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Huang H, Tian Y, Huo Y, Liu Y, Yang W, Li Y, Zhuo M, Xiang D, Li C, Yi G, Liu S. The Autophagy-Related Musa acuminata Protein MaATG8F Interacts with MaATG4B, Regulating Banana Disease Resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4. J Fungi (Basel) 2024; 10:91. [PMID: 38392763 PMCID: PMC10890345 DOI: 10.3390/jof10020091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Banana is one of the most important fruits in the world due to its status as a major food source for more than 400 million people. Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes substantial losses of banana crops every year, and molecular host resistance mechanisms are currently unknown. We here performed a genomewide analysis of the autophagy-related protein 8 (ATG8) family in a wild banana species. The banana genome was found to contain 10 MaATG8 genes. Four MaATG8s formed a gene cluster in the distal part of chromosome 4. Phylogenetic analysis of ATG8 families in banana, Arabidopsis thaliana, citrus, rice, and ginger revealed five major phylogenetic clades shared by all of these plant species, demonstrating evolutionary conservation of the MaATG8 families. The transcriptomic analysis of plants infected with Foc TR4 showed that nine of the MaATG8 genes were more highly induced in resistant cultivars than in susceptible cultivars. Finally, MaATG8F was found to interact with MaATG4B in vitro (with yeast two-hybrid assays), and MaATG8F and MaATG4B all positively regulated banana resistance to Foc TR4. Our study provides novel insights into the structure, distribution, evolution, and expression of the MaATG8 family in bananas. Furthermore, the discovery of interactions between MaATG8F and MaATG4B could facilitate future research of disease resistance genes for the genetic improvement of bananas.
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Affiliation(s)
- Huoqing Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Yuzhen Tian
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yile Huo
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Yushan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Wenlong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Yuqing Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Mengxia Zhuo
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Dandan Xiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Siwen Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Research Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
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Kim WJ, Kim W, Kim Y, Cheong H, Kim SJ. Coordinated recruitment of conserved defense-signaling pathways in PVY O-Infected Nicotiana benthamiana. Plant Signal Behav 2023; 18:2252972. [PMID: 37655790 PMCID: PMC10478736 DOI: 10.1080/15592324.2023.2252972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
Potato virus Y (PVY) is an aphid-transmitted potyvirus that affects economically important solanaceous species. In this study, the phenomena and mechanisms following infection with PVY were investigated in tobacco (Nicotiana benthamiana). In tobacco plants, infection with a mild strain of PVY (PVYO) induced stunted growth in the first two leaves at the shoot apex starting 7 days post-infection (dpi), and mosaic symptoms began to appear on newly developing young leaves at 14 dpi. Using enzyme-linked immunosorbent assay and ultrastructure analysis, we confirmed that viral particles accumulated only in the upper developing leaves of infected plants. We analyzed reactive oxygen species (ROS) generation in leaves from the bottom to the top of the plants to investigate whether delayed symptom development in leaves was associated with a defense response to the virus. In addition, the ultrastructural analysis confirmed the increase of ATG4 and ATG8, which are autophagy markers by endoplasmic reticulum (ER) stress, and the expression of genes involved in viral RNA suppression. Overall, our results suggested that viral RNA silencing and induced autophagy may play a role in the inhibition of viral symptom development in host plants in response to PVYO infection.
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Affiliation(s)
- Won-Jin Kim
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju, Republic of Korea
| | - Woong Kim
- Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Youngsoon Kim
- Plant Cell Research Institute of BIO-FD&C, Co., Ltd., Incheon, Republic of Korea
| | - Hyeonsook Cheong
- Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Seok-Jun Kim
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju, Republic of Korea
- Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
- Institute of Well-Aging Medicare, Chosun University, Gwangju, Republic of Korea
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3
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Mishra A, Varshney A, Mishra S. Regulation of Atg8 membrane deconjugation by cysteine proteases in the malaria parasite Plasmodium berghei. Cell Mol Life Sci 2023; 80:344. [PMID: 37910326 DOI: 10.1007/s00018-023-05004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
During macroautophagy, the Atg8 protein is conjugated to phosphatidylethanolamine (PE) in autophagic membranes. In Apicomplexan parasites, two cysteine proteases, Atg4 and ovarian tumor unit (Otu), have been identified to delipidate Atg8 to release this protein from membranes. Here, we investigated the role of cysteine proteases in Atg8 conjugation and deconjugation and found that the Plasmodium parasite consists of both activities. We successfully disrupted the genes individually; however, simultaneously, they were refractory to deletion and essential for parasite survival. Mutants lacking Atg4 and Otu showed normal blood and mosquito stage development. All mice infected with Otu KO sporozoites became patent; however, Atg4 KO sporozoites either failed to establish blood infection or showed delayed patency. Through in vitro and in vivo analysis, we found that Atg4 KO sporozoites invade and normally develop into early liver stages. However, nuclear and organelle differentiation was severely hampered during late stages and failed to mature into hepatic merozoites. We found a higher level of Atg8 in Atg4 KO parasites, and the deconjugation of Atg8 was hampered. We confirmed Otu localization on the apicoplast; however, parasites lacking Otu showed no visible developmental defects. Our data suggest that Atg4 is the primary deconjugating enzyme and that Otu cannot replace its function completely because it cleaves the peptide bond at the N-terminal side of glycine, thereby irreversibly inactivating Atg8 during its recycling. These findings highlight a role for the Atg8 deconjugation pathway in organelle biogenesis and maintenance of the homeostatic cellular balance.
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Affiliation(s)
- Akancha Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aastha Varshney
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Crespo JL, Pérez-Pérez ME. Monitoring of ATG4 Protease Activity During Autophagy in the Model Microalga Chlamydomonas reinhardtii. Methods Mol Biol 2022; 2447:205-220. [PMID: 35583784 DOI: 10.1007/978-1-0716-2079-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Deciphering the molecular mechanisms underlying the regulation of the ATG4 protease is essential to understand the regulation of ATG8 lipidation, a key step in the biogenesis of the autophagosome and hence in autophagy progression. Here, we describe two complementary approaches to monitor ATG4 proteolytic activity in the model green alga Chlamydomonas reinhardtii: an in vitro assay using recombinant ATG4 and recombinant ATG8 as substrate, and a cell-free assay using soluble total protein extract from Chlamydomonas and recombinant Chlamydomonas ATG8 as substrate. Both assays are followed by non-reducing SDS-PAGE and immuno-blot analysis. Given the high evolutionary conservation of the ATG8 maturation process, these assays have also been validated to monitor ATG4 activity in yeast using Chlamydomonas ATG8 as substrate.
