in homeostatic bone remodeling and pathological bone resorption. Emerging evidence suggests an important role of epigenetic regulation in osteoclastogenesis. In this study, we investigated the role of DOT1L, which regulates gene expression epigenetically by histone H3K79 methylation (H3K79me), during osteoclast formation. Using RANKL-induced RAW264.7 macrophage cells as an osteoclast differentiation model, we found that DOT1L and H3K79me2 levels were upregulated during osteoclast differentiation. Small molecule inhibitor- (EPZ5676 or EPZ004777) or short hairpin RNA-mediated reduction in DOT1L expression promoted osteoclast differentiation and resorption. In addition, DOT1L inhibition increased osteoclast surface area and accelerated bone-mass reduction in a mouse ovariectomy (OVX) model of osteoporosis without alter osteoblast differentiation. DOT1L inhibition increase reactive oxygen species (ROS) generation and autophagy activity, and cell migration in pre-osteoclasts. Moreover, it strengthened expression of osteoclast fusion and resorption-related protein CD9 and MMP9 in osteoclasts derived from RAW264.7. Our findings support a new mechanism of DOT1L-regulated, H3K79me2-mediated, epigenetic regulation of osteoclast differentiation, implicating DOT1L as a new therapeutic target for osteoclast dysregulation-induced disease.
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Affiliation(s)
- Yanpan Gao
- State Key Laboratory of Medical Molecular Biology & Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Wei Ge
- State Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Abreu S, Kriegenburg F, Gómez-Sánchez R, Mari M, Sánchez-Wandelmer J, Skytte Rasmussen M, Soares Guimarães R, Zens B, Schuschnig M, Hardenberg R, Peter M, Johansen T, Kraft C, Martens S, Reggiori F. Conserved Atg8 recognition sites mediate Atg4 association with autophagosomal membranes and Atg8 deconjugation. EMBO Rep 2017; 18:765-780. [PMID: 28330855 DOI: 10.15252/embr.201643146] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 02/12/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
Abstract
Deconjugation of the Atg8/LC3 protein family members from phosphatidylethanolamine (PE) by Atg4 proteases is essential for autophagy progression, but how this event is regulated remains to be understood. Here, we show that yeast Atg4 is recruited onto autophagosomal membranes by direct binding to Atg8 via two evolutionarily conserved Atg8 recognition sites, a classical LC3-interacting region (LIR) at the C-terminus of the protein and a novel motif at the N-terminus. Although both sites are important for Atg4-Atg8 interaction in vivo, only the new N-terminal motif, close to the catalytic center, plays a key role in Atg4 recruitment to autophagosomal membranes and specific Atg8 deconjugation. We thus propose a model where Atg4 activity on autophagosomal membranes depends on the cooperative action of at least two sites within Atg4, in which one functions as a constitutive Atg8 binding module, while the other has a preference toward PE-bound Atg8.
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Affiliation(s)
- Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mads Skytte Rasmussen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Rodrigo Soares Guimarães
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bettina Zens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Claudine Kraft
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands .,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
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Wang P, Sun X, Jia X, Ma F. Apple autophagy-related protein MdATG3s afford tolerance to multiple abiotic stresses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:53-64. [PMID: 28167039 DOI: 10.1016/j.plantsci.2016.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/28/2016] [Accepted: 12/08/2016] [Indexed: 05/02/2023]
Abstract
The efficient degradation system of autophagy in plant cells has important roles in removing and recycling intracellular components during normal development or under environmental stresses. Formation of autophagosomes requires the conjugation of ubiquitin-like protein ATG8 to phosphatidylethanolamine (PE). We isolated two ubiquitin-conjugating enzyme E2-like ATG3 homologues from Malus domestica - MdATG3a and MdATG3b - that are crucial for ATG8-PE conjugation. Both share a conserved N-terminal, as well as the catalytic and C-terminal domains of ATG3 with HPC and FLKF motifs. Each promoter was isolated from genomic DNA and contained several cis-acting elements that are involved in responses to environmental stresses or hormones. In addition to having the same cellular localization in the nucleus and cytoplasm, MdATG3a and MdATG3b showed similar expression patterns toward leaf senescence, nitrogen starvation, drought, salinity, and oxidative stress at the transcriptional level. Ectopic expression of either in Arabidopsis conferred tolerance to osmotic or salinity stress and also improved growth performance under nitrogen- or carbon-starvation. Callus lines of 'Orin' apple that over-expressed MdATG3b also displayed better growth performance when nutrient supplies were limited. These overall results demonstrate that, as important autophagy genes, overexpression of MdATG3s can afford tolerance to multiple abiotic stresses at the cellular and whole-plant level.
