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Cai J, Zhou H, Liu M, Zhang D, Lv J, Xue H, Zhou H, Zhang W. Host immunity and intracellular bacteria evasion mechanisms: Enhancing host-directed therapies with drug delivery systems. Int J Antimicrob Agents 2025; 65:107492. [PMID: 40107461 DOI: 10.1016/j.ijantimicag.2025.107492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 03/04/2025] [Accepted: 03/10/2025] [Indexed: 03/22/2025]
Abstract
Host-directed therapies (HDTs) have been investigated as a potential solution to combat intracellular and drug-resistant bacteria. HDTs stem from extensive research on the intricate interactions between the host and intracellular bacteria, leading to a treatment approach that relies on immunoregulation. To improve the bioavailability and safety of HDTs, researchers have utilized diverse drug delivery systems (DDS) to encapsulate and transport therapeutic agents to target cells. In this review, we first introduce the three mechanisms of bactericidal action and intracellular bacterial evasion: autophagy, reactive oxygen species (ROS), and inflammatory cytokines, with a particular focus on autophagy. Special attention is given to the detailed mechanism of xenophagy in clearing intracellular bacteria, a crucial selective autophagy process that specifically targets and degrades intracellular pathogens. Following this, we present the application of DDS to modulate these regulatory methods for intracellular bacteria elimination. By integrating insights from immunology and nanomedicine, this review highlights the emerging role of DDS in advancing HDTs for intracellular bacterial infections and paving the way for innovative therapeutic interventions.
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Affiliation(s)
- Jiayang Cai
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Han Zhou
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Mingwei Liu
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Dingjian Zhang
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Jingxuan Lv
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Haokun Xue
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Houcheng Zhou
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China
| | - Wenli Zhang
- Department of Pharmaceutics, China Pharmaceutical University, Jiangsu, China.
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2
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Ullern H, Schnur P, Boccara CN, Knævelsrud H. Rest, Repair, Repeat: The Complex Relationship of Autophagy and Sleep. J Mol Biol 2025:169227. [PMID: 40409707 DOI: 10.1016/j.jmb.2025.169227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 05/13/2025] [Accepted: 05/18/2025] [Indexed: 05/25/2025]
Abstract
Autophagy and sleep are two evolutionary conserved mechanisms across the animal kingdom. Autophagy is a pathway for the degradation of cytoplasmic material in the lysosome, playing important roles in the homeostasis and health of the organism. On the other hand, sleep is a homeostatically regulated state with numerous presumed essential roles, including the restoration of tissue and physiological functions, such as brain waste clearance via the activation of the glymphatic systems. Given that sleep and autophagy are crucial processes tightly linked to homeostasis and maintenance of good health, understanding how they interact is of great interest, especially as sleep quality decreases in our modern 24-hour societies. Autophagy represents a promising target for therapeutic interventions in this context. Here, we review the contrasted and complementary roles of autophagy and sleep in maintaining homeostasis. Specifically, we focus on recent evidence suggesting that sleep impairment may increase autophagy, while autophagosome levels may modulate the amount of sleep. We discuss outstanding questions at the intersection of these two fields, highlighting methodological shortcomings in the current literature. Overcoming these limitations will be instrumental to design new experiments with the aim of answering one of the greatest mysteries of our time - why do we sleep?
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Affiliation(s)
- Halvor Ullern
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Paulina Schnur
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Norwegian Centre for Molecular Biosciences and Medicine (NCMBM), University of Oslo, Oslo, Norway
| | - Charlotte N Boccara
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Norwegian Centre for Molecular Biosciences and Medicine (NCMBM), University of Oslo, Oslo, Norway; Department of Neurology, Clinical Neuroscience, Oslo University Hospital (OUS), Norway.
| | - Helene Knævelsrud
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Norway.
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3
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Gross AS, Raffeiner M, Zeng Y, Üstün S, Dagdas Y. Autophagy in Plant Health and Disease. ANNUAL REVIEW OF PLANT BIOLOGY 2025; 76:197-227. [PMID: 39841933 DOI: 10.1146/annurev-arplant-060324-094912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2025]
Abstract
Autophagy has emerged as an essential quality control pathway in plants that selectively and rapidly removes damaged or unwanted cellular components to maintain cellular homeostasis. It can recycle a broad range of cargoes, including entire organelles, protein aggregates, and even invading microbes. It involves the de novo biogenesis of a new cellular compartment, making it intimately linked to endomembrane trafficking pathways. Autophagy is induced by a wide range of biotic and abiotic stress factors, and autophagy mutant plants are highly sensitive to stress, making it an attractive target for improving plant stress resilience. Here, we critically discuss recent discoveries related to plant autophagy and highlight open questions and future research areas.
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Affiliation(s)
- Angelina S Gross
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria;
- Current affiliation: Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Margot Raffeiner
- Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yonglun Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Suayib Üstün
- Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yasin Dagdas
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria;
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4
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Cabrera-Serrano AJ, Sánchez-Maldonado JM, González-Olmedo C, Carretero-Fernández M, Díaz-Beltrán L, Gutiérrez-Bautista JF, García-Verdejo FJ, Gálvez-Montosa F, López-López JA, García-Martín P, Pérez EM, Sánchez-Rovira P, Reyes-Zurita FJ, Sainz J. Crosstalk Between Autophagy and Oxidative Stress in Hematological Malignancies: Mechanisms, Implications, and Therapeutic Potential. Antioxidants (Basel) 2025; 14:264. [PMID: 40227235 PMCID: PMC11939785 DOI: 10.3390/antiox14030264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 02/19/2025] [Accepted: 02/19/2025] [Indexed: 04/15/2025] Open
Abstract
Autophagy is a fundamental cellular process that maintains homeostasis by degrading damaged components and regulating stress responses. It plays a crucial role in cancer biology, including tumor progression, metastasis, and therapeutic resistance. Oxidative stress, similarly, is key to maintaining cellular balance by regulating oxidants and antioxidants, with its disruption leading to molecular damage. The interplay between autophagy and oxidative stress is particularly significant, as reactive oxygen species (ROS) act as both inducers and by-products of autophagy. While autophagy can function as a tumor suppressor in early cancer stages, it often shifts to a pro-tumorigenic role in advanced disease, aiding cancer cell survival under adverse conditions such as hypoxia and nutrient deprivation. This dual role is mediated by several signaling pathways, including PI3K/AKT/mTOR, AMPK, and HIF-1α, which coordinate the balance between autophagic activity and ROS production. In this review, we explore the mechanisms by which autophagy and oxidative stress interact across different hematological malignancies. We discuss how oxidative stress triggers autophagy, creating a feedback loop that promotes tumor survival, and how autophagic dysregulation leads to increased ROS accumulation, exacerbating tumorigenesis. We also examine the therapeutic implications of targeting the autophagy-oxidative stress axis in cancer. Current strategies involve modulating autophagy through specific inhibitors, enhancing ROS levels with pro-oxidant compounds, and combining these approaches with conventional therapies to overcome drug resistance. Understanding the complex relationship between autophagy and oxidative stress provides critical insights into novel therapeutic strategies aimed at improving cancer treatment outcomes.
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Affiliation(s)
- Antonio José Cabrera-Serrano
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
| | - José Manuel Sánchez-Maldonado
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18012 Granada, Spain
| | - Carmen González-Olmedo
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Medical Oncology Unit, University Hospital of Jaén, 23007 Jaén, Spain
| | - María Carretero-Fernández
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
| | - Leticia Díaz-Beltrán
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Medical Oncology Unit, University Hospital of Jaén, 23007 Jaén, Spain
| | - Juan Francisco Gutiérrez-Bautista
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology and Immunology III, University of Granada, 18016 Granada, Spain
| | - Francisco José García-Verdejo
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Medical Oncology Unit, University Hospital of Jaén, 23007 Jaén, Spain
| | - Fernando Gálvez-Montosa
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Medical Oncology Unit, University Hospital of Jaén, 23007 Jaén, Spain
| | - José Antonio López-López
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Medical Oncology Unit, University Hospital of Jaén, 23007 Jaén, Spain
| | - Paloma García-Martín
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
- Campus de la Salud Hospital, PTS, 18016 Granada, Spain
| | - Eva María Pérez
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
- Campus de la Salud Hospital, PTS, 18016 Granada, Spain
| | - Pedro Sánchez-Rovira
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Medical Oncology Unit, University Hospital of Jaén, 23007 Jaén, Spain
| | - Fernando Jesús Reyes-Zurita
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18012 Granada, Spain
| | - Juan Sainz
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS, 18016 Granada, Spain; (A.J.C.-S.); (J.M.S.-M.); (C.G.-O.); (M.C.-F.); (L.D.-B.); (J.F.G.-B.); (F.J.G.-V.); (F.G.-M.); (J.A.L.-L.); (E.M.P.); (P.S.-R.)