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Affiliation(s)
- José L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Sevilla, Spain
| | - M Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Sevilla, Spain.
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5
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De Brasi-Velasco S, López-Vidal O, Martí MC, Ortiz-Espín A, Sevilla F, Jiménez A. Autophagy Is Involved in the Viability of Overexpressing Thioredoxin o1 Tobacco BY-2 Cells under Oxidative Conditions. Antioxidants (Basel) 2021; 10:1884. [PMID: 34942987 DOI: 10.3390/antiox10121884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 01/06/2023] Open
Abstract
Autophagy is an essential process for the degradation of non-useful components, although the mechanism involved in its regulation is less known in plants than in animal systems. Redox regulation of autophagy components is emerging as a possible key mechanism with thioredoxins (TRXs) proposed as involved candidates. In this work, using overexpressing PsTRXo1 tobacco cells (OEX), which present higher viability than non-overexpressing cells after H2O2 treatment, we examine the functional interaction of autophagy and PsTRXo1 in a collaborative response. OEX cells present higher gene expression of the ATG (Autophagy related) marker ATG4 and higher protein content of ATG4, ATG8, and lipidated ATG8 as well as higher ATG4 activity than control cells, supporting the involvement of autophagy in their response to H2O2. In this oxidative situation, autophagy occurs in OEX cells as is evident from an accumulation of autolysosomes and ATG8 immunolocalization when the E-64d autophagy inhibitor is used. Interestingly, cell viability decreases in the presence of the inhibitor, pointing to autophagy as being involved in cell survival. The in vitro interaction of ATG4 and PsTRXo1 proteins is confirmed by dot-blot and co-immunoprecipitation assays as well as the redox regulation of ATG4 activity by PsTRXo1. These findings extend the role of TRXs in mediating the redox regulation of the autophagy process in plant cells.
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6
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Zhou Y, Wang Z, Huang Y, Bai C, Zhang X, Fang M, Ju Z, Liu B. Membrane dynamics of ATG4B and LC3 in autophagosome formation. J Mol Cell Biol 2021; 13:853-863. [PMID: 34562084 PMCID: PMC8800521 DOI: 10.1093/jmcb/mjab059] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/14/2022] Open
Abstract
The biogenesis of autophagosomes provides the basis for macroautophagy to capture and degrade intracellular cargoes. Binding of the autophagy-related protein ATG8/LC3 to autophagic membranes is essential to autophagosome formation, which involves the specific and dynamic processing of ATG8/LC3 by cysteine protease ATG4. However, to date, the mechanism whereby ATG4 is recruited to the membranes, the interaction of ATG4 and ATG8/LC3 on the membranes, and its role in the growth of phagophore are not completely understood. Here, we used fluorescence recovery after photobleaching to monitor the turnover of GFP-tagged ATG4B and LC3B in living animal cells. The data show that ATG4B localizes to early autophagic membranes in an LC3B-dependent manner. During autophagy, ATG4B and LC3B undergo rapid cytosol/isolation membrane exchange but not at the cytosol/completed autophagosome. In addition, ATG4B activity controls the efficiency of autophagosome formation by impacting the membrane binding/dissociation of LC3B. These data suggest that ATG4 and LC3 play interdependent roles in the formation of autophagosomes.
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Affiliation(s)
- Yuanyuan Zhou
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Zhenkun Wang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Yijia Huang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Chujie Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Bone and Soft Tissue Tumor, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xianli Zhang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Mengdie Fang
- College of Bioengineering, Hangzhou Medical College, Hangzhou 310013, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Bo Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
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7
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Martínez-García GG, Pérez RF, Fernández ÁF, Durand S, Kroemer G, Mariño G. Autophagy Deficiency by Atg4B Loss Leads to Metabolomic Alterations in Mice. Metabolites 2021; 11:metabo11080481. [PMID: 34436422 PMCID: PMC8399495 DOI: 10.3390/metabo11080481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/18/2022] Open
Abstract
Autophagy is an essential protective mechanism that allows mammalian cells to cope with a variety of stressors and contributes to maintaining cellular and tissue homeostasis. Due to these crucial roles and also to the fact that autophagy malfunction has been described in a wide range of pathologies, an increasing number of in vivo studies involving animal models targeting autophagy genes have been developed. In mammals, total autophagy inactivation is lethal, and constitutive knockout models lacking effectors of this route are not viable, which has hindered so far the analysis of the consequences of a systemic autophagy decline. Here, we take advantage of atg4b−/− mice, an autophagy-deficient model with only partial disruption of the process, to assess the effects of systemic reduction of autophagy on the metabolome. We describe for the first time the metabolic footprint of systemic autophagy decline, showing that impaired autophagy results in highly tissue-dependent alterations that are more accentuated in the skeletal muscle and plasma. These changes, which include changes in the levels of amino-acids, lipids, or nucleosides, sometimes resemble those that are frequently described in conditions like aging, obesity, or cardiac damage. We also discuss different hypotheses on how impaired autophagy may affect the metabolism of several tissues in mammals.
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Affiliation(s)
- Gemma G. Martínez-García
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología (IUOPA), 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Raúl F. Pérez
- Instituto Universitario de Oncología (IUOPA), 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), 33940 El Entrego, Spain
- Departamento de Biología de Organismos y Sistemas (BOS), Facultad de Biología, Universidad de Oviedo, 33006 Oviedo, Spain
- Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), 28029 Madrid, Spain
| | - Álvaro F. Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Sylvere Durand
- Centre de Recherche des Cordeliers, INSERM, U1138, F-75006 Paris, France; (S.D.); (G.K.)
- Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, F-75006 Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, F-75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, F-94805 Villejuif, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, INSERM, U1138, F-75006 Paris, France; (S.D.); (G.K.)
- Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, F-75006 Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, F-75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, F-94805 Villejuif, France
| | - Guillermo Mariño
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología (IUOPA), 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Correspondence: ; Tel.: +34-985-652-416; Fax: +349-856-524-19
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8
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Nguyen TN, Padman BS, Lazarou M. ATG4s: above and beyond the Atg8-family protein lipidation system. Autophagy 2021; 17:2648-2650. [PMID: 34308753 DOI: 10.1080/15548627.2021.1953263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The sole proteases of the macroautophagy/autophagy machinery, the ATG4s, contribute to autophagosome formation by cleaving Atg8-family protein members (LC3/GABARAPs) which enables Atg8-family protein lipidation and de-lipidation. Our recent work reveals that ATG4s can also promote phagophore growth independently of their protease activity and of Atg8-family proteins. ATG4s and their proximity partners including ARFIP2 and LRBA function to promote trafficking of ATG9A to mitochondria during PINK1-PRKN mitophagy. Through the development of a 3D electron microscopy framework utilizing FIB-SEM and artificial intelligence (termed AIVE: Artificial Intelligence-directed Voxel Extraction), we show that ATG4s promote ER-phagophore contacts during the lipid-transfer phase of autophagosome biogenesis, which requires ATG2B and ATG9A to support phagophore growth. We also discovered that ATG4s are not essential for removal of Atg8-family proteins from autolysosomes, but they can function as deubiquitinase-like enzymes to counteract the conjugation of Atg8-family proteins to other proteins, a process that we have termed ATG8ylation (also known as LC3ylation). These discoveries demonstrate the duality of the ATG4 family in driving autophagosome formation by functioning as both autophagy proteases and trafficking factors, while simultaneously raising questions about the putative roles of ATG8ylation in cell biology.
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Affiliation(s)
- Thanh Ngoc Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Benjamin Scott Padman
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
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9
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Abstract
Atg8-family protein lipidation is the most commonly used marker for monitoring autophagy. During macroautophagy, Atg8-family proteins are specifically conjugated to phosphatidylethanolamine (PE) in forming, double-membrane autophagosomes. A distinct, non-canonical autophagy pathway also operates, characterized by the Conjugation of ATG8s to endolysosomal Single Membranes (CASM). In our new study, we show that CASM is associated with the alternative conjugation of Atg8-family proteins to phosphatidylserine (PS), and PE, in response to various cellular stimuli. We also discover differences in the regulation of conjugation to PE and PS by ATG4s, and altered dynamics between the two species. The identification of alternative Atg8-family protein PS lipidation opens up exciting new questions on the roles, regulation and biology of Atg8-family proteins during non-canonical autophagy.
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Affiliation(s)
- Joanne Durgan
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK
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10
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Affiliation(s)
- Isaac Tamargo-Gómez
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gemma G Martínez-García
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - María F Suárez
- Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Alvaro F Fernández
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Universidad de Oviedo, Oviedo, Spain
| | - Guillermo Mariño
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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11
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Nguyen TN, Padman BS, Zellner S, Khuu G, Uoselis L, Lam WK, Skulsuppaisarn M, Lindblom RSJ, Watts EM, Behrends C, Lazarou M. ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system. Mol Cell 2021; 81:2013-2030.e9. [PMID: 33773106 DOI: 10.1016/j.molcel.2021.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/20/2020] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
The sequestration of damaged mitochondria within double-membrane structures termed autophagosomes is a key step of PINK1/Parkin mitophagy. The ATG4 family of proteases are thought to regulate autophagosome formation exclusively by processing the ubiquitin-like ATG8 family (LC3/GABARAPs). We discover that human ATG4s promote autophagosome formation independently of their protease activity and of ATG8 family processing. ATG4 proximity networks reveal a role for ATG4s and their proximity partners, including the immune-disease protein LRBA, in ATG9A vesicle trafficking to mitochondria. Artificial intelligence-directed 3D electron microscopy of phagophores shows that ATG4s promote phagophore-ER contacts during the lipid-transfer phase of autophagosome formation. We also show that ATG8 removal during autophagosome maturation does not depend on ATG4 activity. Instead, ATG4s can disassemble ATG8-protein conjugates, revealing a role for ATG4s as deubiquitinating-like enzymes. These findings establish non-canonical roles of the ATG4 family beyond the ATG8 lipidation axis and provide an AI-driven framework for rapid 3D electron microscopy.
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Affiliation(s)
- Thanh Ngoc Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| | - Benjamin Scott Padman
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Susanne Zellner
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Grace Khuu
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Louise Uoselis
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Wai Kit Lam
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Marvin Skulsuppaisarn
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Runa S J Lindblom
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Emily M Watts
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
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12
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Durgan J, Lystad AH, Sloan K, Carlsson SR, Wilson MI, Marcassa E, Ulferts R, Webster J, Lopez-Clavijo AF, Wakelam MJ, Beale R, Simonsen A, Oxley D, Florey O. Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine. Mol Cell 2021; 81:2031-2040.e8. [PMID: 33909989 PMCID: PMC8122138 DOI: 10.1016/j.molcel.2021.03.020] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/15/2021] [Accepted: 03/16/2021] [Indexed: 01/22/2023]
Abstract
Autophagy is a fundamental catabolic process that uses a unique post-translational modification, the conjugation of ATG8 protein to phosphatidylethanolamine (PE). ATG8 lipidation also occurs during non-canonical autophagy, a parallel pathway involving conjugation of ATG8 to single membranes (CASM) at endolysosomal compartments, with key functions in immunity, vision, and neurobiology. It is widely assumed that CASM involves the same conjugation of ATG8 to PE, but this has not been formally tested. Here, we discover that all ATG8s can also undergo alternative lipidation to phosphatidylserine (PS) during CASM, induced pharmacologically, by LC3-associated phagocytosis or influenza A virus infection, in mammalian cells. Importantly, ATG8-PS and ATG8-PE adducts are differentially delipidated by the ATG4 family and bear different cellular dynamics, indicating significant molecular distinctions. These results provide important insights into autophagy signaling, revealing an alternative form of the hallmark ATG8 lipidation event. Furthermore, ATG8-PS provides a specific "molecular signature" for the non-canonical autophagy pathway.