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Affiliation(s)
- Ping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xun Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
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38
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Jacomin AC, Samavedam S, Promponas V, Nezis IP. iLIR database: A web resource for LIR motif-containing proteins in eukaryotes. Autophagy 2016; 12:1945-1953. [PMID: 27484196 PMCID: PMC5079668 DOI: 10.1080/15548627.2016.1207016] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Atg8-family proteins are the best-studied proteins of the core autophagic machinery. They are essential for the elongation and closure of the phagophore into a proper autophagosome. Moreover, Atg8-family proteins are associated with the phagophore from the initiation of the autophagic process to, or just prior to, the fusion between autophagosomes with lysosomes. In addition to their implication in autophagosome biogenesis, they are crucial for selective autophagy through their ability to interact with selective autophagy receptor proteins necessary for the specific targeting of substrates for autophagic degradation. In the past few years it has been revealed that Atg8-interacting proteins include not only receptors but also components of the core autophagic machinery, proteins associated with vesicles and their transport, and specific proteins that are selectively degraded by autophagy. Atg8-interacting proteins contain a short linear LC3-interacting region/LC3 recognition sequence/Atg8-interacting motif (LIR/LRS/AIM) motif which is responsible for their interaction with Atg8-family proteins. These proteins are referred to as LIR-containing proteins (LIRCPs). So far, many experimental efforts have been carried out to identify new LIRCPs, leading to the characterization of some of them in the past 10 years. Given the need for the identification of LIRCPs in various organisms, we developed the iLIR database ( https://ilir.warwick.ac.uk ) as a freely available web resource, listing all the putative canonical LIRCPs identified in silico in the proteomes of 8 model organisms using the iLIR server, combined with a Gene Ontology (GO) term analysis. Additionally, a curated text-mining analysis of the literature permitted us to identify novel putative LICRPs in mammals that have not previously been associated with autophagy.
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Affiliation(s)
| | - Siva Samavedam
- a School of Life Sciences, University of Warwick , Coventry , UK
| | - Vasilis Promponas
- b Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus , Nicosia , Cyprus
| | - Ioannis P Nezis
- a School of Life Sciences, University of Warwick , Coventry , UK
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Zhuang L, Ma Y, Wang Q, Zhang J, Zhu C, Zhang L, Xu X. Atg3 Overexpression Enhances Bortezomib-Induced Cell Death in SKM-1 Cell. PLoS One 2016; 11:e0158761. [PMID: 27391105 PMCID: PMC4938461 DOI: 10.1371/journal.pone.0158761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/21/2016] [Indexed: 12/19/2022] Open
Abstract
Background Myelodysplastic syndrome (MDS) is a group of heterogeneous hematopoietic stem cell malignancies with a high risk of transformation into acute myeloid leukemia (AML). Clonal evolutions are significantly associated with transformation to AML. According to a gene expression microarray, atg3 is downregulated in MDS patients progressing to leukemia, but less is known about the function of Atg3 in the survival and death of MSD/AML cells. Moreover, the role of autophagy as a result of bortezomib treatment is controversial. The current study was designed to investigate the function of Atg3 in SKM-1 cells and to study the effect of Atg3 on cell viability and cell death following bortezomib treatment. Methods Four leukemia cell lines (SKM-1, THP-1, NB4 and K562) and two healthy patients’ bone marrow cells were analyzed for Atg3 expression via qRT-PCR and Western blotting analysis. The role of Atg3 in SKM-1 cell survival and cell death was analyzed by CCK-8 assay, trypan blue exclusion assay, DAPI staining and Annexin V/PI dual staining with or without bortezomib treatment. Western blotting analysis was used to detect proteins in autophagic and caspase signaling pathways. Electron microscopy was used to observe ultrastructural changes after Atg3 overexpression. Results Downregulation of Atg3 expression was detected in four leukemia cell lines compared with healthy bone marrow cells. Atg3 mRNA was significantly decreased in MDS patients’ bone marrow cells. Overexpression of Atg3 in SKM-1 cells resulted in AKT-mTOR-dependent autophagy, a significant reduction in cell proliferation and increased cell death, which could be overcome by the autophagy inhibitor 3-MA. SKM-1 cells overexpressing Atg3 were hypersensitive to bortezomib treatment at different concentrations via autophagic cell death and enhanced sensitivity to apoptosis in the SKM-1 cell line. Following treatment with 3-MA, the sensitivity of Atg3-overexpressing cells to bortezomib treatment was reduced. Atg3 knockdown blocked cell growth inhibition and cell death induced by bortezomib. Conclusion Our preliminary study of Atg3 in the high-risk MDS cell line suggests that Atg3 might be possibly a critical regulator of autophagic cell death and a gene target for therapeutic interventions in MDS.