- Instituto de Investigación Biosanitaria IBs.Granada, 18012 Granada, Spain;
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18012 Granada, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
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5
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Wu Y, Xu R, Zhuang X. Multifaceted Roles of the ATG8 Protein Family in Plant Autophagy: From Autophagosome Biogenesis to Cargo Recognition. J Mol Biol 2025:168981. [PMID: 39909236 DOI: 10.1016/j.jmb.2025.168981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/25/2025] [Accepted: 01/30/2025] [Indexed: 02/07/2025]
Abstract
In plant cells, autophagy is an essential quality control process by forming a double-membrane structure named the autophagosome, which envelopes and transports the cargoes to the vacuole for degradation/recycling. Autophagy-related (ATG) 8, a key regulator in autophagy, exerts multifunctional roles during autophagy. ATG8 anchors on the phagophore membrane through the ATG8 conjugation system and participates in different steps during autophagosome formation. Accumulating evidence has demonstrated that ATG8 cooperates with other ATG or non-ATG proteins in autophagosome biogenesis. Meanwhile, ATG8 plays an important role in cargo recognition, which is mainly attributed by the specific interactions between ATG8 and the selective autophagy receptors (SARs) or cargos for selective autophagy. Emerging roles of ATG8 in non-canonical autophagy have been recently reported in plants for different stress adaptations. Here, we review the diverse functions of ATG8 in plants, focusing on autophagosome biogenesis and cargo recognition in canonical and non-canonical autophagy.
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Affiliation(s)
- Yixin Wu
- AoE Centre for Organelle Biogenesis and Function, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rui Xu
- AoE Centre for Organelle Biogenesis and Function, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaohong Zhuang
- AoE Centre for Organelle Biogenesis and Function, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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6
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Chen Y, Liu M, Wei H, Guo J, Zhang S, Bu X, Chen S, Zhang D, Guan S. Alcohol induces hepatocytes necroptosis through the LC3/RIPK1/RIPK3 pathway. Food Chem Toxicol 2023; 182:114124. [PMID: 37898230 DOI: 10.1016/j.fct.2023.114124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Excessive alcohol consumption leads to serious liver injury. Necroptosis is a programmed cell death form, which has been confirmed to be involved in alcoholic liver injury. However, the exact mechanism remains still unclear. In this study, we found that ethanol caused hepatocytes necroptosis by activating receptor-interacting serine/threonine-protein kinase 1 and 3 (RIPK1 and RIPK3). Meanwhile, autophagy was activated in ethanol-treated hepatocytes. Accumulative studies have demonstrated a possible link between autophagy and necroptosis. Microtubule-associated protein 1 light chain 3 (LC3), an autophagy marker protein, is essential for autophagosome biogenesis/maturation. But little attention has been paid to its functional role. In this study, we explored whether LC3 was involved in ethanol-induced necroptosis. The data showed that LC3 interacted with RIPK1 and RIPK3 in ethanol-treated AML12 cells and mice liver by co-immunoprecipitation (co-IP) and colocalization assay. Ethanol-induced necrosome formation and subsequent necroptosis were alleviated in hepatocytes by knockdown of LC3 or autophagy inhibitor 3-methyladenine (3-MA). These results demonstrated that LC3 accumulation facilitated the formation of necrosome by LC3-RIPK1 and LC3-RIPK3 interactions, eventually caused hepatocytes necroptosis after acute ethanol exposure. Our current research could potentially offer a new understanding of the intricate mechanisms involved in the development of acute alcoholic liver injury.
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Affiliation(s)
- Yuelin Chen
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Meitong Liu
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Hongdi Wei
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Jiakang Guo
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Shengzhuo Zhang
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Xiujuan Bu
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Shanshan Chen
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China
| | - Duoduo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Shuang Guan
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, 130062, People's Republic of China; Key Laboratory of Zoonosis, Ministry of Education College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, People's Republic of China.
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7
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Luo ZY, Jiang TX, Zhang T, Xu P, Qiu XB. Ubiquitin Ligase Nrdp1 Controls Autophagy-Associated Acrosome Biogenesis and Mitochondrial Arrangement during Spermiogenesis. Cells 2023; 12:2211. [PMID: 37759433 PMCID: PMC10527437 DOI: 10.3390/cells12182211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 09/29/2023] Open
Abstract
Autophagy is critical to acrosome biogenesis and mitochondrial quality control, but the underlying mechanisms remain unclear. The ubiquitin ligase Nrdp1/RNF41 promotes ubiquitination of the mitophagy-associated Parkin and interacts with the pro-autophagic protein SIP/CacyBP. Here, we report that global deletion of Nrdp1 leads to formation of the round-headed sperm and male infertility by disrupting autophagy. Quantitative proteome analyses demonstrated that the expression of many proteins associated with mitochondria, lysosomes, and acrosomes was dysregulated in either spermatids or sperm of the Nrdp1-deficient mice. Deletion of Nrdp1 increased the levels of Parkin but decreased the levels of SIP, the mitochondrial fission protein Drp1 and the mitochondrial protein Tim23 in sperm, accompanied by the inhibition of autophagy, the impairment of acrosome biogenesis and the disruption of mitochondrial arrangement in sperm. Thus, our results uncover an essential role of Nrdp1 in spermiogenesis and male fertility by promoting autophagy, providing important clues to cope with the related male reproductive diseases.
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Affiliation(s)
- Zi-Yu Luo
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China; (Z.-Y.L.); (T.-X.J.)
| | - Tian-Xia Jiang
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China; (Z.-Y.L.); (T.-X.J.)
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China;
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China;
| | - Xiao-Bo Qiu
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China; (Z.-Y.L.); (T.-X.J.)
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8
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A export and delivery at the cell periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549521. [PMID: 37502979 PMCID: PMC10370099 DOI: 10.1101/2023.07.18.549521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans -Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative L C3-Interacting R egion (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B, but not other members, of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Re-introduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, re-introducing tepsin with a mutated LIR motif or missing N-terminus does not fully rescue altered ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; delivery of ATG9A-positive vesicles at the cell periphery; and in overall maintenance of autophagosome structure.
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9
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Kwarteng DO, Gangoda M, Kooijman EE. The effect of methylated phosphatidylethanolamine derivatives on the ionization properties of signaling phosphatidic acid. Biophys Chem 2023; 296:107005. [PMID: 36934676 DOI: 10.1016/j.bpc.2023.107005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
Phosphatidylethanolamine (PE) and Phosphatidylcholine (PC) are the most abundant glycerophospholipids in eukaryotic membranes. The differences in the physicochemical properties of their headgroups have contrasting modulatory effects on their interaction with intracellular macromolecules. As such, their overall impact on membrane structure and function differs significantly. Enzymatic methylation of PE's amine headgroup produces two methylated derivatives namely monomethyl PE (MMPE) and dimethyl PE (DMPE) which have physicochemical properties that generally range between that of PE and PC. Additionally, their influence on membrane properties differs from both PE and PC. Although variations in headgroup methylation have been reported to affect signaling pathways, the direct influence that these differences exert on the ionization properties of signaling phospholipids have not been investigated. Here, we briefly review membrane function and structure that are mediated by the differences in headgroup methylation between PE, MMPE, DMPE and PC. In addition, using 31P MAS NMR, we investigate the effect of these four phospholipids on the ionization properties of the ubiquitous signaling anionic lipid phosphatidic acid (PA). Our results show that PA's ionization properties are differentially affected by changes in phospholipid headgroup methylation. This could have important implications for PA-protein binding and hence physiological functions in cells where signaling events lead to changes in abundance of methylated PE derivatives in the membrane.
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Affiliation(s)
- Desmond Owusu Kwarteng
- Department of Biological Sciences, Kent State University, P.O. Box 5190, Kent, OH 44242, USA.
| | - Mahinda Gangoda
- Department of Chemistry & Biochemistry, Kent State University, P.O. Box 5190, Kent, OH 44242, USA
| | - Edgar E Kooijman
- Department of Biological Sciences, Kent State University, P.O. Box 5190, Kent, OH 44242, USA.
