1
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Cheng X, Shen S. Transcriptional reprogramming in oral squamous cell carcinoma. Sci Rep 2025; 15:18210. [PMID: 40414942 DOI: 10.1038/s41598-025-01364-w] [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: 08/20/2024] [Accepted: 05/06/2025] [Indexed: 05/27/2025] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a prevalent form of cancer globally. This disease is characterized by its complex genetic underpinnings, involving the intricate regulation of multiple genes. Genetic factors influence cellular processes such as growth, differentiation, and apoptosis of oral mucosal cells, thereby promoting or inhibiting tumor formation and progression. Furthermore, environmental factors-including smoking, alcohol consumption, and human papillomavirus (HPV) infection-can significantly increase the risk of developing OSCC. These external influences can impact the disease in several ways. Delayed clinical detection and the absence of specific biomarkers, coupled with expensive treatment alternatives, contribute to poor prognoses among OSCC patients. Thus, identifying OSCC biomarkers has become imperative. This study investigates publicly accessible sequencing data of oral mucosal tissues from four distinct datasets-GSE23558, GSE30784, GSE36090, and GSE51010-archived in the Gene Expression Omnibus (GEO) database. By analyzing these datasets, which encompass a range of genetic profiles and experimental conditions, the study seeks to uncover critical biomarkers and molecular pathways involved in the early stages of OSCC development. The primary objective is to identify pivotal genes linked to the onset of OSCC. The findings provide preliminary evidence for therapeutic targets in OSCC and may serve as a robust foundation for subsequent biological research endeavors.
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Affiliation(s)
- Xianyang Cheng
- School of Stomatology, Jinan University, Guangzhou, 510000, China
| | - Shan Shen
- Department of Stomatology, The First Affiliated Hospital of Jinan University, Guangzhou, 510000, China.
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2
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Otoda T, Aihara KI, Takayama T. Lysosomal Stress in Cardiovascular Diseases: Therapeutic Potential of Cardiovascular Drugs and Future Directions. Biomedicines 2025; 13:1053. [PMID: 40426881 PMCID: PMC12109370 DOI: 10.3390/biomedicines13051053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2025] [Revised: 03/29/2025] [Accepted: 04/24/2025] [Indexed: 05/29/2025] Open
Abstract
Lysosomal dysfunction has emerged as a central contributor to the pathogenesis of cardiovascular diseases (CVDs), particularly due to its involvement in chronic inflammation, lipid dysregulation, and oxidative stress. This review highlights the multifaceted roles of lysosomes in CVD pathophysiology, focusing on key mechanisms such as NLRP3 inflammasome activation, TFEB-mediated autophagy regulation, ferroptosis, and the role of apolipoprotein M (ApoM) in preserving lysosomal integrity. Additionally, we discuss how impaired lysosomal acidification, mediated by V-ATPase, contributes to lipid-induced cardiac dysfunction. Therapeutically, several pharmacological agents, such as statins, SGLT2 inhibitors, TRPML1 agonists, resveratrol, curcumin, and ferroptosis modulators (e.g., GLS1 activators and icariin), have demonstrated promise in restoring lysosomal function, enhancing autophagic flux, and reducing inflammatory and oxidative injury in both experimental models and early clinical settings. However, key challenges remain, including limitations in drug delivery systems, the absence of lysosome-specific biomarkers, and insufficient clinical validation of these strategies. Future research should prioritize the development of reliable diagnostic tools for lysosomal dysfunction, the optimization of targeted drug delivery, and large-scale clinical trials to validate therapeutic efficacy. Incorporating lysosome-modulating approaches into standard cardiovascular care may offer a new precision medicine paradigm for managing CVD progression.