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Affiliation(s)
- Joanne Durgan
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Alf H Lystad
- Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | | | - Sven R Carlsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | | | | | - Judith Webster
- Mass Spectrometry Facility, Babraham Institute, Cambridge, UK
| | | | - Michael J Wakelam
- Signalling Programme, Babraham Institute, Cambridge, UK; Lipidomics Facility, Babraham Institute, Cambridge, UK
| | | | - Anne Simonsen
- Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, Cambridge, UK
| | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK.
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13
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Pérez-Pérez ME, Lemaire SD, Crespo JL. The ATG4 protease integrates redox and stress signals to regulate autophagy. J Exp Bot 2021; 72:3340-3351. [PMID: 33587749 DOI: 10.1093/jxb/erab063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Autophagy is a highly conserved degradative pathway that ensures cellular homeostasis through the removal of damaged or useless intracellular components including proteins, membranes, or even entire organelles. A main hallmark of autophagy is the biogenesis of autophagosomes, double-membrane vesicles that engulf and transport to the vacuole the material to be degraded and recycled. The formation of autophagosomes responds to integrated signals produced as a consequence of metabolic reactions or different types of stress and is mediated by the coordinated action of core autophagy-related (ATG) proteins. ATG4 is a key Cys-protease with a dual function in both ATG8 lipidation and free ATG8 recycling whose balance is crucial for proper biogenesis of the autophagosome. ATG4 is conserved in the green lineage, and its regulation by different post-translational modifications has been reported in the model systems Chlamydomonas reinhardtii and Arabidopsis. In this review, we discuss the major role of ATG4 in the integration of stress and redox signals that regulate autophagy in algae and plants.
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Affiliation(s)
- María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Avda. Américo Vespucio, Sevilla, Spain
| | - Stéphane D Lemaire
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
- CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - José L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Avda. Américo Vespucio, Sevilla, Spain
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14
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Wang M, Jing J, Li H, Liu J, Yuan Y, Sun L. The expression characteristics and prognostic roles of autophagy-related genes in gastric cancer. PeerJ 2021; 9:e10814. [PMID: 33604190 PMCID: PMC7866901 DOI: 10.7717/peerj.10814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background Autophagy is an evolutionally highly conserved process, accompanied by the dynamic changes of various molecules, which is necessary for the orderly degradation and recycling of cellular components. The aim of the study was to identify the role of autophagy-related (ATG) genes in the occurrence and development of gastric cancer (GC). Methods Data from Oncomine dataset was used for the differential expression analysis between cancer and normal tissues. The association of ATG genes expression with clinicopathologic indicators was evaluated by The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database. Moreover, using the TCGA datasets, the prognostic role of ATG genes was assessed. A nomogram was further built to assess the independent prognostic factors. Results The expression of autophagy-related genes AMBRA1, ATG4B, ATG7, ATG10, ATG12, ATG16L2, GABARAPL2, GABARAPL1, ULK4 and WIPI2 showed differences between cancer and normal tissues. After verification, ATG14 and ATG4D were significantly associated with TNM stage. ATG9A, ATG2A, and ATG4D were associated with T stage. VMP1 and ATG4A were low-expressed in patients without lymph node metastasis. No gene in autophagy pathway was associated with M stage. Further multivariate analysis suggested that ATG4D and MAP1LC3C were independent prognostic factors for GC. The C-index of nomogram was 0.676 and the 95% CI was 0.628 to 0.724. Conclusion Our study provided a comprehensive illustration of ATG genes expression characteristics in GC. Abnormal expressions of the ubiquitin-like conjugated system in ATG genes plays a key role in the occurrence of GC. ATG8/LC3 sub-system may play an important role in development and clinical outcome of GC. In the future, it is necessary to further elucidate the alterations of specific ATG8/LC3 forms in order to provide insights for the discovery, diagnosis, or targeting for GC.
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Affiliation(s)
- Mengya Wang
- Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Hao Li
- Department of Clinical Laboratory, the First Hospital of China Medical University, Shenyang, China
| | - Jingwei Liu
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
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15
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Xia F, Liu P, Li M. The regulatory factors and pathological roles of autophagy-related protein 4 in diverse diseases: Recent research advances. Med Res Rev 2020; 41:1644-1675. [PMID: 33314291 DOI: 10.1002/med.21772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
Macroautophagy (autophagy) is an evolutionarily conserved and dynamic degradation/recycling pathway in which portions of the cytoplasm, such as dysfunctional proteins and surplus organelles, are engulfed by double-membrane bound vesicles through a lysosome-dependent process. As the only proteolytic enzyme of the core mammalian autophagy proteins, autophagy-related protein 4 (ATG4) primes newly synthesized pro-light chain 3 (LC3) to form LC3-I that attaches to phosphatidylethanolamine and delipidates LC3-PE to LC3-I for recycling. Besides autophagy, ATG4 has been shown to be involved in regulating various biological and pathological processes. The roles of ATG4 in cancer therapy, a methodology for ATG4 activity detection, and the discovery of chemical modulators have been well-reviewed. However, a comprehensive summary on how ATG4 is regulated by multiple factors and, thereby, how ATG4 influences autophagy or other pathways remains lacking. In this paper, we summarize multiple processes and molecules that regulate the activity of ATG4, such as micro-RNAs, posttranslational modifications, and small molecules. Additionally, we focus on the relationship between ATG4 and diverse diseases, including cancer, neurodegeneration, microbial infection, and other diseases. It provides insight regarding potential ATG4-targeted therapeutic opportunities, which could be beneficial for future studies and human health.