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10
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Shen ZF, Li L, Zhu XM, Liu XH, Klionsky DJ, Lin FC. Current opinions on mitophagy in fungi. Autophagy 2023; 19:747-757. [PMID: 35793406 PMCID: PMC9980689 DOI: 10.1080/15548627.2022.2098452] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/02/2022] Open
Abstract
Mitophagy, as one of the most important cellular processes to ensure quality control of mitochondria, aims at transporting damaged, aging, dysfunctional or excess mitochondria to vacuoles (plants and fungi) or lysosomes (mammals) for degradation and recycling. The normal functioning of mitophagy is critical for cellular homeostasis from yeasts to humans. Although the role of mitophagy has been well studied in mammalian cells and in certain model organisms, especially the budding yeast Saccharomyces cerevisiae, our understanding of its significance in other fungi, particularly in pathogenic filamentous fungi, is still at the preliminary stage. Recent studies have shown that mitophagy plays a vital role in spore production, vegetative growth and virulence of pathogenic fungi, which are very different from its roles in mammal and yeast. In this review, we summarize the functions of mitophagy for mitochondrial quality and quantity control, fungal growth and pathogenesis that have been reported in the field of molecular biology over the past two decades. These findings may help researchers and readers to better understand the multiple functions of mitophagy and provide new perspectives for the study of mitophagy in fungal pathogenesis.Abbreviations: AIM/LIR: Atg8-family interacting motif/LC3-interacting region; BAR: Bin-Amphiphysin-Rvs; BNIP3: BCL2 interacting protein 3; CK2: casein kinase 2; Cvt: cytoplasm-to-vacuole targeting; ER: endoplasmic reticulum; IMM: inner mitochondrial membrane; mETC: mitochondrial electron transport chain; OMM: outer mitochondrial membrane; OPTN: optineurin; PAS: phagophore assembly site; PD: Parkinson disease; PE: phosphatidylethanolamine; PHB2: prohibitin 2; PX: Phox homology; ROS, reactive oxygen species; TM: transmembrane.
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Affiliation(s)
- Zi-Fang Shen
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiao-Hong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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11
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Ibrahim T, Khandare V, Mirkin FG, Tumtas Y, Bubeck D, Bozkurt TO. AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs. PLoS Biol 2023; 21:e3001962. [PMID: 36753519 PMCID: PMC9907853 DOI: 10.1371/journal.pbio.3001962] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/15/2022] [Indexed: 02/09/2023] Open
Abstract
Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here, we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized noncanonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms.
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Affiliation(s)
- Tarhan Ibrahim
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Virendrasinh Khandare
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Agrotechnology and Food Sciences, Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Federico Gabriel Mirkin
- Department of Life Sciences, Imperial College London, London, United Kingdom
- INGEBI-CONICET, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Yasin Tumtas
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tolga O. Bozkurt
- Department of Life Sciences, Imperial College London, London, United Kingdom
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12
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Fahie KMM, Papanicolaou KN, Zachara NE. Integration of O-GlcNAc into Stress Response Pathways. Cells 2022; 11:3509. [PMID: 36359905 PMCID: PMC9654274 DOI: 10.3390/cells11213509] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
The modification of nuclear, mitochondrial, and cytosolic proteins by O-linked βN-acetylglucosamine (O-GlcNAc) has emerged as a dynamic and essential post-translational modification of mammalian proteins. O-GlcNAc is cycled on and off over 5000 proteins in response to diverse stimuli impacting protein function and, in turn, epigenetics and transcription, translation and proteostasis, metabolism, cell structure, and signal transduction. Environmental and physiological injury lead to complex changes in O-GlcNAcylation that impact cell and tissue survival in models of heat shock, osmotic stress, oxidative stress, and hypoxia/reoxygenation injury, as well as ischemic reperfusion injury. Numerous mechanisms that appear to underpin O-GlcNAc-mediated survival include changes in chaperone levels, impacts on the unfolded protein response and integrated stress response, improvements in mitochondrial function, and reduced protein aggregation. Here, we discuss the points at which O-GlcNAc is integrated into the cellular stress response, focusing on the roles it plays in the cardiovascular system and in neurodegeneration.
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Affiliation(s)
- Kamau M. M. Fahie
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kyriakos N. Papanicolaou
- Department of Medicine, Division of Cardiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natasha E. Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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13
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Zhang Y, Liu X, Klionsky DJ, Lu B, Zhong Q. Manipulating autophagic degradation in human diseases: from mechanisms to interventions. LIFE MEDICINE 2022; 1:120-148. [PMID: 39871921 PMCID: PMC11749641 DOI: 10.1093/lifemedi/lnac043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/08/2022] [Indexed: 01/29/2025]
Abstract
Targeted degradation, having emerged as a powerful and promising strategy in drug discovery in the past two decades, has provided a solution for many once undruggable targets involved in various diseases. While earlier targeted degradation tools, as exemplified by PROteolysis-TArgeting Chimera (PROTAC), focused on harnessing the ubiquitin-proteasome system, novel approaches that aim to utilize autophagy, a potent, lysosome-dependent degradation pathway, have also surfaced recently as promising modalities. In this review, we first introduce the mechanisms that establish selectivity in autophagy, which provides the rationales for autophagy-based targeted degradation; we also provide an overview on the panoply of cellular machinery involved in this process, an arsenal that could be potentially harnessed. On this basis, we propose four strategies for designing autophagy-based targeted degraders, including Tagging Targets, Directly Engaging Targets, Initiating Autophagy at Targets, and Phagophore-Tethering to Targets. We introduce the current frontiers in this field, including AUtophagy-TArgeting Chimera (AUTAC), Targeted Protein Autophagy (TPA), AUTOphagy-TArgeting Chimera (AUTOTAC, not to be confused with AUTAC), AuTophagosome TEthering Compound (ATTEC), and other experimental approaches as case studies for each strategy. Finally, we put forward a workflow for generating autophagy-based degraders and some important questions that may guide and inspire the process.
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Affiliation(s)
- Yiqing Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 20025, China
| | - Xiaoxia Liu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 20025, China
| | - Daniel J Klionsky
- Department of Molecular, Cellular, and Developmental Biology, and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Boxun Lu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 20025, China
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14
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The caspase-6-p62 axis modulates p62 droplets based autophagy in a dominant-negative manner. Cell Death Differ 2021; 29:1211-1227. [PMID: 34862482 PMCID: PMC9178044 DOI: 10.1038/s41418-021-00912-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022] Open
Abstract
SQSTM1/p62, as a major autophagy receptor, forms droplets that are critical for cargo recognition, nucleation, and clearance. p62 droplets also function as liquid assembly platforms to allow the formation of autophagosomes at their surfaces. It is unknown how p62-droplet formation is regulated under physiological or pathological conditions. Here, we report that p62-droplet formation is selectively blocked by inflammatory toxicity, which induces cleavage of p62 by caspase-6 at a novel cleavage site D256, a conserved site across human, mouse, rat, and zebrafish. The N-terminal cleavage product is relatively stable, whereas the C-terminal product appears undetectable. Using a variety of cellular models, we show that the p62 N-terminal caspase-6 cleavage product (p62-N) plays a dominant-negative role to block p62-droplet formation. In vitro p62 phase separation assays confirm this observation. Dominant-negative regulation of p62-droplet formation by caspase-6 cleavage attenuates p62 droplets dependent autophagosome formation. Our study suggests a novel pathway to modulate autophagy through the caspase-6–p62 axis under certain stress stimuli.
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15
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Bo T, Kang Y, Liu Y, Xu J, Wang W. Atg5 Regulates Selective Autophagy of the Parental Macronucleus during Tetrahymena Sexual Reproduction. Cells 2021; 10:3071. [PMID: 34831293 PMCID: PMC8623110 DOI: 10.3390/cells10113071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
Nuclear autophagy is an important selective autophagy process. The selective autophagy of sexual development micronuclei (MICs) and the programmed nuclear degradation of parental macronucleus (paMAC) occur during sexual reproduction in Tetrahymena thermophila. The molecular regulatory mechanism of nuclear selective autophagy is unclear. In this study, the autophagy-related protein Atg5 was identified from T. thermophila. Atg5 was localized in the cytoplasm in the early sexual-development stage and was localized in the paMAC in the late sexual-development stage. During this stage, the degradation of meiotic products of MIC was delayed in atg5i mutants. Furthermore, paMAC was abnormally enlarged and delayed or failed to degrade. The expression level and lipidation of Atg8.2 significantly decreased in the mutants. All these results indicated that Atg5 was involved in the regulation of the selective autophagy of paMAC by regulating Atg8.2 in Tetrahymena.
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Affiliation(s)
- Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (T.B.); (Y.K.); (Y.L.); (J.X.)
| | - Yu Kang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (T.B.); (Y.K.); (Y.L.); (J.X.)
| | - Ya Liu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (T.B.); (Y.K.); (Y.L.); (J.X.)
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (T.B.); (Y.K.); (Y.L.); (J.X.)
- College of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (T.B.); (Y.K.); (Y.L.); (J.X.)