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Affiliation(s)
- Toshiki Otoda
- Division of General Medicine, Department of Internal Medicine, Nihon University School of Medicine, 30-1 Oyaguchikamicho, Itabashi, Tokyo 173-8610, Japan;
- Department of Community Medicine and Medical Science, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan;
| | - Ken-ichi Aihara
- Department of Community Medicine and Medical Science, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan;
| | - Tadateru Takayama
- Division of General Medicine, Department of Internal Medicine, Nihon University School of Medicine, 30-1 Oyaguchikamicho, Itabashi, Tokyo 173-8610, Japan;
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3
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Gong GQ, Anandapadamanaban M, Islam MS, Hay IM, Bourguet M, Špokaitė S, Dessus AN, Ohashi Y, Perisic O, Williams RL. Making PI3K superfamily enzymes run faster. Adv Biol Regul 2025; 95:101060. [PMID: 39592347 DOI: 10.1016/j.jbior.2024.101060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 11/16/2024] [Indexed: 11/28/2024]
Abstract
The phosphoinositide 3-kinase (PI3K) superfamily includes lipid kinases (PI3Ks and type III PI4Ks) and a group of PI3K-like Ser/Thr protein kinases (PIKKs: mTOR, ATM, ATR, DNA-PKcs, SMG1 and TRRAP) that have a conserved C-terminal kinase domain. A common feature of the superfamily is that they have very low basal activity that can be greatly increased by a range of regulatory factors. Activators reconfigure the active site, causing a subtle realignment of the N-lobe of the kinase domain relative to the C-lobe. This realignment brings the ATP-binding loop in the N-lobe closer to the catalytic residues in the C-lobe. In addition, a conserved C-lobe feature known as the PIKK regulatory domain (PRD) also can change conformation, and PI3K activators can alter an analogous PRD-like region. Recent structures have shown that diverse activating influences can trigger these conformational changes, and a helical region clamping onto the kinase domain transmits regulatory interactions to bring about the active site realignment for more efficient catalysis. A recent report of a small-molecule activator of PI3Kα for application in nerve regeneration suggests that flexibility of these regulatory elements might be exploited to develop specific activators of all PI3K superfamily members. These activators could have roles in wound healing, anti-stroke therapy and treating neurodegeneration. We review common structural features of the PI3K superfamily that may make them amenable to activation.
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Affiliation(s)
- Grace Q Gong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; University College London Cancer Institute, University College London, London, UK
| | | | - Md Saiful Islam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Iain M Hay
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Maxime Bourguet
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Saulė Špokaitė
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Antoine N Dessus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Yohei Ohashi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Olga Perisic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Roger L Williams
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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4
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Cui Z, Esposito A, Napolitano G, Ballabio A, Hurley JH. Structural basis for growth factor and nutrient signal integration on the lysosomal membrane by mTORC1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.15.623810. [PMID: 39605743 PMCID: PMC11601357 DOI: 10.1101/2024.11.15.623810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1), which consists of mTOR, Raptor, and mLST8, receives signaling inputs from growth factor signals and nutrients. These signals are mediated by the Rheb and Rag small GTPases, respectively, which activate mTORC1 on the cytosolic face of the lysosome membrane. We biochemically reconstituted the activation of mTORC1 on membranes by physiological submicromolar concentrations of Rheb, Rags, and Ragulator. We determined the cryo-EM structure and found that Raptor and mTOR directly interact with the membrane at anchor points separated by up to 230 Å across the membrane surface. Full engagement of the membrane anchors is required for maximal activation, which is brought about by alignment of the catalytic residues in the mTOR kinase active site. The observations show at the molecular and atomic scale how converging signals from growth factors and nutrients drive mTORC1 recruitment to and activation on the lysosomal membrane in a three-step process, consisting of (1) Rag-Ragulator-driven recruitment to within ∼100 Å of the lysosomal membrane, (2) Rheb-driven recruitment to within ∼40 Å, and finally (3) direct engagement of mTOR and Raptor with the membrane. The combination of Rheb and membrane engagement leads to full catalytic activation, providing a structural explanation for growth factor and nutrient signal integration at the lysosome.