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Affiliation(s)
- Lin Zhuang
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Ma
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qian Wang
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Zhang
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chen Zhu
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Zhang
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoping Xu
- Department of Hematology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail:
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Li W, Yang Y, Hou X, Zhuang H, Wu Z, Li Z, Guo R, Chen H, Lin C, Zhong W, Chen Y, Wu K, Zhang L, Feng D. MicroRNA-495 regulates starvation-induced autophagy by targeting ATG3. FEBS Lett 2016; 590:726-38. [PMID: 26910393 DOI: 10.1002/1873-3468.12108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/31/2016] [Accepted: 02/08/2016] [Indexed: 12/21/2022]
Abstract
The functions of some essential autophagy genes are regulated by microRNAs. However, an ATG3-modulating microRNA has never been reported. Here we show that the transcription of miR-495 negatively correlates with the translation of ATG3 under nutrient-deprived or rapamycin-treated conditions. miR-495 targets ATG3 and regulates its protein levels under starvation conditions. miR-495 also inhibits starvation-induced autophagy by decreasing the number of autophagosomes and by preventing LC3-I-to-LC3-II transition and P62 degradation. These processes are reversed by the overexpression of an endogenous miR-495 inhibitor. Re-expression of Atg3 without miR-495 response elements restores miR-495-inhibited autophagy. miR-495 sustains cell viability under starvation conditions but has no effect under hypoxia. Moreover, miR-495 inhibits etoposide-induced cell death. In conclusion, miR-495 is involved in starvation-induced autophagy by regulating Atg3.
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Affiliation(s)
- Wen Li
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Yue Yang
- Department of Anesthesiology, Guangdong Medical College, Zhanjiang, China
| | - Xiaoyan Hou
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Haixia Zhuang
- Department of Anesthesiology, Guangdong Medical College, Zhanjiang, China
| | - Zijun Wu
- Department of Cardiovasology, the Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Zhiyi Li
- Department of Anesthesiology, Guangdong Medical College, Zhanjiang, China
| | - Runmin Guo
- Department of Cardiovasology, the Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Hao Chen
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Chunxia Lin
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Wangtao Zhong
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Yusen Chen
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Keng Wu
- Department of Cardiovasology, the Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Liangqing Zhang
- Department of Anesthesiology, Guangdong Medical College, Zhanjiang, China
| | - Du Feng
- Guangdong Key Laboratory of Age-related Cardiac-cerebral Vascular Disease, Institute of Neurology, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
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Induction of Autophagy interferes the tachyzoite to bradyzoite transformation of Toxoplasma gondii. Parasitology 2016; 143:639-45. [DOI: 10.1017/s0031182015001985] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SUMMARYAutophagy process in Toxoplasma gondii plays a vital role in regulating parasite survival or death. Thus, once having an understanding of certain effects of autophagy on the transformation of tachyzoite to bradyzoite this will allow us to elucidate the function of autophagy during parasite development. Herein, we used three TgAtg proteins involved in Atg8 conjugation system, TgAtg3, TgAtg7 and TgAtg8 to evaluate the autophagy level in tachyzoite and bradyzoite of Toxoplasma in vitro based on Pru TgAtg7-HA transgenic strains. We showed that both TgAtg3 and TgAtg8 were expressed at a significantly lower level in bradyzoites than in tachyzoites. Importantly, the number of parasites containing fluorescence-labelled TgAtg8 puncta was significantly reduced in bradyzoites than in tachyzoites, suggesting that autophagy is downregulated in Toxoplasma bradyzoite in vitro. Moreover, after treatment with drugs, bradyzoite-specific gene BAG1 levels decreased significantly in rapamycin-treated bradyzoites and increased significantly in 3-MA-treated bradyzoites in comparison with control bradyzoites, indicating that Toxoplasma autophagy is involved in the transformation of tachyzoite to bradyzoite in vitro. Together, it is suggested that autophagy may serve as a potential strategy to regulate the transformation.