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16
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Huang Y, Feng Y, Cui L, Yang L, Zhang Q, Zhang J, Jiang X, Zhang X, Lv Y, Jia JZ, Zhang DX, Huang YS. Autophagy-Related LC3 Accumulation Interacted Directly With LIR Containing RIPK1 and RIPK3, Stimulating Necroptosis in Hypoxic Cardiomyocytes. Front Cell Dev Biol 2021; 9:679637. [PMID: 34368130 PMCID: PMC8344065 DOI: 10.3389/fcell.2021.679637] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
The exact relationships and detailed mechanisms between autophagy and necroptosis remain obscure. Here, we demonstrated the link between accumulated autophagosome and necroptosis by intervening with autophagic flux. We first confirmed that the LC3 interacting region (LIR) domain is present in the protein sequences of RIPK1 and RIPK3. Mutual effects among LC3, RIPK1, and RIPK3 have been identified in myocardium and cardiomyocytes. Direct LC3-RIPK1 and LC3-RIPK3 interactions were confirmed by pull-down assays, and their interactions were deleted after LIR domain mutation. Moreover, after disrupting autophagic flux under normoxia with bafilomycin A1 treatment, or with LC3 or ATG5 overexpression adenovirus, RIPK1, RIPK3, p-RIPK3, and p-MLKL levels increased, suggesting necroptosis activation. Severe disruptions in autophagic flux were observed under hypoxia and bafilomycin A1 co-treated cardiomyocytes and myocardium and led to more significant activation of necroptosis. Conversely, after alleviating hypoxia-induced autophagic flux impairment with LC3 or ATG5 knockdown adenovirus, the effects of hypoxia on RIPK1 and RIPK3 levels were reduced, which resulted in decreased p-RIPK3 and p-MLKL. Furthermore, necroptosis was inhibited by siRNAs against RIPK1 and RIPK3 under hypoxia or normoxia. Based on our results, LIR domain mediated LC3-RIPK1 and LC3-RIPK3 interaction. Besides, autophagosome accumulation under hypoxia lead to necrosome formation and, in turn, necroptosis, while when autophagic flux was uninterrupted, RIPK1 and RIPK3 were cleared through an autophagy-related pathway which inhibited necroptosis. These findings provide novel insights for the role of LC3 in regulating cardiomyocyte necroptosis, indicating its therapeutic potential in the prevention and treatment of hypoxic myocardial injury and other hypoxia-related diseases.
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Affiliation(s)
- Yao Huang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yanhai Feng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lin Cui
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lei Yang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qiong Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Junhui Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xupin Jiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xingyue Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yanling Lv
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jie-Zhi Jia
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Dong-Xia Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yue-Sheng Huang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Wound Repair, and Institute of Wound Repair, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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17
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Abstract
Selective autophagy is the lysosomal degradation of specific intracellular components sequestered into autophagosomes, late endosomes, or lysosomes through the activity of selective autophagy receptors (SARs). SARs interact with autophagy-related (ATG)8 family proteins via sequence motifs called LC3-interacting region (LIR) motifs in vertebrates and Atg8-interacting motifs (AIMs) in yeast and plants. SARs can be divided into two broad groups: soluble or membrane bound. Cargo or substrate selection may be independent or dependent of ubiquitin labeling of the cargo. In this review, we discuss mechanisms of mammalian selective autophagy with a focus on the unifying principles employed in substrate recognition, interaction with the forming autophagosome via LIR-ATG8 interactions, and the recruitment of core autophagy components for efficient autophagosome formation on the substrate. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Trond Lamark
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway; ,
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway; ,
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18
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Common Principles and Specific Mechanisms of Mitophagy from Yeast to Humans. Int J Mol Sci 2021; 22:ijms22094363. [PMID: 33922020 PMCID: PMC8122514 DOI: 10.3390/ijms22094363] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are double membrane-bound organelles in eukaryotic cells essential to a variety of cellular functions including energy conversion and ATP production, iron-sulfur biogenesis, lipid and amino acid metabolism, and regulating apoptosis and stress responses. Mitochondrial dysfunction is mechanistically linked to several neurodegenerative diseases, cancer, and ageing. Excessive and dysfunctional/damaged mitochondria are degraded by selective autophagic pathways known as mitophagy. Both budding yeast and mammals use the well-conserved machinery of core autophagy-related genes (ATGs) to execute and regulate mitophagy. In mammalian cells, the PINK1-PARKIN mitophagy pathway is a well-studied pathway that senses dysfunctional mitochondria and marks them for degradation in the lysosome. PINK1-PARKIN mediated mitophagy relies on ubiquitin-binding mitophagy adaptors that are non-ATG proteins. Loss-of-function mutations in PINK1 and PARKIN are linked to Parkinson´s disease (PD) in humans, and defective mitophagy is proposed to be a main pathomechanism. Despite the common view that yeast cells lack PINK1- and PARKIN-homologs and that mitophagy in yeast is solely regulated by receptor-mediated mitophagy, some studies suggest that a ubiquitination-dependent mitophagy pathway also exists. Here, we will discuss shared mechanisms between mammals and yeast, how mitophagy in the latter is regulated in a ubiquitin-dependent and -independent manner, and why these pathways are essential for yeast cell survival and fitness under various physiological stress conditions.
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19
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Chang C, Shi X, Jensen LE, Yokom AL, Fracchiolla D, Martens S, Hurley JH. Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy. SCIENCE ADVANCES 2021; 7:7/17/eabg4922. [PMID: 33893090 PMCID: PMC8064641 DOI: 10.1126/sciadv.abg4922] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/05/2021] [Indexed: 05/14/2023]
Abstract
Selective autophagy of damaged mitochondria, protein aggregates, and other cargoes is essential for health. Cargo initiates phagophore biogenesis, which entails the conjugation of LC3 to phosphatidylethanolamine. Current models suggest that clustered ubiquitin chains on a cargo trigger a cascade from autophagic cargo receptors through the core complexes ULK1 and class III phosphatidylinositol 3-kinase complex I, WIPI2, and the ATG7, ATG3, and ATG12ATG5-ATG16L1 machinery of LC3 lipidation. This was tested using giant unilamellar vesicles (GUVs), GST-Ub4 as a model cargo, the cargo receptors NDP52, TAX1BP1, and OPTN, and the autophagy core complexes. All three cargo receptors potently stimulated LC3 lipidation on GUVs. NDP52- and TAX1BP1-induced LC3 lipidation required all components, but not ULK1 kinase activity. However, OPTN bypassed the ULK1 requirement. Thus, cargo-dependent stimulation of LC3 lipidation is common to multiple autophagic cargo receptors, yet the details of core complex engagement vary between the different receptors.
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Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Xiaoshan Shi
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Liv E Jensen
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Adam L Yokom
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Dorotea Fracchiolla
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sascha Martens
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
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20
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Gubas A, Dikic I. A guide to the regulation of selective autophagy receptors. FEBS J 2021; 289:75-89. [PMID: 33730405 DOI: 10.1111/febs.15824] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
Autophagy is a highly conserved catabolic process cells use to maintain their homeostasis by degrading misfolded, damaged and excessive proteins, nonfunctional organelles, foreign pathogens and other cellular components. Hence, autophagy can be nonselective, where bulky portions of the cytoplasm are degraded upon stress, or a highly selective process, where preselected cellular components are degraded. To distinguish between different cellular components, autophagy employs selective autophagy receptors, which will link the cargo to the autophagy machinery, thereby sequestering it in the autophagosome for its subsequent degradation in the lysosome. Autophagy receptors undergo post-translational and structural modifications to fulfil their role in autophagy, or upon executing their role, for their own degradation. We highlight the four most prominent protein modifications - phosphorylation, ubiquitination, acetylation and oligomerisation - that are essential for autophagy receptor recruitment, function and turnover. Understanding the regulation of selective autophagy receptors will provide deeper insights into the pathway and open up potential therapeutic avenues.
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Affiliation(s)
- Andrea Gubas
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
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21
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In vitro reconstitution of autophagic processes. Biochem Soc Trans 2020; 48:2003-2014. [PMID: 32897375 DOI: 10.1042/bst20200130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/17/2022]
Abstract
Autophagy is a lysosomal degradation system that involves de novo autophagosome formation. A lot of factors are involved in autophagosome formation, including dozens of Atg proteins that form supramolecular complexes, membrane structures including vesicles and organelles, and even membraneless organelles. Because these diverse higher-order structural components cooperate to mediate de novo formation of autophagosomes, it is too complicated to be elaborated only by cell biological approaches. Recent trials to regenerate each step of this phenomenon in vitro have started to elaborate on the molecular mechanisms of such a complicated process by simplification. In this review article, we outline the in vitro reconstitution trials in autophagosome formation, mainly focusing on the reports in the past few years and discussing the molecular mechanisms of autophagosome formation by comparing in vitro and in vivo observations.