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5
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Wu B, Huang X, Shi X, Jiang M, Liu H, Zhao L. LAMTOR1 decreased exosomal PD-L1 to enhance immunotherapy efficacy in non-small cell lung cancer. Mol Cancer 2024; 23:184. [PMID: 39223601 PMCID: PMC11367890 DOI: 10.1186/s12943-024-02099-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Great progress has been made in utilizing immune checkpoint blockade (ICB) for the treatment of non-small-cell lung cancer (NSCLC). Therapies targeting programmed cell death protein 1 (PD-1) and its ligand PD-L1, expressed on tumor cells, have demonstrated potential in improving patient survival rates. An unresolved issue involves immune suppression induced by exosomal PD-L1 within the tumor microenvironment (TME), particularly regarding CD8+ T cells. Our study unveiled the crucial involvement of LAMTOR1 in suppressing the exosomes of PD-L1 and promoting CD8+ T cell infiltration in NSCLC. Through its interaction with HRS, LAMTOR1 facilitates PD-L1 lysosomal degradation, thereby reducing exosomal PD-L1 release. Notably, the ability of LAMTOR1 to promote PD-L1 lysosomal degradation relies on a specific ubiquitination site and an HRS binding sequence. The findings suggest that employing LAMTOR1 to construct peptides could serve as a promising strategy for bolstering the efficacy of immunotherapy in NSCLC. The discovery and comprehension of how LAMTOR1 inhibits the release of exosomal PD-L1 offer insights into potential therapeutic strategies for improving immunotherapy. It is imperative to conduct further research and clinical trials to investigate the feasibility and efficacy of targeting LAMTOR1 in NSCLC treatment.
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Affiliation(s)
- Bo Wu
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, 110136, China
| | - Xin Huang
- Department of General practice medicine, Shengjing Hospital of China Medical University, Shenyang, 110022, China
| | - Xiang Shi
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China
| | - Meixi Jiang
- Department of Neurology, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hongxu Liu
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, China.
| | - Li Zhao
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, 110136, China.
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6
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Chiu TY, Lazar DC, Wang WW, Wozniak JM, Jadhav AM, Li W, Gazaniga N, Theofilopoulos AN, Teijaro JR, Parker CG. Chemoproteomic development of SLC15A4 inhibitors with anti-inflammatory activity. Nat Chem Biol 2024; 20:1000-1011. [PMID: 38191941 PMCID: PMC11228132 DOI: 10.1038/s41589-023-01527-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]
Abstract
SLC15A4 is an endolysosome-resident transporter linked with autoinflammation and autoimmunity. Specifically, SLC15A4 is critical for Toll-like receptors (TLRs) 7-9 as well as nucleotide-binding oligomerization domain-containing protein (NOD) signaling in several immune cell subsets. Notably, SLC15A4 is essential for the development of systemic lupus erythematosus in murine models and is associated with autoimmune conditions in humans. Despite its therapeutic potential, the availability of quality chemical probes targeting SLC15A4 functions is limited. In this study, we used an integrated chemical proteomics approach to develop a suite of chemical tools, including first-in-class functional inhibitors, for SLC15A4. We demonstrate that these inhibitors suppress SLC15A4-mediated endolysosomal TLR and NOD functions in a variety of human and mouse immune cells; we provide evidence of their ability to suppress inflammation in vivo and in clinical settings; and we provide insights into their mechanism of action. Our findings establish SLC15A4 as a druggable target for the treatment of autoimmune and autoinflammatory conditions.
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Affiliation(s)
- Tzu-Yuan Chiu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel C Lazar
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wesley W Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Appaso M Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathalia Gazaniga
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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7
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Cheng L, Guo L, Zou T, Yang Y, Tao R, Liu S. Research progress on oncoprotein hepatitis B X‑interacting protein (Review). Mol Med Rep 2024; 29:89. [PMID: 38577934 PMCID: PMC11019400 DOI: 10.3892/mmr.2024.13213] [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: 11/29/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
Hepatitis B X‑interacting protein (HBXIP) is a membrane protein located on the lysosomal surface and encoded by the Lamtor gene. It is expressed by a wide range of tumor types, including breast cancer, esophageal squamous cell carcinoma and hepatocellular carcinoma, and its expression is associated with certain clinicopathological characteristics. In the past decade, research on the oncogenic mechanisms of HBXIP has increased and the function of HBXIP in normal cells has been gradually elucidated. In the present review, the following was discussed: The normal physiological role of the HBXIP carcinogenic mechanism; the clinical significance of high levels of HBXIP expression in different tumors; HBXIP regulation of transcription, post‑transcription and post‑translation processes in tumors; the role of HBXIP in improving the antioxidant capacity of tumor cells; the inhibition of ferroptosis of tumor cells and regulating the metabolic reprogramming of tumor cells; and the role of HBXIP in promoting the malignant progression of tumors. In conclusion, the present review summarized the existing knowledge of HBXIP, established its carcinogenic mechanism and discussed future related research on HBXIP.