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42
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Bento CF, Renna M, Ghislat G, Puri C, Ashkenazi A, Vicinanza M, Menzies FM, Rubinsztein DC. Mammalian Autophagy: How Does It Work? Annu Rev Biochem 2016; 85:685-713. [PMID: 26865532 DOI: 10.1146/annurev-biochem-060815-014556] [Citation(s) in RCA: 529] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autophagy is a conserved intracellular pathway that delivers cytoplasmic contents to lysosomes for degradation via double-membrane autophagosomes. Autophagy substrates include organelles such as mitochondria, aggregate-prone proteins that cause neurodegeneration and various pathogens. Thus, this pathway appears to be relevant to the pathogenesis of diverse diseases, and its modulation may have therapeutic value. Here, we focus on the cell and molecular biology of mammalian autophagy and review the key proteins that regulate the process by discussing their roles and how these may be modulated by posttranslational modifications. We consider the membrane-trafficking events that impact autophagy and the questions relating to the sources of autophagosome membrane(s). Finally, we discuss data from structural studies and some of the insights these have provided.
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Affiliation(s)
- Carla F Bento
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Maurizio Renna
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Ghita Ghislat
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Claudia Puri
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Avraham Ashkenazi
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Mariella Vicinanza
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Fiona M Menzies
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
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Chen D, Lin J, Liu Y, Li X, Chen G, Hua Q, Nie Q, Hu X, Tan F. Identification of TgAtg8-TgAtg3 interaction in Toxoplasma gondii. Acta Trop 2016; 153:79-85. [PMID: 26407821 DOI: 10.1016/j.actatropica.2015.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/02/2015] [Accepted: 09/21/2015] [Indexed: 12/25/2022]
Abstract
Autophagy is a catabolic process in eukaryotic cells involved in the targeted degradation of cellular organelles and the cytoplasm. Recent works in Toxoplasma gondii suggest that the autophagy processes may serve as an important pathway in modulating parasite survival or death. As an important modulator of Atg8 lipidation and autophagy, Atg8-Atg3 interaction has been attracting increasing attention. However, there is no direct evidence that TgAtg8-TgAtg3 interaction occurs in the parasite. In this study, we firstly found TgAtg8 partially colocalized with TgAtg3 in GFP-TgAtg8 transgenic strains using IFA. Then, lysates from GFP-TgAtg8 tachyzoites were directly subject to large-scale tandem affinity purification with anti-GFP antibody. Western blot and tandem mass spectrometry (MS/MS) analysis determined the interaction between TgAtg8 and TgAtg3. Additionally, we performed real-time interaction analysis with a surface plasmon resonance biosensor using BIAcore system. As expected, the result demonstrated a concentration-dependent increases in resonance signals and indicated the TgAtg8 could bind directly TgAtg3 in vitro. Noteworthily, A KD of 34.9nM obtained from TgAtg8-TgAtg3 interaction indicate a high-affinity between Atg8-Atg3 in Toxoplasma. Furthermore, homology modeling and sequence alignment showed that TgAtg8 has greatest sequence and structural conservation. Within TgAtg3, this protein possesses the core E2 enzymatic activity structure and a truncated handle region which may contain AIM sequence. Taken together, our findings would help elucidate the formation mechanism of autophagosome in Toxoplasma and provide a possibility for looking into parasitic drug targets.
