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Shang Z, Zhang S, Wang J, Zhou L, Zhang X, Billadeau DD, Yang P, Zhang L, Zhou F, Bai P, Jia D. TRIM25 predominately associates with anti-viral stress granules. Nat Commun 2024; 15:4127. [PMID: 38750080 PMCID: PMC11096359 DOI: 10.1038/s41467-024-48596-4] [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: 07/02/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Stress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25's ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
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Affiliation(s)
- Zehua Shang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lili Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Xinyue Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Peiguo Yang
- School of Life Sciences, Westlake University, Hangzhou, 310024, 310030, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 100850, Beijing, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China.
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2
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Chatzichristofi A, Sagris V, Pallaris A, Eftychiou M, Kalvari I, Price N, Theodosiou T, Iliopoulos I, Nezis IP, Promponas VJ. LIRcentral: a manually curated online database of experimentally validated functional LIR motifs. Autophagy 2023; 19:3189-3200. [PMID: 37530436 PMCID: PMC10621281 DOI: 10.1080/15548627.2023.2235851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.eu), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource. Information incorporated in LIRcentral is useful for accomplishing a variety of research tasks, including: (i) guiding wet biology researchers for the characterization of novel instances of LIR motifs, (ii) giving bioinformaticians/computational biologists access to high-quality LIR motifs for building novel prediction methods for LIR motifs and LIR containing proteins (LIRCPs) and (iii) performing analyses to better understand the biological importance/features of functional LIR motifs. We welcome feedback on the LIRcentral content and functionality by all interested researchers and anticipate this work to spearhead a community effort for sustaining this resource which will further promote progress in studying LIR motifs/LIRCPs.Abbreviations: AIM, Atg8-family interacting motif; Atg8, autophagy related 8; GABARAP, GABA type A receptor-associated protein; LIR, LC3-interacting region; LIRCP, LIR-containing protein; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PMID, PubMed identifier; PPI, protein-protein interaction; SLiM, short linear motif.
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Affiliation(s)
- Agathangelos Chatzichristofi
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Vasileios Sagris
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Aristos Pallaris
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Marios Eftychiou
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioanna Kalvari
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Nicholas Price
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Theodosios Theodosiou
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | | | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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Chi S, Zhang T, Pan Y, Niu S, Zhao L, Gu Z, Liu Q, Jin A, Wang W, Tan S. Time-restricted feeding alleviates metabolic implications of circadian disruption by regulating gut hormone release and brown fat activation. Food Funct 2023; 14:10443-10458. [PMID: 37916301 DOI: 10.1039/d3fo02063k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Individuals with rotating and night shift work are highly susceptible to developing metabolic disorders such as obesity and diabetes. This is primarily attributed to disruptions in the circadian rhythms caused by activities and irregular eating habits. Time-restricted feeding (tRF) limits the daily eating schedules and has been demonstrated to markedly improve several metabolic disorders. Although an intricate relationship exists between tRF and circadian rhythms, the underlying specific mechanism remains elusive. We used a sleep disruption device for activity interference and established a model of circadian rhythm disorder in mice with different genetic backgrounds. We found that circadian rhythm disruption led to abnormal hormone secretion in the gut and elevated insulin resistance. tRF improved metabolic abnormalities caused by circadian rhythm disruption, primarily by restoring the gut hormone secretion rhythm and activating brown fat thermogenesis. The crucial function of brown fat in tRF was confirmed using a mouse model with brown fat removal. We demonstrated that chenodeoxycholic acid (CDCA) effectively improved circadian rhythm disruption-induced metabolic disorders by restoring brown fat activation. Our findings demonstrate the potential benefits of CDCA in reversing metabolic disadvantages associated with irregular circadian rhythms.