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Affiliation(s)
- Fan Xia
- Department of Pharmacology and Toxicology, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peiqing Liu
- Department of Pharmacology and Toxicology, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Min Li
- Department of Pharmacology and Toxicology, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
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16
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Abstract
Macroautophagy/autophagy plays a dual role in many physiological processes of multicellular eukaryotes. In plants, autophagy can be used by both host and pathogen for a beneficiary infection outcome. Plants employ a two-tier innate immune system to defend against invading pathogens. Cell surface localized pattern recognition receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and launch pattern-triggered immunity (PTI) to provide broad-spectrum resistance. Pathogens inject a battery of effector proteins into their hosts to counter PTI and compromise the primary immune response. Hosts induce a second layer of defense called effector-triggered immunity (ETI) to counter the effects of these effectors. In addition to ETI and PTI, autophagy is emerging as a central cellular process modulated by both host and pathogens toward their respective advantage. Pathogens lacking the ability to inject effectors are compromised in virulence. However, molecular targets and biochemical characterization of most of these effector proteins remain elusive. In a recent paper we presented a systematic analysis of interaction between autophagy proteins of Arabidopsis thaliana with effectors from bacterial, fungal, oomycete and nematode pathogens. Abbreviations: ATG, autophagy related; BiFC, bimolecular fluorescence complementation; ETI, effector-triggered immunity; PAMPs, pathogen-associated molecular patterns; PTI, pattern-triggered immunity.
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Affiliation(s)
- Neeraj K Lal
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California , Davis, CA, USA
| | - Burinrutt Thanasuwat
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California , Davis, CA, USA
| | - Barry Chan
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California , Davis, CA, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California , Davis, CA, USA
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17
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Herhaus L, Bhaskara RM, Lystad AH, Gestal‐Mato U, Covarrubias‐Pinto A, Bonn F, Simonsen A, Hummer G, Dikic I. TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Rep 2020; 21:e48317. [PMID: 31709703 PMCID: PMC6945063 DOI: 10.15252/embr.201948317] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Autophagy is a highly conserved catabolic process through which defective or otherwise harmful cellular components are targeted for degradation via the lysosomal route. Regulatory pathways, involving post-translational modifications such as phosphorylation, play a critical role in controlling this tightly orchestrated process. Here, we demonstrate that TBK1 regulates autophagy by phosphorylating autophagy modifiers LC3C and GABARAP-L2 on surface-exposed serine residues (LC3C S93 and S96; GABARAP-L2 S87 and S88). This phosphorylation event impedes their binding to the processing enzyme ATG4 by destabilizing the complex. Phosphorylated LC3C/GABARAP-L2 cannot be removed from liposomes by ATG4 and are thus protected from ATG4-mediated premature removal from nascent autophagosomes. This ensures a steady coat of lipidated LC3C/GABARAP-L2 throughout the early steps in autophagosome formation and aids in maintaining a unidirectional flow of the autophagosome to the lysosome. Taken together, we present a new regulatory mechanism of autophagy, which influences the conjugation and de-conjugation of LC3C and GABARAP-L2 to autophagosomes by TBK1-mediated phosphorylation.
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Affiliation(s)
- Lina Herhaus
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Ramachandra M Bhaskara
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Alf Håkon Lystad
- Department of Molecular MedicineFaculty of MedicineInstitute of Basic Medical Sciences and Centre for Cancer Cell ReprogrammingInstitute of Clinical MedicineUniversity of OsloOsloNorway
| | - Uxía Gestal‐Mato
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
| | | | - Florian Bonn
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
- Present address:
Immundiagnostik AGBensheimGermany
| | - Anne Simonsen
- Department of Molecular MedicineFaculty of MedicineInstitute of Basic Medical Sciences and Centre for Cancer Cell ReprogrammingInstitute of Clinical MedicineUniversity of OsloOsloNorway
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsFrankfurt am MainGermany
- Institute for BiophysicsGoethe UniversityFrankfurt am MainGermany
| | - Ivan Dikic
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesRiedberg Campus, Goethe University FrankfurtFrankfurt am MainGermany
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18
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Agrotis A, Ketteler R. On ATG4B as Drug Target for Treatment of Solid Tumours-The Knowns and the Unknowns. Cells 2019; 9:cells9010053. [PMID: 31878323 PMCID: PMC7016753 DOI: 10.3390/cells9010053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Autophagy is an evolutionary conserved stress survival pathway that has been shown to play an important role in the initiation, progression, and metastasis of multiple cancers; however, little progress has been made to date in translation of basic research to clinical application. This is partially due to an incomplete understanding of the role of autophagy in the different stages of cancer, and also to an incomplete assessment of potential drug targets in the autophagy pathway. While drug discovery efforts are on-going to target enzymes involved in the initiation phase of the autophagosome, e.g., unc51-like autophagy activating kinase (ULK)1/2, vacuolar protein sorting 34 (Vps34), and autophagy-related (ATG)7, we propose that the cysteine protease ATG4B is a bona fide drug target for the development of anti-cancer treatments. In this review, we highlight some of the recent advances in our understanding of the role of ATG4B in autophagy and its relevance to cancer, and perform a critical evaluation of ATG4B as a druggable cancer target.
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19
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Fu Y, Huang Z, Hong L, Lu JH, Feng D, Yin XM, Li M. Targeting ATG4 in Cancer Therapy. Cancers (Basel) 2019; 11:E649. [PMID: 31083460 DOI: 10.3390/cancers11050649] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a lysosome-mediated degradation pathway that enables the degradation and recycling of cytoplasmic components to sustain metabolic homoeostasis. Recently, autophagy has been reported to have an astonishing number of connections to cancer, as tumor cells require proficient autophagy in response to metabolic and therapeutic stresses to sustain cell proliferation. Autophagy-related gene 4 (ATG4) is essential for autophagy by affecting autophagosome formation through processing full-length microtubule-associated protein 1A/1B-light chain 3 (pro-LC3) and lipidated LC3. An increasing amount of evidence suggests that ATG4B expression is elevated in certain types of cancer, implying that ATG4B is a potential anticancer target. In this review, we address the central roles of ATG4B in the autophagy machinery and in targeted cancer therapy. Specifically, we discuss how pharmacologically inhibiting ATG4B can benefit cancer therapies.