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Yamamoto H, Shima T, Yamaguchi M, Mochizuki Y, Hoshida H, Kakuta S, Kondo-Kakuta C, Noda NN, Inagaki F, Itoh T, Akada R, Ohsumi Y. The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy. J Biol Chem 2015; 290:29506-18. [PMID: 26442587 DOI: 10.1074/jbc.m115.684233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 11/06/2022] Open
Abstract
Autophagy is a conserved degradation process in which autophagosomes are generated by cooperative actions of multiple autophagy-related (Atg) proteins. Previous studies using the model yeast Saccharomyces cerevisiae have provided various insights into the molecular basis of autophagy; however, because of the modest stability of several Atg proteins, structural and biochemical studies have been limited to a subset of Atg proteins, preventing us from understanding how multiple Atg proteins function cooperatively in autophagosome formation. With the goal of expanding the scope of autophagy research, we sought to identify a novel organism with stable Atg proteins that would be advantageous for in vitro analyses. Thus, we focused on a newly isolated thermotolerant yeast strain, Kluyveromyces marxianus DMKU3-1042, to utilize as a novel system elucidating autophagy. We developed experimental methods to monitor autophagy in K. marxianus cells, identified the complete set of K. marxianus Atg homologs, and confirmed that each Atg homolog is engaged in autophagosome formation. Biochemical and bioinformatic analyses revealed that recombinant K. marxianus Atg proteins have superior thermostability and solubility as compared with S. cerevisiae Atg proteins, probably due to the shorter primary sequences of KmAtg proteins. Furthermore, bioinformatic analyses showed that more than half of K. marxianus open reading frames are relatively short in length. These features make K. marxianus proteins broadly applicable as tools for structural and biochemical studies, not only in the autophagy field but also in other fields.
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Affiliation(s)
- Hayashi Yamamoto
- From the Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503,
| | - Takayuki Shima
- From the Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503
| | - Masaya Yamaguchi
- the Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0812
| | - Yuh Mochizuki
- the Laboratory of In Silico Functional Genomics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501
| | - Hisashi Hoshida
- the Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Ube 755-8611, and
| | - Soichiro Kakuta
- From the Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503
| | - Chika Kondo-Kakuta
- From the Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503
| | - Nobuo N Noda
- the Institute of Microbial Chemistry, Tokyo 141-0021, Japan
| | - Fuyuhiko Inagaki
- the Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0812
| | - Takehiko Itoh
- the Laboratory of In Silico Functional Genomics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501
| | - Rinji Akada
- the Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Ube 755-8611, and
| | - Yoshinori Ohsumi
- From the Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503,
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45
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Abstract
The formation of the autophagosome, a landmark event in autophagy, is accomplished by the concerted actions of Atg proteins. The initial step of starvation-induced autophagy in yeast is the assembly of the Atg1 complex, which, with the help of other Atg groups, recruits Atg conjugation systems and initiates the formation of the autophagosome. In this review, we describe from a structural-biological point of view the structure, interaction, and molecular roles of Atg proteins, especially those in the Atg1 complex and in the Atg conjugation systems.
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Affiliation(s)
- Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan;
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46
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Juris L, Montino M, Rube P, Schlotterhose P, Thumm M, Krick R. PI3P binding by Atg21 organises Atg8 lipidation. EMBO J 2015; 34:955-73. [PMID: 25691244 DOI: 10.15252/embj.201488957] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 01/28/2015] [Indexed: 11/09/2022] Open
Abstract
Autophagosome biogenesis requires two ubiquitin-like conjugation systems. One couples ubiquitin-like Atg8 to phosphatidylethanolamine, and the other couples ubiquitin-like Atg12 to Atg5. Atg12~Atg5 then forms a heterodimer with Atg16. Membrane recruitment of the Atg12~Atg5/Atg16 complex defines the Atg8 lipidation site. Lipidation requires a PI3P-containing precursor. How PI3P is sensed and used to coordinate the conjugation systems remained unclear. Here, we show that Atg21, a WD40 β-propeller, binds via PI3P to the preautophagosomal structure (PAS). Atg21 directly interacts with the coiled-coil domain of Atg16 and with Atg8. This latter interaction requires the conserved F5K6-motif in the N-terminal helical domain of Atg8, but not its AIM-binding site. Accordingly, the Atg8 AIM-binding site remains free to mediate interaction with its E2 enzyme Atg3. Atg21 thus defines PI3P-dependently the lipidation site by linking and organising the E3 ligase complex and Atg8 at the PAS.