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Affiliation(s)
- Sensen Chi
- Department of Immunology, School of Basic Medicine Sciences, Chongqing Medical University, Chongqing 400010, China.
| | - Taoyuan Zhang
- Department of Immunology, School of Basic Medicine Sciences, Chongqing Medical University, Chongqing 400010, China.
| | - Yu Pan
- Department of Immunology, School of Basic Medicine Sciences, Chongqing Medical University, Chongqing 400010, China.
| | - Shenghui Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Zili Gu
- Department of Radiology, Leiden University Medical Center, 2333ZA, Leiden, The Netherlands
| | - Qi Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Aishun Jin
- Department of Immunology, School of Basic Medicine Sciences, Chongqing Medical University, Chongqing 400010, China.
| | - Wang Wang
- Department of Immunology, School of Basic Medicine Sciences, Chongqing Medical University, Chongqing 400010, China.
| | - Shuai Tan
- Department of Immunology, School of Basic Medicine Sciences, Chongqing Medical University, Chongqing 400010, China.
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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4
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Tang Q, Liu M, Zhao H, Chen L. Glycogen-binding protein STBD1: Molecule and role in pathophysiology. J Cell Physiol 2023; 238:2010-2025. [PMID: 37435888 DOI: 10.1002/jcp.31078] [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: 02/21/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023]
Abstract
Starch-binding domain-containing protein 1 (STBD1) is a glycogen-binding protein discovered in skeletal muscle gene differential expression that is pivotal to cellular energy metabolism. Recent studies have indicated that STBD1 is involved in many physiological processes, such as glycophagy, glycogen accumulation, and lipid droplet formation. Moreover, dysregulation of STBD1 causes multiple diseases, including cardiovascular disease, metabolic disease, and even cancer. Deletions and/or mutations in STBD1 promote tumorigenesis. Therefore, STBD1 has garnered considerable interest in the pathology community. In this review, we first summarized the current understanding of STBD1, including its structure, subcellular localization, tissue distribution, and biological functions. Next, we examined the roles and molecular mechanisms of STBD1 in related diseases. Based on available research, we discussed the novel function and future of STBD1, including its potential application as a therapeutic target in glycogen-related diseases. Given the significance of STBD1 in energy metabolism, an in-depth understanding of the protein is crucial for understanding physiological processes and developing therapeutic strategies for related diseases.
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Affiliation(s)
- Qiannan Tang
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, Hengyang Medical School, University of South China, Hengyang, China
| | - Meiqing Liu
- Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Central Laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Hong Zhao
- Nursing College, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Linxi Chen
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, Hengyang Medical School, University of South China, Hengyang, China
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5
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Nieto-Torres JL, Zaretski S, Liu T, Adams PD, Hansen M. Post-translational modifications of ATG8 proteins - an emerging mechanism of autophagy control. J Cell Sci 2023; 136:jcs259725. [PMID: 37589340 PMCID: PMC10445744 DOI: 10.1242/jcs.259725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Autophagy is a recycling mechanism involved in cellular homeostasis with key implications for health and disease. The conjugation of the ATG8 family proteins, which includes LC3B (also known as MAP1LC3B), to autophagosome membranes, constitutes a hallmark of the canonical autophagy process. After ATG8 proteins are conjugated to the autophagosome membranes via lipidation, they orchestrate a plethora of protein-protein interactions that support key steps of the autophagy process. These include binding to cargo receptors to allow cargo recruitment, association with proteins implicated in autophagosome transport and autophagosome-lysosome fusion. How these diverse and critical protein-protein interactions are regulated is still not well understood. Recent reports have highlighted crucial roles for post-translational modifications of ATG8 proteins in the regulation of ATG8 functions and the autophagy process. This Review summarizes the main post-translational regulatory events discovered to date to influence the autophagy process, mostly described in mammalian cells, including ubiquitylation, acetylation, lipidation and phosphorylation, as well as their known contributions to the autophagy process, physiology and disease.