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Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S. Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 2020; 369:eaaz7714. [PMID: 32883836 PMCID: PMC7610778 DOI: 10.1126/science.aaz7714] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/16/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Autophagosomes form de novo in a manner that is incompletely understood. Particularly enigmatic are autophagy-related protein 9 (Atg9)-containing vesicles that are required for autophagy machinery assembly but do not supply the bulk of the autophagosomal membrane. In this study, we reconstituted autophagosome nucleation using recombinant components from yeast. We found that Atg9 proteoliposomes first recruited the phosphatidylinositol 3-phosphate kinase complex, followed by Atg21, the Atg2-Atg18 lipid transfer complex, and the E3-like Atg12-Atg5-Atg16 complex, which promoted Atg8 lipidation. Furthermore, we found that Atg2 could transfer lipids for Atg8 lipidation. In selective autophagy, these reactions could potentially be coupled to the cargo via the Atg19-Atg11-Atg9 interactions. We thus propose that Atg9 vesicles form seeds that establish membrane contact sites to initiate lipid transfer from compartments such as the endoplasmic reticulum.
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Affiliation(s)
- Justyna Sawa-Makarska
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Verena Baumann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Veronika Nogellova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Christine Abert
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martin Graef
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
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23
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The Roles of Ubiquitin in Mediating Autophagy. Cells 2020; 9:cells9092025. [PMID: 32887506 PMCID: PMC7564124 DOI: 10.3390/cells9092025] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Ubiquitination, the post-translational modification essential for various intracellular processes, is implicated in multiple aspects of autophagy, the major lysosome/vacuole-dependent degradation pathway. The autophagy machinery adopted the structural architecture of ubiquitin and employs two ubiquitin-like protein conjugation systems for autophagosome biogenesis. Ubiquitin chains that are attached as labels to protein aggregates or subcellular organelles confer selectivity, allowing autophagy receptors to simultaneously bind ubiquitinated cargos and autophagy-specific ubiquitin-like modifiers (Atg8-family proteins). Moreover, there is tremendous crosstalk between autophagy and the ubiquitin-proteasome system. Ubiquitination of autophagy-related proteins or regulatory components plays significant roles in the precise control of the autophagy pathway. In this review, we summarize and discuss the molecular mechanisms and functions of ubiquitin and ubiquitination, in the process and regulation of autophagy.
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24
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Wesch N, Kirkin V, Rogov VV. Atg8-Family Proteins-Structural Features and Molecular Interactions in Autophagy and Beyond. Cells 2020; 9:E2008. [PMID: 32882854 PMCID: PMC7564214 DOI: 10.3390/cells9092008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a common name for a number of catabolic processes, which keep the cellular homeostasis by removing damaged and dysfunctional intracellular components. Impairment or misbalance of autophagy can lead to various diseases, such as neurodegeneration, infection diseases, and cancer. A central axis of autophagy is formed along the interactions of autophagy modifiers (Atg8-family proteins) with a variety of their cellular counter partners. Besides autophagy, Atg8-proteins participate in many other pathways, among which membrane trafficking and neuronal signaling are the most known. Despite the fact that autophagy modifiers are well-studied, as the small globular proteins show similarity to ubiquitin on a structural level, the mechanism of their interactions are still not completely understood. A thorough analysis and classification of all known mechanisms of Atg8-protein interactions could shed light on their functioning and connect the pathways involving Atg8-proteins. In this review, we present our views of the key features of the Atg8-proteins and describe the basic principles of their recognition and binding by interaction partners. We discuss affinity and selectivity of their interactions as well as provide perspectives for discovery of new Atg8-interacting proteins and therapeutic approaches to tackle major human diseases.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London, Sutton SM2 5NG, UK;
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
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25
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Fracchiolla D, Chang C, Hurley JH, Martens S. A PI3K-WIPI2 positive feedback loop allosterically activates LC3 lipidation in autophagy. J Cell Biol 2020; 219:e201912098. [PMID: 32437499 PMCID: PMC7337497 DOI: 10.1083/jcb.201912098] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/18/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Autophagy degrades cytoplasmic cargo by its delivery to lysosomes within double membrane autophagosomes. Synthesis of the phosphoinositide PI(3)P by the autophagic class III phosphatidylinositol-3 kinase complex I (PI3KC3-C1) and conjugation of ATG8/LC3 proteins to phagophore membranes by the ATG12-ATG5-ATG16L1 (E3) complex are two critical steps in autophagosome biogenesis, connected by WIPI2. Here, we present a complete reconstitution of these events. On giant unilamellar vesicles (GUVs), LC3 lipidation is strictly dependent on the recruitment of WIPI2 that in turn depends on PI(3)P. Ectopically targeting E3 to membranes in the absence of WIPI2 is insufficient to support LC3 lipidation, demonstrating that WIPI2 allosterically activates the E3 complex. PI3KC3-C1 and WIPI2 mutually promote the recruitment of each other in a positive feedback loop. When both PI 3-kinase and LC3 lipidation reactions were performed simultaneously, positive feedback between PI3KC3-C1 and WIPI2 led to rapid LC3 lipidation with kinetics similar to that seen in cellular autophagosome formation.
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Affiliation(s)
- Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Vienna BioCenter, Vienna, Austria
| | - Chunmei Chang
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA
| | - James H. Hurley
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Vienna BioCenter, Vienna, Austria
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26
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Martens S, Fracchiolla D. Activation and targeting of ATG8 protein lipidation. Cell Discov 2020; 6:23. [PMID: 32377373 PMCID: PMC7198486 DOI: 10.1038/s41421-020-0155-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022] Open
Abstract
ATG8 family proteins are evolutionary conserved ubiquitin-like modifiers, which become attached to the headgroup of the membrane lipid phosphatidylethanolamine in a process referred to as lipidation. This reaction is carried out analogous to the conjugation of ubiquitin to its target proteins, involving the E1-like ATG7, the E2-like ATG3 and the E3-like ATG12-ATG5-ATG16 complex, which determines the site of lipidation. ATG8 lipidation is a hallmark of autophagy where these proteins are involved in autophagosome formation, the fusion of autophagosomes with lysosomes and cargo selection. However, it has become evident that ATG8 lipidation also occurs in processes that are not directly related to autophagy. Here we discuss recent insights into the targeting of ATG8 lipidation in autophagy and other pathways with special emphasis on the recruitment and activation of the E3-like complex.
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Affiliation(s)
- Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria
| | - Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria
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27
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GABARAPL2 Is Critical for Growth Restriction of Toxoplasma gondii in HeLa Cells Treated with Gamma Interferon. Infect Immun 2020; 88:IAI.00054-20. [PMID: 32094251 DOI: 10.1128/iai.00054-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 02/11/2020] [Indexed: 12/16/2022] Open
Abstract
Gamma interferon (IFN-γ)-induced innate immune responses play important roles in the inhibition of Toxoplasma gondii infection. It has been reported that IFN-γ stimulates non-acidification-dependent growth restriction of T. gondii in HeLa cells, but the mechanism remains unclear. Here, we found that γ-aminobutyric acid (GABA) receptor-associated protein-like 2 (GABARAPL2) plays a critical role in parasite restriction in IFN-γ-treated HeLa cells. GABARAPL2 is recruited to membrane structures surrounding parasitophorous vacuoles (PV). Autophagy adaptors are required for the proper localization and function of GABARAPL2 in the IFN-γ -induced immune response. These findings provide further understanding of a noncanonical autophagy pathway responsible for IFN-γ-dependent inhibition of T. gondii growth in human HeLa cells and demonstrate the critical role of GABARAPL2 in this response.
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28
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Ke PY. Mitophagy in the Pathogenesis of Liver Diseases. Cells 2020; 9:cells9040831. [PMID: 32235615 PMCID: PMC7226805 DOI: 10.3390/cells9040831] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a catabolic process involving vacuolar sequestration of intracellular components and their targeting to lysosomes for degradation, thus supporting nutrient recycling and energy regeneration. Accumulating evidence indicates that in addition to being a bulk, nonselective degradation mechanism, autophagy may selectively eliminate damaged mitochondria to promote mitochondrial turnover, a process termed “mitophagy”. Mitophagy sequesters dysfunctional mitochondria via ubiquitination and cargo receptor recognition and has emerged as an important event in the regulation of liver physiology. Recent studies have shown that mitophagy may participate in the pathogenesis of various liver diseases, such as liver injury, liver steatosis/fatty liver disease, hepatocellular carcinoma, viral hepatitis, and hepatic fibrosis. This review summarizes the current knowledge on the molecular regulations and functions of mitophagy in liver physiology and the roles of mitophagy in the development of liver-related diseases. Furthermore, the therapeutic implications of targeting hepatic mitophagy to design a new strategy to cure liver diseases are discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; ; Tel.: +886-3-211-8800 (ext. 5115); Fax: +886-3-211-8700
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
- Division of Allergy, Immunology, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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29
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Yamasaki A, Alam JM, Noshiro D, Hirata E, Fujioka Y, Suzuki K, Ohsumi Y, Noda NN. Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates. Mol Cell 2020; 77:1163-1175.e9. [PMID: 31995729 DOI: 10.1016/j.molcel.2019.12.026] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/22/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022]
Abstract
Clearance of biomolecular condensates by selective autophagy is thought to play a crucial role in cellular homeostasis. However, the mechanism underlying selective autophagy of condensates and whether liquidity determines a condensate's susceptibility to degradation by autophagy remain unknown. Here, we show that the selective autophagic cargo aminopeptidase I (Ape1) undergoes phase separation to form semi-liquid droplets. The Ape1-specific receptor protein Atg19 localizes to the surface of Ape1 droplets both in vitro and in vivo, with the "floatability" of Atg19 preventing its penetration into droplets. In vitro reconstitution experiments reveal that Atg19 and lipidated Atg8 are necessary and sufficient for selective sequestration of Ape1 droplets by membranes. This sequestration is impaired by mutational solidification of Ape1 droplets or diminished ability of Atg19 to float. Taken together, we propose that cargo liquidity and the presence of sufficient amounts of autophagic receptor on cargo are crucial for selective autophagy of biomolecular condensates.