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Affiliation(s)
- Lisa Juris
- Georg-August-University, University Medicine, Institute of Cellular Biochemistry, Goettingen, Germany
| | - Marco Montino
- Georg-August-University, University Medicine, Institute of Cellular Biochemistry, Goettingen, Germany
| | - Peter Rube
- Georg-August-University, University Medicine, Institute of Cellular Biochemistry, Goettingen, Germany
| | - Petra Schlotterhose
- Georg-August-University, University Medicine, Institute of Cellular Biochemistry, Goettingen, Germany
| | - Michael Thumm
- Georg-August-University, University Medicine, Institute of Cellular Biochemistry, Goettingen, Germany
| | - Roswitha Krick
- Georg-August-University, University Medicine, Institute of Cellular Biochemistry, Goettingen, Germany
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47
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Sakoh-Nakatogawa M, Kirisako H, Nakatogawa H, Ohsumi Y. Localization of Atg3 to autophagy-related membranes and its enhancement by the Atg8-family interacting motif to promote expansion of the membranes. FEBS Lett 2015; 589:744-9. [PMID: 25680528 DOI: 10.1016/j.febslet.2015.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/04/2015] [Accepted: 02/04/2015] [Indexed: 11/29/2022]
Abstract
The E2 enzyme Atg3 conjugates the ubiquitin-like protein Atg8 to phosphatidylethanolamine (PE) to drive autophagosome formation in Saccharomyces cerevisiae. In this study, we show that Atg3 localizes to the pre-autophagosomal structure (PAS) and the isolation membrane (IM), providing crucial evidence that Atg8-PE conjugates are produced on these structures. We also find that mutations in the Atg8-family interacting motif (AIM) of Atg3 significantly impairs the PAS/IM localization of Atg3, resulting in inefficient IM expansion. It is suggested that the AIM-mediated PAS/IM localization of Atg3 facilitates membrane expansion in these structures probably by ensuring active production of Atg8-PE on the membranes.
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Affiliation(s)
| | - Hiromi Kirisako
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Hitoshi Nakatogawa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan.
| | - Yoshinori Ohsumi
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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48
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Ngu M, Hirata E, Suzuki K. Visualization of Atg3 during autophagosome formation in Saccharomyces cerevisiae. J Biol Chem 2015; 290:8146-53. [PMID: 25645919 DOI: 10.1074/jbc.m114.626952] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Macroautophagy (autophagy) is a highly conserved cellular recycling process involved in degradation of eukaryotic cellular components. During autophagy, macromolecules and organelles are sequestered into the double-membrane autophagosome and degraded in the vacuole/lysosome. Autophagy-related 8 (Atg8), a core Atg protein essential for autophagosome formation, is a marker of several autophagic structures: the pre-autophagosomal structure (PAS), isolation membrane (IM), and autophagosome. Atg8 is conjugated to phosphatidylethanolamine (PE) through a ubiquitin-like conjugation system to yield Atg8-PE; this reaction is called Atg8 lipidation. Although the mechanisms of Atg8 lipidation have been well studied in vitro, the cellular locale of Atg8 lipidation remains enigmatic. Atg3 is an E2-like enzyme that catalyzes the conjugation reaction between Atg8 and PE. Therefore, we hypothesized that the localization of Atg3 would provide insights about the site of the lipidation reaction. To explore this idea, we constructed functional GFP-tagged Atg3 (Atg3-GFP) by inserting the GFP portion immediately after the handle region of Atg3. During autophagy, Atg3-GFP transiently formed a single dot per cell on the vacuolar membrane. This Atg3-GFP dot colocalized with 2× mCherry-tagged Atg8, demonstrating that Atg3 is localized to autophagic structures. Furthermore, we found that Atg3-GFP is localized to the IM by fine-localization analysis. The localization of Atg3 suggests that Atg3 plays an important role in autophagosome formation at the IM.