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Affiliation(s)
- Jose L. Nieto-Torres
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- Department of Biomedical Sciences, School of Health Sciences and Veterinary, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Moncada, Spain
| | - Sviatlana Zaretski
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Peter D. Adams
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- The Buck Institute for Aging Research, Novato, CA 94945, USA
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6
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Qian L, Ding X, Fan X, Li S, Qiao Y, Zhang X, Li J. Identification and validation of a novel prognostic circadian rhythm-related gene signature for stomach adenocarcinoma. Chronobiol Int 2023; 40:744-758. [PMID: 37122167 DOI: 10.1080/07420528.2023.2205936] [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: 09/14/2022] [Revised: 02/23/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Circadian rhythm genes were reported to be strongly associated with the development and prognosis of circadian rhythm disorders related to stomach adenocarcinoma (STAD), which is one of the most prevalent cancers. This study aimed to identify a circadian rhythm-related gene signature that could help predict STAD outcome. Using bioinformatics analysis approaches, 105 genes were examined in 350 patients with STAD. Overall, six hub-type circadian rhythm-associated genes (GNA11, PER1, SOX14, EZH2, MAGED1, and NR1D1) were identified using univariate and multivariate Cox regression analyses. These genes were then used to build a genetic predictive model, which was further validated using a publicly available dataset (GSE26899). Overall, genes associated with the circadian rhythm were found to be substantially correlated with the characteristics of the STAD patients (grade, sex, and M stage). In addition, the circadian rhythm-related gene signature was significantly associated with the MAPK and Notch signaling pathways, which are known risk factors for poorer STAD outcome. Taken together, these findings suggest that the herein proposed prognostic model based on six circadian rhythm-associated genes may have predictive value and potential application for clinical decision-making and for personalized treatment of STAD.
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Affiliation(s)
- Lei Qian
- Department of Experiment Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaochen Ding
- Department of Experiment Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaoyan Fan
- Department of Experiment Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shisen Li
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China
| | - Yihuan Qiao
- School of Clinical Medicine, Xi'an Medical University, Xi'an, China
| | - Xiaoqun Zhang
- Department of Pharmacy, Shaanxi Provincial Hospital of Chinese Medicine, Xi'an, China
| | - Jipeng Li
- Department of Experiment Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
- Department of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China
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7
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Yong X, Jia G, Liu Z, Zhou C, Yi J, Tang Y, Chen L, Chen L, Wang Y, Sun Q, Billadeau D, Su Z, Jia D. Cryo-EM structure of the Mon1-Ccz1-RMC1 complex reveals molecular basis of metazoan RAB7A activation. Proc Natl Acad Sci U S A 2023; 120:e2301725120. [PMID: 37216550 PMCID: PMC10235969 DOI: 10.1073/pnas.2301725120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Understanding of the evolution of metazoans from their unicellular ancestors is a fundamental question in biology. In contrast to fungi which utilize the Mon1-Ccz1 dimeric complex to activate the small GTPase RAB7A, metazoans rely on the Mon1-Ccz1-RMC1 trimeric complex. Here, we report a near-atomic resolution cryogenic-electron microscopy structure of the Drosophila Mon1-Ccz1-RMC1 complex. RMC1 acts as a scaffolding subunit and binds to both Mon1 and Ccz1 on the surface opposite to the RAB7A-binding site, with many of the RMC1-contacting residues from Mon1 and Ccz1 unique to metazoans, explaining the binding specificity. Significantly, the assembly of RMC1 with Mon1-Ccz1 is required for cellular RAB7A activation, autophagic functions and organismal development in zebrafish. Our studies offer a molecular explanation for the different degree of subunit conservation across species, and provide an excellent example of how metazoan-specific proteins take over existing functions in unicellular organisms.