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Affiliation(s)
- Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Jahangir Md Alam
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Life Science Data Research Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Collaborative Research Institute for Innovative Microbiology, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
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30
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Kirkin V. History of the Selective Autophagy Research: How Did It Begin and Where Does It Stand Today? J Mol Biol 2020; 432:3-27. [PMID: 31082435 PMCID: PMC6971693 DOI: 10.1016/j.jmb.2019.05.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
Abstract
Autophagy, self-eating, is a pivotal catabolic mechanism that ensures homeostasis and survival of the cell in the face of stressors as different as starvation, infection, or protein misfolding. The importance of the research in this field was recognized by the general public after the Nobel Prize for Physiology or Medicine was awarded in 2016 to Yoshinori Ohsumi for discoveries of the mechanisms of autophagy using yeast as a model organism. One of the seminal findings of Ohsumi was on the role ubiquitin-like proteins (UBLs)-Atg5, Atg12, and Atg8-play in the formation of the double-membrane vesicle autophagosome, which is the functional unit of autophagy. Subsequent work by several groups demonstrated that, like the founding member of the UBL family ubiquitin, these small but versatile protein and lipid modifiers interact with a plethora of proteins, which either directly regulate autophagosome formation, for example, components of the Atg1/ULK1 complex, or are involved in cargo recognition, for example, Atg19 and p62/SQSTM1. By tethering the cargo to the UBLs present on the forming autophagosome, the latter proteins were proposed to effectively act as selective autophagy receptors. The discovery of the selective autophagy receptors brought a breakthrough in the autophagy field, supplying the mechanistic underpinning for the formation of an autophagosome selectively around the cytosolic cargo, that is, a protein aggregate, a mitochondrion, or a cytosolic bacterium. In this historical overview, I highlight key steps that the research into selective autophagy has been taking over the past 20 years. I comment on their significance and discuss current challenges in developing more detailed knowledge of the mechanisms of selective autophagy. I will conclude by introducing the new directions that this dynamic research field is taking into its third decade.
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Affiliation(s)
- Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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31
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Turco E, Fracchiolla D, Martens S. Recruitment and Activation of the ULK1/Atg1 Kinase Complex in Selective Autophagy. J Mol Biol 2020; 432:123-134. [PMID: 31351898 PMCID: PMC6971721 DOI: 10.1016/j.jmb.2019.07.027] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 01/26/2023]
Abstract
Autophagy is a major cellular degradation pathway, which mediates the delivery of cytoplasmic cargo material into lysosomes. This is achieved by the specific sequestration of the cargo within double-membrane vesicles, the autophagosomes, which form de novo around this material. Autophagosome formation requires the action of a conserved set of factors, which act in hierarchical manner. The ULK1/Atg1 kinase complex is one of the most upstream acting components of the autophagy machinery. Here we discuss recent insights into the mechanisms of ULK1/Atg1 recruitment and activation at the cargo during selective autophagy. In particular, we will focus on the role of cargo receptors such as p62 and NDP52 during this process and discuss the emerging concept that cargo receptors act upstream of the autophagy machinery during cargo-induced selective autophagy.
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Affiliation(s)
- Eleonora Turco
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
| | - Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
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32
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Johansen T, Lamark T. Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors. J Mol Biol 2020; 432:80-103. [DOI: 10.1016/j.jmb.2019.07.016] [Citation(s) in RCA: 452] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/21/2022]
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33
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Mechanisms of Autophagy in Metabolic Stress Response. J Mol Biol 2020; 432:28-52. [DOI: 10.1016/j.jmb.2019.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 01/17/2023]
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34
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Novel insights into molecular mechanisms of Pseudourostyla cristata encystment using comparative transcriptomics. Sci Rep 2019; 9:19109. [PMID: 31836801 PMCID: PMC6911008 DOI: 10.1038/s41598-019-55608-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/20/2019] [Indexed: 12/17/2022] Open
Abstract
The encystment of many ciliates is an advanced survival strategy against adversity and the most important reason for ciliates existence worldwide. However, the molecular mechanism for the encystment of free-living ciliates is poorly understood. Here, we performed comparative transcriptomic analysis of dormant cysts and trophonts from Pseudourostyla cristata using transcriptomics, qRT-PCR and bioinformatic techniques. We identified 2565 differentially expressed unigenes between the dormant cysts and the trophonts. The total number of differentially expressed genes in GO database was 1752. The differential unigenes noted to the GO terms were 1993. These differential categories were mainly related to polyamine transport, pectin decomposition, cytoplasmic translation, ribosome, respiratory chain, ribosome structure, ion channel activity, and RNA ligation. A total of 224 different pathways were mapped. Among them, 184 pathways were upregulated, while 162 were downregulated. Further investigation showed that the calcium and AMPK signaling pathway had important induction effects on the encystment. In addition, FOXO and ubiquitin-mediated proteolysis signaling pathway jointly regulated the encystment. Based on these findings, we propose a hypothetical signaling network that regulates Pseudourostyla cristata encystment. Overall, these results provide deeper insights into the molecular mechanisms of ciliates encystment and adaptation to adverse environments.
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35
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Fraser J, Simpson J, Fontana R, Kishi‐Itakura C, Ktistakis NT, Gammoh N. Targeting of early endosomes by autophagy facilitates EGFR recycling and signalling. EMBO Rep 2019; 20:e47734. [PMID: 31448519 PMCID: PMC6776898 DOI: 10.15252/embr.201947734] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022] Open
Abstract
Despite recently uncovered connections between autophagy and the endocytic pathway, the role of autophagy in regulating endosomal function remains incompletely understood. Here, we find that the ablation of autophagy-essential players disrupts EGF-induced endocytic trafficking of EGFR. Cells lacking ATG7 or ATG16L1 exhibit increased levels of phosphatidylinositol-3-phosphate (PI(3)P), a key determinant of early endosome maturation. Increased PI(3)P levels are associated with an accumulation of EEA1-positive endosomes where EGFR trafficking is stalled. Aberrant early endosomes are recognised by the autophagy machinery in a TBK1- and Gal8-dependent manner and are delivered to LAMP2-positive lysosomes. Preventing this homeostatic regulation of early endosomes by autophagy reduces EGFR recycling to the plasma membrane and compromises downstream signalling and cell survival. Our findings uncover a novel role for the autophagy machinery in maintaining early endosome function and growth factor sensing.
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Affiliation(s)
- Jane Fraser
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Joanne Simpson
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Rosa Fontana
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | | | | | - Noor Gammoh
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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36
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Kirkin V, Rogov VV. A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway. Mol Cell 2019; 76:268-285. [PMID: 31585693 DOI: 10.1016/j.molcel.2019.09.005] [Citation(s) in RCA: 368] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022]
Abstract
The clearance of surplus, broken, or dangerous components is key for maintaining cellular homeostasis. The failure to remove protein aggregates, damaged organelles, or intracellular pathogens leads to diseases, including neurodegeneration, cancer, and infectious diseases. Autophagy is the evolutionarily conserved pathway that sequesters cytoplasmic components in specialized vesicles, autophagosomes, which transport the cargo to the degradative compartments (vacuoles or lysosomes). Research during the past few decades has elucidated how autophagosomes engulf their substrates selectively. This type of autophagy involves a growing number of selective autophagy receptors (SARs) (e.g., Atg19 in yeasts, p62/SQSTM1 in mammals), which bind to the cargo and simultaneously engage components of the core autophagic machinery via direct interaction with the ubiquitin-like proteins (UBLs) of the Atg8/LC3/GABARAP family and adaptors, Atg11 (in yeasts) or FIP200 (in mammals). In this Review, we critically discuss the biology of the SARs with special emphasis on their interactions with UBLs.