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20
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Hill SE, Kauffman KJ, Krout M, Richmond JE, Melia TJ, Colón-Ramos DA. Maturation and Clearance of Autophagosomes in Neurons Depends on a Specific Cysteine Protease Isoform, ATG-4.2. Dev Cell 2019; 49:251-266.e8. [PMID: 30880001 DOI: 10.1016/j.devcel.2019.02.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 12/17/2018] [Accepted: 02/12/2019] [Indexed: 12/31/2022]
Abstract
In neurons, defects in autophagosome clearance have been associated with neurodegenerative disease. Yet, the mechanisms that coordinate trafficking and clearance of synaptic autophagosomes are poorly understood. Here, we use genetic screens and in vivo imaging in single neurons of C. elegans to identify mechanisms necessary for clearance of synaptic autophagosomes. We observed that autophagy at the synapse can be modulated in vivo by the state of neuronal activity, that autophagosomes undergo UNC-16/JIP3-mediated retrograde transport, and that autophagosomes containing synaptic material mature in the cell body. Through forward genetic screens, we then determined that autophagosome maturation in the cell body depends on the protease ATG-4.2, but not the related ATG-4.1, and that ATG-4.2 can cleave LGG-1/Atg8/GABARAP from membranes. Our studies revealed that ATG-4.2 is specifically necessary for the maturation and clearance of autophagosomes and that defects in transport and ATG-4.2-mediated maturation genetically interact to enhance abnormal accumulation of autophagosomes in neurons.
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Affiliation(s)
- Sarah E Hill
- Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Karlina J Kauffman
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mia Krout
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Janet E Richmond
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Daniel A Colón-Ramos
- Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, 201 Blvd del Valle, San Juan 00901, Puerto Rico.
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21
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Kauffman KJ, Yu S, Jin J, Mugo B, Nguyen N, O'Brien A, Nag S, Lystad AH, Melia TJ. Delipidation of mammalian Atg8-family proteins by each of the four ATG4 proteases. Autophagy 2018; 14:992-1010. [PMID: 29458288 DOI: 10.1080/15548627.2018.1437341] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During macroautophagy/autophagy, mammalian Atg8-family proteins undergo 2 proteolytic processing events. The first exposes a COOH-terminal glycine used in the conjugation of these proteins to lipids on the phagophore, the precursor to the autophagosome, whereas the second releases the lipid. The ATG4 family of proteases drives both cleavages, but how ATG4 proteins distinguish between soluble and lipid-anchored Atg8 proteins is not well understood. In a fully reconstituted delipidation assay, we establish that the physical anchoring of mammalian Atg8-family proteins in the membrane dramatically shifts the way ATG4 proteases recognize these substrates. Thus, while ATG4B is orders of magnitude faster at processing a soluble unprimed protein, all 4 ATG4 proteases can be activated to similar enzymatic activities on lipid-attached substrates. The recognition of lipidated but not soluble substrates is sensitive to a COOH-terminal LIR motif both in vitro and in cells. We suggest a model whereby ATG4B drives very fast priming of mammalian Atg8 proteins, whereas delipidation is inherently slow and regulated by all ATG4 homologs.
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Affiliation(s)
- Karlina J Kauffman
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Shenliang Yu
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Jiaxin Jin
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA.,b Lanzhou University Second Hospital , Lanzhou , Gansu Province , China
| | - Brian Mugo
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Nathan Nguyen
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Aidan O'Brien
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Shanta Nag
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Alf Håkon Lystad
- c Department of Molecular Medicine , Institute of Basic Medical Sciences, University of Oslo , Norway
| | - Thomas J Melia
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
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22
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Skytte Rasmussen M, Mouilleron S, Kumar Shrestha B, Wirth M, Lee R, Bowitz Larsen K, Abudu Princely Y, O'Reilly N, Sjøttem E, Tooze SA, Lamark T, Johansen T. ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. Autophagy 2017; 13:834-853. [PMID: 28287329 PMCID: PMC5446077 DOI: 10.1080/15548627.2017.1287651] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 12/29/2022] Open
Abstract
The cysteine protease ATG4B cleaves off one or more C-terminal residues of the inactive proform of proteins of the ortholog and paralog LC3 and GABARAP subfamilies of yeast Atg8 to expose a C-terminal glycine that is conjugated to phosphatidylethanolamine during autophagosome formation. We show that ATG4B contains a C-terminal LC3-interacting region (LIR) motif important for efficient binding to and cleavage of LC3 and GABARAP proteins. We solved the crystal structures of the GABARAPL1-ATG4B C-terminal LIR complex. Analyses of the structures and in vitro binding assays, using specific point mutants, clearly showed that the ATG4B LIR binds via electrostatic-, aromatic HP1 and hydrophobic HP2 pocket interactions. Both these interactions and the catalytic site-substrate interaction contribute to binding between LC3s or GABARAPs and ATG4B. We also reveal an unexpected role for ATG4B in stabilizing the unlipidated forms of GABARAP and GABARAPL1. In mouse embryonic fibroblast (MEF) atg4b knockout cells, GABARAP and GABARAPL1 were unstable and degraded by the proteasome. Strikingly, the LIR motif of ATG4B was required for stabilization of the unlipidated forms of GABARAP and GABARAPL1 in cells.