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Affiliation(s)
- Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Guowen Jia
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Zhe Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Chunzhuang Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Jiamin Yi
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Yingying Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Li Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Yuan Wang
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Qingxiang Sun
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Daniel D. Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN55905
| | - Zhaoming Su
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
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8
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Vargas JNS, Hamasaki M, Kawabata T, Youle RJ, Yoshimori T. The mechanisms and roles of selective autophagy in mammals. Nat Rev Mol Cell Biol 2023; 24:167-185. [PMID: 36302887 DOI: 10.1038/s41580-022-00542-2] [Citation(s) in RCA: 207] [Impact Index Per Article: 207.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Autophagy is a process that targets various intracellular elements for degradation. Autophagy can be non-selective - associated with the indiscriminate engulfment of cytosolic components - occurring in response to nutrient starvation and is commonly referred to as bulk autophagy. By contrast, selective autophagy degrades specific targets, such as damaged organelles (mitophagy, lysophagy, ER-phagy, ribophagy), aggregated proteins (aggrephagy) or invading bacteria (xenophagy), thereby being importantly involved in cellular quality control. Hence, not surprisingly, aberrant selective autophagy has been associated with various human pathologies, prominently including neurodegeneration and infection. In recent years, considerable progress has been made in understanding mechanisms governing selective cargo engulfment in mammals, including the identification of ubiquitin-dependent selective autophagy receptors such as p62, NBR1, OPTN and NDP52, which can bind cargo and ubiquitin simultaneously to initiate pathways leading to autophagy initiation and membrane recruitment. This progress opens the prospects for enhancing selective autophagy pathways to boost cellular quality control capabilities and alleviate pathology.
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Affiliation(s)
- Jose Norberto S Vargas
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
| | - Tsuyoshi Kawabata
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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9
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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: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [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
- * E-mail: (DB); (TOB)
| | - Tolga O. Bozkurt
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (DB); (TOB)
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10
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Zhang S, Yazaki E, Sakamoto H, Yamamoto H, Mizushima N. Evolutionary diversification of the autophagy-related ubiquitin-like conjugation systems. Autophagy 2022; 18:2969-2984. [PMID: 35427200 PMCID: PMC9673942 DOI: 10.1080/15548627.2022.2059168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two autophagy-related (ATG) ubiquitin-like conjugation systems, the ATG12 and ATG8 systems, play important roles in macroautophagy. While multiple duplications and losses of the ATG conjugation system proteins are found in different lineages, the extent to which the underlying systems diversified across eukaryotes is not fully understood. Here, in order to understand the evolution of the ATG conjugation systems, we constructed a transcriptome database consisting of 94 eukaryotic species covering major eukaryotic clades and systematically identified ATG conjugation system components. Both ATG10 and the C-terminal glycine of ATG12 are essential for the canonical ubiquitin-like conjugation of ATG12 and ATG5. However, loss of ATG10 or the C-terminal glycine of ATG12 occurred at least 16 times in a wide range of lineages, suggesting that possible covalent-to-non-covalent transition is not limited to the species that we previously reported such as Alveolata and some yeast species. Some species have only the ATG8 system (with conjugation enzymes) or only ATG8 (without conjugation enzymes). More than 10 species have ATG8 homologs without the conserved C-terminal glycine, and Tetrahymena has an ATG8 homolog with a predicted transmembrane domain, which may be able to anchor to the membrane independent of the ATG conjugation systems. We discuss the possibility that the ancestor of the ATG12 and ATG8 systems is more similar to ATG8. Overall, our study offers a whole picture of the evolution and diversity of the ATG conjugation systems among eukaryotes, and provides evidence that functional diversifications of the systems are more common than previously thought.Abbreviations: APEAR: ATG8-PE association region; ATG: autophagy-related; LIR: LC3-interacting region; NEDD8: neural precursor cell expressed, developmentally down-regulated gene 8; PE: phosphatidylethanolamine; SAMP: small archaeal modifier protein; SAR: Stramenopiles, Alveolata, and Rhizaria; SMC: structural maintenance of chromosomes; SUMO: small ubiquitin like modifier; TACK: Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota; UBA: ubiquitin like modifier activating enzyme; UFM: ubiquitin fold modifier; URM: ubiquitin related modifier.