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Affiliation(s)
- Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London, Sutton SM2 5NG, UK.
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany.
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37
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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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38
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Dudley LJ, Cabodevilla AG, Makar AN, Sztacho M, Michelberger T, Marsh JA, Houston DR, Martens S, Jiang X, Gammoh N. Intrinsic lipid binding activity of ATG16L1 supports efficient membrane anchoring and autophagy. EMBO J 2019; 38:e100554. [PMID: 30936093 PMCID: PMC6484409 DOI: 10.15252/embj.2018100554] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 02/04/2019] [Accepted: 03/07/2019] [Indexed: 01/06/2023] Open
Abstract
Membrane targeting of autophagy-related complexes is an important step that regulates their activities and prevents their aberrant engagement on non-autophagic membranes. ATG16L1 is a core autophagy protein implicated at distinct phases of autophagosome biogenesis. In this study, we dissected the recruitment of ATG16L1 to the pre-autophagosomal structure (PAS) and showed that it requires sequences within its coiled-coil domain (CCD) dispensable for homodimerisation. Structural and mutational analyses identified conserved residues within the CCD of ATG16L1 that mediate direct binding to phosphoinositides, including phosphatidylinositol 3-phosphate (PI3P). Mutating putative lipid binding residues abrogated the localisation of ATG16L1 to the PAS and inhibited LC3 lipidation. On the other hand, enhancing lipid binding of ATG16L1 by mutating negatively charged residues adjacent to the lipid binding motif also resulted in autophagy inhibition, suggesting that regulated recruitment of ATG16L1 to the PAS is required for its autophagic activity. Overall, our findings indicate that ATG16L1 harbours an intrinsic ability to bind lipids that plays an essential role during LC3 lipidation and autophagosome maturation.
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Affiliation(s)
- Leo J Dudley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ainara G Cabodevilla
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Agata N Makar
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Martin Sztacho
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Tim Michelberger
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Joseph A Marsh
- Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Xuejun Jiang
- Cell Biology Department, Memorial Sloan Kettering Cancer Centre, New York, NY, USA
| | - Noor Gammoh
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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39
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Turco E, Witt M, Abert C, Bock-Bierbaum T, Su MY, Trapannone R, Sztacho M, Danieli A, Shi X, Zaffagnini G, Gamper A, Schuschnig M, Fracchiolla D, Bernklau D, Romanov J, Hartl M, Hurley JH, Daumke O, Martens S. FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates. Mol Cell 2019; 74:330-346.e11. [PMID: 30853400 PMCID: PMC6477179 DOI: 10.1016/j.molcel.2019.01.035] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/13/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022]
Abstract
The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that disordered residues 326-380 of p62 directly interact with the C-terminal region (CTR) of FIP200. Crystal structure determination shows that the FIP200 CTR contains a dimeric globular domain that we designated the "Claw" for its shape. The interaction of p62 with FIP200 is mediated by a positively charged pocket in the Claw, enhanced by p62 phosphorylation, mutually exclusive with the binding of p62 to LC3B, and it promotes degradation of ubiquitinated cargo by autophagy. Furthermore, the recruitment of the FIP200 CTR slows the phase separation of ubiquitinated proteins by p62 in a reconstituted system. Our data provide the molecular basis for a crosstalk between cargo condensation and autophagosome formation.
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Affiliation(s)
- Eleonora Turco
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marie Witt
- Department of Crystallography, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Christine Abert
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Tobias Bock-Bierbaum
- Department of Crystallography, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Ming-Yuan Su
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Riccardo Trapannone
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Martin Sztacho
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Alberto Danieli
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Xiaoshan Shi
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabriele Zaffagnini
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Annamaria Gamper
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Daniel Bernklau
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Julia Romanov
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Markus Hartl
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oliver Daumke
- Department of Crystallography, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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40
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Ke PY. Diverse Functions of Autophagy in Liver Physiology and Liver Diseases. Int J Mol Sci 2019; 20:E300. [PMID: 30642133 PMCID: PMC6358975 DOI: 10.3390/ijms20020300] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/05/2019] [Accepted: 01/08/2019] [Indexed: 01/09/2023] Open
Abstract
Autophagy is a catabolic process by which eukaryotic cells eliminate cytosolic materials through vacuole-mediated sequestration and subsequent delivery to lysosomes for degradation, thus maintaining cellular homeostasis and the integrity of organelles. Autophagy has emerged as playing a critical role in the regulation of liver physiology and the balancing of liver metabolism. Conversely, numerous recent studies have indicated that autophagy may disease-dependently participate in the pathogenesis of liver diseases, such as liver hepatitis, steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma. This review summarizes the current knowledge on the functions of autophagy in hepatic metabolism and the contribution of autophagy to the pathophysiology of liver-related diseases. Moreover, the impacts of autophagy modulation on the amelioration of the development and progression of liver diseases are also discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan.
- Division of Allergy, Immunology, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan.
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41
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Abstract
Autophagy research frequently requires the determination of protein-protein interactions. The experimental system described in this chapter allows a simple, versatile, and quantitative in vitro analysis of interactions between recombinant cargo receptor and Atg8 proteins by fluorescence microscopy. The assay can be easily modified to study other protein-protein interactions. The purified autophagy receptor is recruited to affinity resins via a suitable tag and then added to fluorescently labeled ATG8 in solution. The relative strength of the interaction can be assessed by determination of the fluorescence intensity on the surface of the bead at an equilibrium binding state. Thereby different interaction partners can be quantitatively compared, and weak or interactions with high off rates can be detected and quantified.
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Affiliation(s)
- Christine Abert
- 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.
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42
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Ke PY. The Multifaceted Roles of Autophagy in Flavivirus-Host Interactions. Int J Mol Sci 2018; 19:ijms19123940. [PMID: 30544615 PMCID: PMC6321027 DOI: 10.3390/ijms19123940] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 02/06/2023] Open
Abstract
Autophagy is an evolutionarily conserved cellular process in which intracellular components are eliminated via lysosomal degradation to supply nutrients for organelle biogenesis and metabolic homeostasis. Flavivirus infections underlie multiple human diseases and thus exert an immense burden on public health worldwide. Mounting evidence indicates that host autophagy is subverted to modulate the life cycles of flaviviruses, such as hepatitis C virus, dengue virus, Japanese encephalitis virus, West Nile virus and Zika virus. The diverse interplay between autophagy and flavivirus infection not only regulates viral growth in host cells but also counteracts host stress responses induced by viral infection. In this review, we summarize the current knowledge on the role of autophagy in the flavivirus life cycle. We also discuss the impacts of virus-induced autophagy on the pathogeneses of flavivirus-associated diseases and the potential use of autophagy as a therapeutic target for curing flavivirus infections and related human diseases.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan.
- Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan.
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43
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Moparthi SB, Wollert T. Reconstruction of destruction – in vitro reconstitution methods in autophagy research. J Cell Sci 2018; 132:132/4/jcs223792. [DOI: 10.1242/jcs.223792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
Autophagy is one of the most elaborative membrane remodeling systems in eukaryotic cells. Its major function is to recycle cytoplasmic material by delivering it to lysosomes for degradation. To achieve this, a membrane cisterna is formed that gradually captures cargo such as organelles or protein aggregates. The diversity of cargo requires autophagy to be highly versatile to adapt the shape of the phagophore to its substrate. Upon closure of the phagophore, a double-membrane-surrounded autophagosome is formed that eventually fuses with lysosomes. In response to environmental cues such as cytotoxicity or starvation, bulk cytoplasm can be captured and delivered to lysosomes. Autophagy thus supports cellular survival under adverse conditions. During the past decades, groundbreaking genetic and cell biological studies have identified the core machinery involved in the process. In this Review, we are focusing on in vitro reconstitution approaches to decipher the details and spatiotemporal control of autophagy, and how such studies contributed to our current understanding of the pathways in yeast and mammals. We highlight studies that revealed the function of the autophagy machinery at a molecular level with respect to its capacity to remodel membranes.
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Affiliation(s)
- Satish Babu Moparthi
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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44
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Danieli A, Martens S. p62-mediated phase separation at the intersection of the ubiquitin-proteasome system and autophagy. J Cell Sci 2018; 131:131/19/jcs214304. [PMID: 30287680 DOI: 10.1242/jcs.214304] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The degradation of misfolded proteins is essential for cellular homeostasis. Misfolded proteins are normally degraded by the ubiquitin-proteasome system (UPS), and selective autophagy serves as a backup mechanism when the UPS is overloaded. Selective autophagy mediates the degradation of harmful material by its sequestration within double-membrane organelles called autophagosomes. The selectivity of autophagic processes is mediated by cargo receptors, which link the cargo to the autophagosomal membrane. The p62 cargo receptor (SQSTM1) has a main function during the degradation of misfolded, ubiquitylated proteins by selective autophagy; here it functions to phase separate these proteins into larger condensates and tether them to the autophagosomal membrane. Recent work has given us crucial insights into the mechanism of action of the p62 cargo receptor during selective autophagy and how its activity can be integrated with the UPS. We will discuss these recent insights in the context of protein quality control and the emerging concept of cellular organization mediated by phase transitions.