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Affiliation(s)
- Mads Skytte Rasmussen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | | | - Birendra Kumar Shrestha
- 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
| | - Rebecca Lee
- Structural Biology, The Francis Crick Institute, London, UK
| | - Kenneth Bowitz Larsen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Yakubu Abudu Princely
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nicola O'Reilly
- Peptide Chemistry Science Technology Platform, 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
| | - 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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23
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Wei CC, Luo Z, Song YF, Pan YX, Wu K, You WJ. Identification of autophagy related genes LC3 and ATG4 from yellow catfish Pelteobagrus fulvidraco and their transcriptional responses to waterborne and dietborne zinc exposure. Chemosphere 2017; 175:228-238. [PMID: 28222377 DOI: 10.1016/j.chemosphere.2017.02.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Autophagy mediates the regulation of lipid metabolism. Moreover, our recent study indicated that waterborne and dietborne zinc (Zn) exposure differentially influenced lipid metabolism in a fish species of significance for aquaculture, yellow catfish Pelteobagrus fulvidraco, but further mechanism remained unknown. The hypothesis of the present study is that autophagy mediated the Zn-induced changes of lipid metabolism of yellow catfish subjected to different exposure pathways. To this end, we cloned key genes involved in autophagy in yellow catfish, explored their mRNA expressions in responses to different Zn exposure pathways. Full-length cDNA sequences of two LC3 subtypes and six ATG4 isoforms were isolated from yellow catfish. More ATG4 members were firstly identified in fish that might have arisen by teleost-specific whole genome duplication events. All of these members shared similar domain structure to their orthologous genes of vertebrates. Their mRNAs were widely expressed in various tissues, but at variable levels. Extra Zn addition in water or diets induced (P < 0.05) mRNA expression of ATG4Da, ATG4Db and LC3B. Considering their important roles of these genes in lipid metabolism, ATG4Da, ATG4Db and LC3B may mediate the changes of Zn-induced hepatic lipid metabolism of yellow catfish under different Zn exposure pathways. For the first time, we characterized the full-length cDNA sequences of six ATG4 isoforms and two LC3 subtypes, determined their tissue expression profiles and transcriptional responses to different Zn exposure pathways, which would contribute to our understanding of the molecular basis of autophagy, and also provide new insights into physiological responses to different Zn exposure pathways.
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Affiliation(s)
- Chuan-Chuan Wei
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
| | - Yu-Feng Song
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Ya-Xiong Pan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Wu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Jing You
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
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24
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Antonelli M, Strappazzon F, Arisi I, Brandi R, D'Onofrio M, Sambucci M, Manic G, Vitale I, Barilà D, Stagni V. ATM kinase sustains breast cancer stem-like cells by promoting ATG4C expression and autophagy. Oncotarget 2017; 8:21692-21709. [PMID: 28423511 PMCID: PMC5400616 DOI: 10.18632/oncotarget.15537] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/23/2017] [Indexed: 12/14/2022] Open
Abstract
The efficacy of Ataxia-Telangiectasia Mutated (ATM) kinase signalling inhibition in cancer therapy is tempered by the identification of new emerging functions of ATM, which suggests that the role of this protein in cancer progression is complex. We recently demonstrated that this tumor suppressor gene could act as tumor promoting factor in HER2 (Human Epidermal Growth Factor Receptor 2) positive breast cancer. Herein we put in evidence that ATM expression sustains the proportion of cells with a stem-like phenotype, measured as the capability to form mammospheres, independently of HER2 expression levels. Transcriptomic analyses revealed that, in mammospheres, ATM modulates the expression of cell cycle-, DNA repair- and autophagy-related genes. Among these, the silencing of the autophagic gene, autophagy related 4C cysteine peptidase (ATG4C), impairs mammosphere formation similarly to ATM depletion. Conversely, ATG4C ectopic expression in cells silenced for ATM expression, rescues mammospheres growth. Finally, tumor array analyses, performed using public data, identify a significant correlation between ATM and ATG4C expression levels in all human breast cancer subtypes, except for the basal-like one.Overall, we uncover a new connection between ATM kinase and autophagy regulation in breast cancer. We demonstrate that, in breast cancer cells, ATM and ATG4C are essential drivers of mammosphere formation, suggesting that their targeting may improve current approaches to eradicate breast cancer cells with a stem-like phenotype.
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Affiliation(s)
- Martina Antonelli
- Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy.,Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Flavie Strappazzon
- Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy
| | - Ivan Arisi
- Genomics Facility, European Brain Research Institute (EBRI) 'Rita Levi-Montalcini', Rome, Italy
| | - Rossella Brandi
- Genomics Facility, European Brain Research Institute (EBRI) 'Rita Levi-Montalcini', Rome, Italy
| | - Mara D'Onofrio
- Genomics Facility, European Brain Research Institute (EBRI) 'Rita Levi-Montalcini', Rome, Italy
| | - Manolo Sambucci
- Neuroimmunology Unit, Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Gwenola Manic
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Ilio Vitale
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy.,Regina Elena National Cancer Center Institute, Rome, Italy
| | - Daniela Barilà
- Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy.,Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Venturina Stagni
- Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy
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25
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Seo E, Woo J, Park E, Bertolani SJ, Siegel JB, Choi D, Dinesh-Kumar SP. Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4. Autophagy 2016; 12:2054-2068. [PMID: 27540766 PMCID: PMC5103345 DOI: 10.1080/15548627.2016.1217373] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/16/2016] [Accepted: 07/21/2016] [Indexed: 12/27/2022] Open
Abstract
Autophagy is important for degradation and recycling of intracellular components. In a diversity of genera and species, orthologs and paralogs of the yeast Atg4 and Atg8 proteins are crucial in the biogenesis of double-membrane autophagosomes that carry the cellular cargoes to vacuoles and lysosomes. Although many plant genome sequences are available, the ATG4 and ATG8 sequence analysis is limited to some model plants. We identified 28 ATG4 and 116 ATG8 genes from the available 18 different plant genome sequences. Gene structures and protein domain sequences of ATG4 and ATG8 are conserved in plant lineages. Phylogenetic analyses classified ATG8s into 3 subgroups suggesting divergence from the common ancestor. The ATG8 expansion in plants might be attributed to whole genome duplication, segmental and dispersed duplication, and purifying selection. Our results revealed that the yeast Atg4 processes Arabidopsis ATG8 but not human LC3A (HsLC3A). In contrast, HsATG4B can process yeast and plant ATG8s in vitro but yeast and plant ATG4s cannot process HsLC3A. Interestingly, in Nicotiana benthamiana plants the yeast Atg8 is processed compared to HsLC3A. However, HsLC3A is processed when coexpressed with HsATG4B in plants. Molecular modeling indicates that lack of processing of HsLC3A by plant and yeast ATG4 is not due to lack of interaction with HsLC3A. Our in-depth analyses of ATG4 and ATG8 in the plant lineage combined with results of cross-kingdom ATG8 processing by ATG4 further support the evolutionarily conserved maturation of ATG8. Broad ATG8 processing by HsATG4B and lack of processing of HsLC3A by yeast and plant ATG4s suggest that the cross-kingdom ATG8 processing is determined by ATG8 sequence rather than ATG4.