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Affiliation(s)
- Sidi Zhang
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Euki Yazaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Saitama, Japan
| | - Hirokazu Sakamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,CONTACT Noboru Mizushima Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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11
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Glycophagy – the physiological perspective on a newly characterized glycogen-selective autophagy. CURRENT OPINION IN PHYSIOLOGY 2022. [DOI: 10.1016/j.cophys.2022.100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Koutsifeli P, Varma U, Daniels LJ, Annandale M, Li X, Neale JPH, Hayes S, Weeks KL, James S, Delbridge LMD, Mellor KM. Glycogen-autophagy: Molecular machinery and cellular mechanisms of glycophagy. J Biol Chem 2022; 298:102093. [PMID: 35654138 PMCID: PMC9249846 DOI: 10.1016/j.jbc.2022.102093] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/21/2022] [Accepted: 05/16/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy is an essential cellular process involving degradation of superfluous or defective macromolecules and organelles as a form of homeostatic recycling. Initially proposed to be a “bulk” degradation pathway, a more nuanced appreciation of selective autophagy pathways has developed in the literature in recent years. As a glycogen-selective autophagy process, “glycophagy” is emerging as a key metabolic route of transport and delivery of glycolytic fuel substrate. Study of glycophagy is at an early stage. Enhanced understanding of this major noncanonical pathway of glycogen flux will provide important opportunities for new insights into cellular energy metabolism. In addition, glycogen metabolic mishandling is centrally involved in the pathophysiology of several metabolic diseases in a wide range of tissues, including the liver, skeletal muscle, cardiac muscle, and brain. Thus, advances in this exciting new field are of broad multidisciplinary interest relevant to many cell types and metabolic states. Here, we review the current evidence of glycophagy involvement in homeostatic cellular metabolic processes and of molecular mediators participating in glycophagy flux. We integrate information from a variety of settings including cell lines, primary cell culture systems, ex vivo tissue preparations, genetic disease models, and clinical glycogen disease states.
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Affiliation(s)
- Parisa Koutsifeli
- Department of Physiology, University of Auckland, Auckland, New Zealand; Department of Anatomy & Physiology, University of Melbourne, Melbourne, Australia
| | - Upasna Varma
- Department of Anatomy & Physiology, University of Melbourne, Melbourne, Australia
| | - Lorna J Daniels
- Department of Physiology, University of Auckland, Auckland, New Zealand; Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Marco Annandale
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Xun Li
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Joshua P H Neale
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Sarah Hayes
- Department of Anatomy & Physiology, University of Melbourne, Melbourne, Australia
| | - Kate L Weeks
- Department of Anatomy & Physiology, University of Melbourne, Melbourne, Australia; Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia; Department of Diabetes, Monash University, Melbourne, Australia
| | - Samuel James
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Lea M D Delbridge
- Department of Physiology, University of Auckland, Auckland, New Zealand; Department of Anatomy & Physiology, University of Melbourne, Melbourne, Australia.
| | - Kimberley M Mellor
- Department of Physiology, University of Auckland, Auckland, New Zealand; Department of Anatomy & Physiology, University of Melbourne, Melbourne, Australia; Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
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13
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Fan H, He Y, Xiang J, Zhou J, Wan X, You J, Du K, Li Y, Cui L, Wang Y, Zhang C, Bu Y, Lei Y. ROS generation attenuates the anti-cancer effect of CPX on cervical cancer cells by inducing autophagy and inhibiting glycophagy. Redox Biol 2022; 53:102339. [PMID: 35636017 PMCID: PMC9144037 DOI: 10.1016/j.redox.2022.102339] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 01/07/2023] Open
Abstract
Cervical cancer is one of the most common gynecological malignancies with poor prognosis due to constant chemoresistance and repeated relapse. Ciclopirox olamine (CPX), a synthetic antifungal agent, has recently been identified to be a promising anti-cancer candidate. However, the detailed mechanisms related to its anti-cancer effects remain unclear and need to be further elucidated. In this study, we found that CPX could induce proliferation inhibition in cervical cancer cells by targeting PARK7. Further results demonstrated that CPX could induce cytoprotective autophagy by downregulating the expression of PARK7 to activate PRKAA1 or by PARK7-independent accumulation of ROS to inhibit mTOR signaling. Meanwhile, CPX treatment increased the glycogen clustering and glycophagy in cervical cancer cells. The presence of N-acetyl-l-cysteine (NAC), a ROS scavenger, led to further clustering of glycogen in cells by reducing autophagy and enhancing glycophagy, which promoted CPX-induced inhibition of cervical cancer cell proliferation. Together, our study provides new insights into the molecular mechanisms of CPX in the anti-cancer therapy and opens new avenues for the glycophagy in cancer therapeutics. CPX induces cytoprotective autophagy and inhibits proliferation of cervical cancer cells by targeting PARK7. ROS generation attenuates the anticancer effect of CPX by inducing cytoprotective autophagy and inhibiting glycophagy. ROS-triggered glycogen clustering and inactivation of YAP1 are involved in the anti-cancer effects of CPX.