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Affiliation(s)
- Alberto Danieli
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
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45
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Mylka V, Deckers J, Ratman D, De Cauwer L, Thommis J, De Rycke R, Impens F, Libert C, Tavernier J, Vanden Berghe W, Gevaert K, De Bosscher K. The autophagy receptor SQSTM1/p62 mediates anti-inflammatory actions of the selective NR3C1/glucocorticoid receptor modulator compound A (CpdA) in macrophages. Autophagy 2018; 14:2049-2064. [PMID: 30215534 PMCID: PMC6984772 DOI: 10.1080/15548627.2018.1495681] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Glucocorticoids are widely used to treat inflammatory disorders; however, prolonged use of glucocorticoids results in side effects including osteoporosis, diabetes and obesity. Compound A (CpdA), identified as a selective NR3C1/glucocorticoid receptor (nuclear receptor subfamily 3, group C, member 1) modulator, exhibits an inflammation-suppressive effect, largely in the absence of detrimental side effects. To understand the mechanistic differences between the classic glucocorticoid dexamethasone (DEX) and CpdA, we looked for proteins oppositely regulated in bone marrow-derived macrophages using an unbiased proteomics approach. We found that the autophagy receptor SQSTM1 but not NR3C1 mediates the anti-inflammatory action of CpdA. CpdA drives SQSTM1 upregulation by recruiting the NFE2L2 transcription factor to its promoter. In contrast, the classic NR3C1 ligand dexamethasone recruits NR3C1 to the Sqstm1 promoter and other NFE2L2-controlled gene promoters, resulting in gene downregulation. Both DEX and CpdA induce autophagy, with marked different autophagy characteristics and morphology. Suppression of LPS-induced Il6 and Ccl2 genes by CpdA in macrophages is hampered upon Sqstm1 silencing, confirming that SQSTM1 is essential for the anti-inflammatory capacity of CpdA, at least in this cell type. Together, these results demonstrate how off-target mechanisms of selective NR3C1 ligands may contribute to a more efficient anti-inflammatory therapy.
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Affiliation(s)
- Viacheslav Mylka
- a Receptor Research Laboratories, Nuclear Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Julie Deckers
- a Receptor Research Laboratories, Nuclear Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,f Inflammation Research Center , VIB, Ghent University , Ghent , Belgium
| | - Dariusz Ratman
- a Receptor Research Laboratories, Nuclear Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Lode De Cauwer
- a Receptor Research Laboratories, Nuclear Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Jonathan Thommis
- a Receptor Research Laboratories, Nuclear Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Riet De Rycke
- f Inflammation Research Center , VIB, Ghent University , Ghent , Belgium.,g Department of Biomedical Molecular Biology , Ghent University , Ghent , Belgium.,h Department of Plant Systems Biology , VIB , Ghent , Belgium.,i Department of Plant Biotechnology and Bioinformatics , Ghent University , Ghent , Belgium
| | - Francis Impens
- c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,j VIB Proteomics Core , VIB , Ghent , Belgium
| | - Claude Libert
- f Inflammation Research Center , VIB, Ghent University , Ghent , Belgium.,g Department of Biomedical Molecular Biology , Ghent University , Ghent , Belgium
| | - Jan Tavernier
- b Receptor Research Laboratories, Cytokine Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Wim Vanden Berghe
- e PPES lab Protein Science, Proteomics & Epigenetic Signaling , Department Biomedical Sciences - University of Antwerp , Wilrijk , Belgium
| | - Kris Gevaert
- c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
| | - Karolien De Bosscher
- a Receptor Research Laboratories, Nuclear Receptor Lab , Ghent University , Ghent , Belgium.,c Department of Biochemistry , VIB-UGent Center for Medical Biotechnology , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium
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46
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Roles of ubiquitin in autophagy and cell death. Semin Cell Dev Biol 2018; 93:125-135. [PMID: 30195063 PMCID: PMC6854449 DOI: 10.1016/j.semcdb.2018.09.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/28/2018] [Accepted: 09/03/2018] [Indexed: 01/12/2023]
Abstract
The balance between cell survival and cell death is often lost in human pathologies such as inflammation and cancer. Autophagy plays a critical role in cell survival: essential nutrients are generated by autophagy-dependent degradation and recycling of cellular garbage. On the other hand, cell death is induced by different programs, such as apoptosis, pyroptosis, and necroptosis. Emerging evidence is revealing how cell survival and cell death pathways are coordinated to determine cell fate. For instance, posttranslational modification of proteins with ubiquitin regulates many steps of autophagy and cell death pathways. In this review article, we will discuss how the ubiquitin system influences cell death and autophagy.
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47
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Lawrence RE, Cho KF, Rappold R, Thrun A, Tofaute M, Kim DJ, Moldavski O, Hurley JH, Zoncu R. A nutrient-induced affinity switch controls mTORC1 activation by its Rag GTPase-Ragulator lysosomal scaffold. Nat Cell Biol 2018; 20:1052-1063. [PMID: 30061680 PMCID: PMC6279252 DOI: 10.1038/s41556-018-0148-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/20/2018] [Indexed: 12/31/2022]
Abstract
A key step in nutrient sensing is the activation of the master growth regulator, mTORC1 kinase, on the surface of lysosomes. Nutrients enable mTORC1 scaffolding by a complex composed of the Rag GTPases (Rags) and Ragulator, but the underlying mechanism of mTORC1 capture is poorly understood. Combining dynamic imaging in cells and reconstituted systems, we uncover an affinity switch that controls mTORC1 lifetime and activation at the lysosome. Nutrients destabilize the Rag-Ragulator interface, causing cycling of the Rags between lysosome-bound Ragulator and the cytoplasm, and rendering mTORC1 capture contingent on simultaneous engagement of two Rag-binding interfaces. Rag GTPase domains trigger cycling by coordinately weakening binding of the C-terminal domains to Ragulator in a nucleotide-controlled manner. Cancer-specific Rag mutants override release from Ragulator and enhance mTORC1 recruitment and signaling output. Cycling in the active state sets the Rags apart from most signaling GTPases, and provides a mechanism to attenuate mTORC1 signaling.
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Affiliation(s)
- Rosalie E Lawrence
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Kelvin F Cho
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Ronja Rappold
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Anna Thrun
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Marie Tofaute
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Do Jin Kim
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Ofer Moldavski
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA. .,The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA.
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48
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Zientara-Rytter K, Subramani S. AIM/LIR-based fluorescent sensors-new tools to monitor mAtg8 functions. Autophagy 2018; 14:1074-1078. [PMID: 29749795 DOI: 10.1080/15548627.2018.1454238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Macroautophagy/autophagy, a catabolic process by which cytoplasmic materials are degraded and recycled in lysosomes/vacuoles, remains a rapidly expanding research topic with the need for constantly improved methodologies to study each step of this pathway. Recently Lee and colleagues, as well as Stolz et al., independently reported the development of new AIM/LIR-based fluorescent sensors, which mark individual endogenous mammalian Atg8-family (mAtg8) proteins without affecting the autophagic flux. When expressed in cells, each sensor selectively recognizes individual mAtg8 isoforms and distinguishes mammalian MAP1LC3/LC3 proteins from the related GABARAPs. Such selectivity was achieved by using various LC3-interacting regions with high binding affinity to either a subgroup, or a specific, mAtg8 isoform as part of the sensor. Here we discuss the utility of these sensors in autophagy research and highlight their strengths, weaknesses and future directions.
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Affiliation(s)
- Katarzyna Zientara-Rytter
- a Section of Molecular Biology, Division of Biological Sciences , University of California San Diego , La Jolla , CA , USA
| | - Suresh Subramani
- a Section of Molecular Biology, Division of Biological Sciences , University of California San Diego , La Jolla , CA , USA
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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: 6.1] [Reference Citation Analysis] [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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An Intervention Target for Myocardial Fibrosis: Autophagy. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6215916. [PMID: 29850542 PMCID: PMC5911341 DOI: 10.1155/2018/6215916] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/07/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
Myocardial fibrosis (MF) is the result of metabolic imbalance of collagen synthesis and metabolism, which is widespread in various cardiovascular diseases. Autophagy is a lysosomal degradation pathway which is highly conserved. In recent years, research on autophagy has been increasing and the researchers have also become cumulatively aware of the specified association between autophagy and MF. This review highlights the role of autophagy in MF and the potential effects through the administration of medicine.
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