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Affiliation(s)
- Eunyoung Seo
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA USA
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Korea
| | - Jongchan Woo
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA USA
| | - Eunsook Park
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA USA
| | - Steven J. Bertolani
- Department of Chemistry and the Genome Center, University of California, Davis, CA USA
| | - Justin B. Siegel
- Department of Chemistry and the Genome Center, University of California, Davis, CA USA
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Korea
| | - Savithramma P. Dinesh-Kumar
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA USA
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26
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Ni Z, Gong Y, Dai X, Ding W, Wang B, Gong H, Qin L, Cheng P, Li S, Lian J, He F. AU4S: a novel synthetic peptide to measure the activity of ATG4 in living cells. Autophagy 2016; 11:403-15. [PMID: 25831015 DOI: 10.1080/15548627.2015.1009773] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
ATG4 plays a key role in autophagy induction, but the methods for monitoring ATG4 activity in living cells are limited. Here we designed a novel fluorescent peptide named AU4S for noninvasive detection of ATG4 activity in living cells, which consists of the cell-penetrating peptide (CPP), ATG4-recognized sequence "GTFG," and the fluorophore FITC. Additionally, an ATG4-resistant peptide AG4R was used as a control. CPP can help AU4S or AG4R to penetrate cell membrane efficiently. AU4S but not AG4R can be recognized and cleaved by ATG4, leading to the change of fluorescence intensity. Therefore, the difference between AU4S- and AG4R-measured fluorescence values in the same sample, defined as "F-D value," can reflect ATG4 activity. By detecting the F-D values, we found that ATG4 activity paralleled LC3B-II levels in rapamycin-treated cells, but neither paralleled LC3B-II levels in starved cells nor presented a correlation with LC3B-II accumulation in WBCs from healthy donors or leukemia patients. However, when DTT was added to the system, ATG4 activity not only paralleled LC3B-II levels in starved cells in the presence or absence of autophagy inhibitors, but also presented a positive correlation with LC3B-II accumulation in WBCs from leukemia patients (R(2) = 0.5288). In conclusion, this study provides a convenient, rapid, and quantitative method to monitor ATG4 activity in living cells, which may be beneficial to basic and clinical research on autophagy.
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Key Words
- 3-MA, 3-methyladenine
- AG4R, ATG4-resistant peptide
- ATG4
- ATG4, autophagy-related 4, cysteine peptidase
- AU4S
- AU4S, autophagy-related 4 substrate
- Ac, acetyl
- CFP, cyan fluorescent protein
- CPP, cell-penetrating peptide
- CQ, chloroquine
- DTT, dithiothreitol
- EBSS, Earle's balanced salt solution
- FITC, fluorescein isothiocyanate
- HIV, human immunodeficiency virus
- LC3
- MAP1LC3/LC3, microtubule-associated protein 1 light chain 3
- NAC, N-acetyl-L-cysteine
- NRK, normal rat kidney cell line
- PAGE, polyacrylamide gel electrophoresis
- PBS, phosphate-buffered saline
- PE, phosphatidylethanolamine
- PLA2, phospholipase A2
- PMSF, phenylmethanesulfonyl fluoride
- PtdIns3K, phosphatidylinositol 3-kinase
- ROS
- ROS, reactive oxygen species
- SDS, sodium dodecyl sulfate
- WBCs, white blood cells
- YFP, yellow fluorescent protein
- autophagy
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Affiliation(s)
- Zhenhong Ni
- a Department of Biochemistry and Molecular Biology; College of Basic Medical Sciences ; Third Military Medical University ; Chongqing , China
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27
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Kong-Hap MA, Mouammine A, Daher W, Berry L, Lebrun M, Dubremetz JF, Besteiro S. Regulation of ATG8 membrane association by ATG4 in the parasitic protist Toxoplasma gondii. Autophagy 2013; 9:1334-48. [PMID: 23748741 DOI: 10.4161/auto.25189] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In the process of autophagy, the Atg8 protein is conjugated, through a ubiquitin-like system, to the lipid phosphatidylethanolamine (PE) to associate with the membrane of forming autophagosomes. There, it plays a crucial role in the genesis of these organelles and in autophagy in general. In most eukaryotes, the cysteine peptidase Atg4 processes the C terminus of cytosolic Atg8 to regulate its association with autophagosomal membranes and also delipidates Atg8 to release this protein from membranes. The parasitic protist Toxoplasma gondii contains a functional, yet apparently reduced, autophagic machinery. T. gondii Atg8 homolog, in addition to a cytosolic and occasionally autophagosomal localization, also localizes to the apicoplast, a nonphotosynthetic plastid bounded by four membranes. Our attempts to interfere with TgATG8 function showed that it appears to be essential for parasite multiplication inside its host cell. This protein also displays a peculiar C terminus that does not seem to necessitate processing prior to membrane association and yet an unusually large Toxoplasma homolog of ATG4 is predicted in the parasite genome. A TgATG4 conditional expression mutant that we have generated is severely affected in growth, and displays significant alterations at the organellar level, noticeably with a fragmentation of the mitochondrial network and a loss of the apicoplast. TgATG4-depleted parasites appear to be defective in the recycling of membrane-bound TgATG8. Overall, our data highlight a role for the TgATG8 conjugation pathway in maintaining the homeostasis of the parasite's organelles and suggest that Toxoplasma has evolved a specialized autophagic machinery with original regulation.
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Affiliation(s)
- Marie A Kong-Hap
- UMR 5235 CNRS; Universités de Montpellier 1 et 2; Dynamique des Interactions Membranaires Normales et Pathologiques; Montpellier, France
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