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Affiliation(s)
- Hui Fan
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Yujia He
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, 610041, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Junqi Xiang
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Jing Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Xinyan Wan
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Jiawei You
- Department of Basic Medicine, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Kailong Du
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Yue Li
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Lin Cui
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Yitao Wang
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Chundong Zhang
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Yunlong Lei
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China.
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14
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Aziz S, Rasheed F, Zahra R, König S. Gastric Cancer Pre-Stage Detection and Early Diagnosis of Gastritis Using Serum Protein Signatures. Molecules 2022; 27:molecules27092857. [PMID: 35566209 PMCID: PMC9099457 DOI: 10.3390/molecules27092857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Background: A gastric cancer (GC) diagnosis relies on histopathology. Endoscopy rates are increasing. Helicobacter pylori infection is a major GC risk factor. In an effort to elucidate abundant blood biomarkers, and potentially reduce the number of diagnostic surgical interventions, we investigated sera and biopsies from a cohort of 219 H. pylori positive and negative patients diagnosed with GC, gastritis, and ulcers. This allowed the comparative investigation of the different gastroduodenal diseases, and the exclusion of protein changes resulting from bacterial infection or inflammation of the gastric mucosa when searching for GC-dependent proteins. Methods: High-definition mass spectrometry-based expression analysis of tryptically digested proteins was performed, followed by multivariate statistical and network analyses for the different disease groups, with respect to H. pylori infection status. Significantly regulated proteins differing more than two-fold between groups were shortlisted, and their role in gastritis and GC discussed. Results: We present data of comparative protein analyses of biopsies and sera from patients suffering from mild to advanced gastritis, ulcers, and early to advanced GC, in conjunction with a wealth of metadata, clinical information, histopathological evaluation, and H. pylori infection status. We used samples from pre-malignant stages to extract prospective serum markers for early-stage GC, and present a 29-protein marker panel containing, amongst others, integrin β-6 and glutathione peroxidase. Furthermore, ten serum markers specific for advanced GC, independent of H. pylori infection, are provided. They include CRP, protein S100A9, and kallistatin. The majority of these proteins were previously discussed in the context of cancer or GC. In addition, we detected hypoalbuminemia and increased fibrinogen serum levels in gastritis. Conclusion: Two protein panels were suggested for the development of multiplex tests for GC serum diagnostics. For most of the elements contained in these panels, individual commercial tests are available. Thus, we envision the design of multi-protein assays, incorporating several to all of the panel members, in order to gain a level of specificity that cannot be achieved by testing a single protein alone. As their development and validation will take time, gastritis diagnosis based on the fibrinogen to albumin serum ratio may be a quick way forward. Its determination at the primary/secondary care level for early diagnosis could significantly reduce the number of referrals to endoscopy. Preventive measures are in high demand. The protein marker panels presented in this work will contribute to improved GC diagnostics, once they have been transferred from a research result to a practical tool.