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Affiliation(s)
- Meipin Ngu
- From the Department of Integrated Biosciences, Graduate School of Frontier Sciences, and
| | - Eri Hirata
- From the Department of Integrated Biosciences, Graduate School of Frontier Sciences, and
| | - Kuninori Suzuki
- From the Department of Integrated Biosciences, Graduate School of Frontier Sciences, and the Bioimaging Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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49
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Ambivero CT, Cilenti L, Main S, Zervos AS. Mulan E3 ubiquitin ligase interacts with multiple E2 conjugating enzymes and participates in mitophagy by recruiting GABARAP. Cell Signal 2014; 26:2921-9. [PMID: 25224329 DOI: 10.1016/j.cellsig.2014.09.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/05/2014] [Indexed: 12/21/2022]
Abstract
Mulan is an E3 ubiquitin ligase embedded in the outer mitochondrial membrane (OMM) with its RING finger facing the cytoplasm and a large domain located in the intermembrane space (IMS). Mulan is known to have an important role in cell growth, cell death, and more recently in mitophagy. The mechanism of its function is poorly understood; but as an E3 ligase it is expected to interact with specific E2 ubiquitin conjugating enzymes and these complexes will bind and ubiquitinate specific substrates. The unique topology of Mulan can provide a direct link of communicating mitochondrial signals to the cytoplasm. Our studies identified four different E2 conjugating enzymes (Ube2E2, Ube2E3, Ube2G2 and Ube2L3) as specific interactors of Mulan. Each of these E2 conjugating enzymes was fused to the RING finger domain of Mulan and used in a modified yeast two-hybrid screen. Several unique interactors for each Mulan-E2 complex were isolated. One such specific interactor of Mulan-Ube2E3 was the GABARAP (GABAA receptor-associated protein). GABARAP is a member of the Atg8 family of proteins that plays a major role in autophagy/mitophagy. The interaction of GABARAP with Mulan-Ube2E3 required an LC3-interacting region (LIR) located in the RING finger domain of Mulan as well as the presence of Ube2E3. The isolation of four different E2 conjugating enzymes, as specific partners of Mulan E3 ligase, suggests that Mulan is involved in multiple biological pathways. In addition, the interaction of GABARAP with Mulan-Ube2E3 supports the role of Mulan as an important regulator of mitophagy and provides a plausible mechanism for its function in this process.
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Affiliation(s)
- Camilla T Ambivero
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
| | - Lucia Cilenti
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
| | - Stacey Main
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
| | - Antonis S Zervos
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA.
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50
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Ghavami S, Sharma P, Yeganeh B, Ojo OO, Jha A, Mutawe MM, Kashani HH, Los MJ, Klonisch T, Unruh H, Halayko AJ. Airway mesenchymal cell death by mevalonate cascade inhibition: integration of autophagy, unfolded protein response and apoptosis focusing on Bcl2 family proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:1259-71. [PMID: 24637330 DOI: 10.1016/j.bbamcr.2014.03.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 02/07/2023]
Abstract
HMG-CoA reductase, the proximal rate-limiting enzyme in the mevalonate pathway, is inhibited by statins. Beyond their cholesterol lowering impact, statins have pleiotropic effects and their use is linked to improved lung health. We have shown that mevalonate cascade inhibition induces apoptosis and autophagy in cultured human airway mesenchymal cells. Here, we show that simvastatin also induces endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) in these cells. We tested whether coordination of ER stress, autophagy and apoptosis determines survival or demise of human lung mesenchymal cells exposed to statin. We observed that simvastatin exposure activates UPR (activated transcription factor 4, activated transcription factor 6 and IRE1α) and caspase-4 in primary human airway fibroblasts and smooth muscle cells. Exogenous mevalonate inhibited apoptosis, autophagy and UPR, but exogenous cholesterol was without impact, indicating that sterol intermediates are involved with mechanisms mediating statin effects. Caspase-4 inhibition decreased simvastatin-induced apoptosis, whereas inhibition of autophagy by ATG7 or ATG3 knockdown significantly increased cell death. In BAX(-/-)/BAK(-/-) murine embryonic fibroblasts, simvastatin-triggered apoptotic and UPR events were abrogated, but autophagy flux was increased leading to cell death via necrosis. Our data indicate that mevalonate cascade inhibition, likely associated with depletion of sterol intermediates, can lead to cell death via coordinated apoptosis, autophagy, and ER stress. The interplay between these pathways appears to be principally regulated by autophagy and Bcl-2-family pro-apoptotic proteins. These findings uncover multiple mechanisms of action of statins that could contribute to refining the use of such agent in treatment of lung disease.
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Affiliation(s)
- Saeid Ghavami
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada; Department of Human Anatomy and Cell Science, University of Manitoba, Canada
| | - Pawan Sharma
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada
| | - Behzad Yeganeh
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada
| | - Oluwaseun O Ojo
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada
| | - Aruni Jha
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada
| | - Mark M Mutawe
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada
| | - Hessam H Kashani
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada
| | - Marek J Los
- Dept. of Clinical & Experimental Medicine, Integrative Regenerative Med. (IGEN) Center, Linköping University, Sweden
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, University of Manitoba, Canada
| | - Helmut Unruh
- Department of Internal Medicine, University of Manitoba, Canada
| | - Andrew J Halayko
- Department of Physiology, University of Manitoba, Canada; Manitoba Institute of Child Health, University of Manitoba, Canada; Department of Internal Medicine, University of Manitoba, Canada.
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