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Affiliation(s)
- Shahid Aziz
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Faisal Rasheed
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence:
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15
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Brennan A, Layfield R, Long J, Williams HEL, Oldham NJ, Scott D, Searle MS. An ALS-associated variant of the autophagy receptor SQSTM1/p62 reprograms binding selectivity toward the autophagy-related hATG8 proteins. J Biol Chem 2022; 298:101514. [PMID: 34929165 PMCID: PMC8762078 DOI: 10.1016/j.jbc.2021.101514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/29/2022] Open
Abstract
Recognition of human autophagy-related 8 (hATG8) proteins by autophagy receptors represents a critical step within this cellular quality control system. Autophagy impairment is known to be a pathogenic mechanism in the motor neuron disorder amyotrophic lateral sclerosis (ALS). Overlapping but specific roles of hATG8 proteins belonging to the LC3 and GABARAP subfamilies are incompletely understood, and binding selectivity is typically overlooked. We previously showed that an ALS-associated variant of the SQSTM1/p62 (p62) autophagy receptor bearing an L341V mutation within its ATG8-interacting motif (AIM) impairs recognition of LC3B in vitro, yielding an autophagy-deficient phenotype. Improvements in understanding of hATG8 recognition by AIMs now distinguish LC3-interaction and GABARAP-interaction motifs and predict the effects of L341V substitution may extend beyond loss of function to biasing AIM binding preference. Through biophysical analyses, we confirm impaired binding of the L341V-AIM mutant to LC3A, LC3B, GABARAP, and GABARAPL1. In contrast, p62 AIM interactions with LC3C and GABARAPL2 are unaffected by this mutation. Isothermal titration calorimetry and NMR investigations provided insights into the entropy-driven GABARAPL2/p62 interaction and how the L341V mutation may be tolerated. Competition binding demonstrated reduced association of the L341V-AIM with one hATG8 manifests as a relative increase in association with alternate hATG8s, indicating effective reprogramming of hATG8 selectivity. These data highlight how a single AIM peptide might compete for binding with different hATG8s and suggest that the L341V-AIM mutation may be neomorphic, representative of a disease mechanism that likely extends into other human disorders.
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Affiliation(s)
- Andrew Brennan
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Robert Layfield
- School of Life Sciences, University of Nottingham Medical School, Nottingham, UK.
| | - Jed Long
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Huw E L Williams
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Neil J Oldham
- School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Daniel Scott
- School of Life Sciences, University of Nottingham Medical School, Nottingham, UK.
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK.
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16
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Zhao L, Zhong K, Zhao J, Yong X, Tong A, Jia D. SARS-CoV-2 spike protein harnesses SNX27-mediated endocytic recycling pathway. MedComm (Beijing) 2021; 2:798-809. [PMID: 34909756 PMCID: PMC8661858 DOI: 10.1002/mco2.92] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 is an enveloped positive-sense RNA virus that depends on host factors for all stages of its life. Membrane receptor ACE2 is a well-established factor for SARS-CoV-2 docking. In addition to ACE2, whole-genome genetic screens have identified additional proteins, such as endosomal trafficking regulators SNX27 and retromer, as key host factors required for SARS-CoV-2 infection. However, it is poorly understood how SARS-CoV-2 utilize host endocytic transport pathways to produce productive infection. Here, we report that SNX27 interacts with the SARS-CoV-2 spike (S) protein to facilitate S protein surface expression. Interestingly, S protein binds to the PDZ domain of SNX27, although it does not contain a PDZ-binding motif (PDZbm). Either abrogation of the SNX27 PDZ domain or S protein "MTSC" motif, which is critical for SNX27 binding, decreases surface expression of S protein and viral production. Collectively, our study highlights a novel approach utilized by SARS-CoV-2 to facilitate virion trafficking to establish virus infection.
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Affiliation(s)
- Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Kunhong Zhong
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan UniversityChengduChina
| | - Jia Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan UniversityChengduChina
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenDepartment of PaediatricsState Key Laboratory of Biotherapy and Collaborative Innovation Center of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
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17
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Kotlyar M, Pastrello C, Ahmed Z, Chee J, Varyova Z, Jurisica I. IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. Nucleic Acids Res 2021; 50:D640-D647. [PMID: 34755877 PMCID: PMC8728267 DOI: 10.1093/nar/gkab1034] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/13/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
Improved bioassays have significantly increased the rate of identifying new protein-protein interactions (PPIs), and the number of detected human PPIs has greatly exceeded early estimates of human interactome size. These new PPIs provide a more complete view of disease mechanisms but precise understanding of how PPIs affect phenotype remains a challenge. It requires knowledge of PPI context (e.g. tissues, subcellular localizations), and functional roles, especially within pathways and protein complexes. The previous IID release focused on PPI context, providing networks with comprehensive tissue, disease, cellular localization, and druggability annotations. The current update adds developmental stages to the available contexts, and provides a way of assigning context to PPIs that could not be previously annotated due to insufficient data or incompatibility with available context categories (e.g. interactions between membrane and cytoplasmic proteins). This update also annotates PPIs with conservation across species, directionality in pathways, membership in large complexes, interaction stability (i.e. stable or transient), and mutation effects. Enrichment analysis is now available for all annotations, and includes multiple options; for example, context annotations can be analyzed with respect to PPIs or network proteins. In addition to tabular view or download, IID provides online network visualization. This update is available at http://ophid.utoronto.ca/iid.
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Affiliation(s)
- Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Justin Chee
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Zofia Varyova
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON M5S 1A4, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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18
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The Emerging Roles of Autophagy in Human Diseases. Biomedicines 2021; 9:biomedicines9111651. [PMID: 34829881 PMCID: PMC8615641 DOI: 10.3390/biomedicines9111651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 01/18/2023] Open
Abstract
Autophagy, a process of cellular self-digestion, delivers intracellular components including superfluous and dysfunctional proteins and organelles to the lysosome for degradation and recycling and is important to maintain cellular homeostasis. In recent decades, autophagy has been found to help fight against a variety of human diseases, but, at the same time, autophagy can also promote the procession of certain pathologies, which makes the connection between autophagy and diseases complex but interesting. In this review, we summarize the advances in understanding the roles of autophagy in human diseases and the therapeutic methods targeting autophagy and discuss some of the remaining questions in this field, focusing on cancer, neurodegenerative diseases, infectious diseases and metabolic disorders.
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19
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Zhang W, Han Z, Xue Y, Jia D. iCAL: a new pipeline to investigate autophagy selectivity and cancer. Autophagy 2021; 17:1799-1801. [PMID: 34176435 DOI: 10.1080/15548627.2021.1939972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Macroautophagy/autophagy can selectively degrade misfolded proteins, damaged organelles and other cargoes. It is conceivable that alteration of the degradation processes could disrupt normal cellular signaling and contribute to human diseases such as cancer. To explore the link between aberrant autophagy selectivity and human cancer, we have developed a pipeline called "inference of cancer-associated LC3-interacting region-containing proteins" (iCAL), which integrates a sequence-based predictor, a model-based computational method, publicly available cancer mutations, and multiple experimental approaches. Using iCAL, we have identified 222 LIR motif-associated mutations (LAMs) in 148 LIR-containing proteins (LIRCPs), and validated that LAMs in ATG4B, STBD1, EHMT2 and BRAF impair their interactions with LC3 and/or autophagy activities. Moreover, we uncovered that STBD1, a previously poorly-characterized protein, inhibits tumor growth via metabolism reprogramming in cancer cells. A patient-derived mutation in STBD1 (W203C) disrupts the interaction with LC3 and promotes tumor growth. Taken together, iCAL provides an exciting new avenue to discover novel autophagy pathways that contribute to carcinogenesis.
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Affiliation(s)
- Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhu Han
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
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