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Affiliation(s)
- Lei Cheng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Lijuan Guo
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Teng Zou
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Yisong Yang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Ran Tao
- Department of Anatomy, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Shuangping Liu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
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8
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Zhao L, Gao N, Peng X, Chen L, Meng T, Jiang C, Jin J, Zhang J, Duan Q, Tian H, Weng L, Wang X, Tan X, Li Y, Qin H, Yuan J, Ge X, Deng L, Wang P. TRAF4-Mediated LAMTOR1 Ubiquitination Promotes mTORC1 Activation and Inhibits the Inflammation-Induced Colorectal Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2301164. [PMID: 38229144 DOI: 10.1002/advs.202301164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/28/2023] [Indexed: 01/18/2024]
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) is a conserved serine/threonine kinase that integrates various environmental signals to regulate cell growth and metabolism. mTORC1 activation requires tethering to lysosomes by the Ragulator-Rag complex. However, the dynamic regulation of the interaction between Ragulator and Rag guanosine triphosphatase (GTPase) remains unclear. In this study, that LAMTOR1, an essential component of Ragulator, is dynamically ubiquitinated depending on amino acid abundance is reported. It is found that the E3 ligase TRAF4 directly interacts with LAMTOR1 and catalyzes the K63-linked polyubiquitination of LAMTOR1 at K151. Ubiquitination of LAMTOR1 by TRAF4 promoted its binding to Rag GTPases and enhanced mTORC1 activation, K151R knock-in or TRAF4 knock-out blocks amino acid-induced mTORC1 activation and accelerates the development of inflammation-induced colon cancer. This study revealed that TRAF4-mediated LAMTOR1 ubiquitination is a regulatory mechanism for mTORC1 activation and provides a therapeutic target for diseases involving mTORC1 dysregulation.
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Affiliation(s)
- Linlin Zhao
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Ni Gao
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Xiaoping Peng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Lei Chen
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Tong Meng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200940, P. R. China
| | - Cong Jiang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Jiali Jin
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Jiawen Zhang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Qiuhui Duan
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Hongling Tian
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Linjun Weng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Xinbo Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Xiao Tan
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Yaxu Li
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Huanlong Qin
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200092, P. R. China
- Research Institute of Intestinal Diseases, Tongji University School of Medicine, Shanghai, 200092, P. R. China
| | - Jian Yuan
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200092, P. R. China
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, P. R. China
| | - Xin Ge
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200092, P. R. China
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9
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Bagh MB, Appu AP, Sadhukhan T, Mondal A, Plavelil N, Raghavankutty M, Supran AM, Sadhukhan S, Liu A, Mukherjee AB. Disruption of lysosomal nutrient sensing scaffold contributes to pathogenesis of a fatal neurodegenerative lysosomal storage disease. J Biol Chem 2024; 300:105641. [PMID: 38211816 PMCID: PMC10862020 DOI: 10.1016/j.jbc.2024.105641] [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: 06/06/2023] [Revised: 11/27/2023] [Accepted: 12/17/2023] [Indexed: 01/13/2024] Open
Abstract
The ceroid lipofuscinosis neuronal 1 (CLN1) disease, formerly called infantile neuronal ceroid lipofuscinosis, is a fatal hereditary neurodegenerative lysosomal storage disorder. This disease is caused by loss-of-function mutations in the CLN1 gene, encoding palmitoyl-protein thioesterase-1 (PPT1). PPT1 catalyzes depalmitoylation of S-palmitoylated proteins for degradation and clearance by lysosomal hydrolases. Numerous proteins, especially in the brain, require dynamic S-palmitoylation (palmitoylation-depalmitoylation cycles) for endosomal trafficking to their destination. While 23 palmitoyl-acyl transferases in the mammalian genome catalyze S-palmitoylation, depalmitoylation is catalyzed by thioesterases such as PPT1. Despite these discoveries, the pathogenic mechanism of CLN1 disease has remained elusive. Here, we report that in the brain of Cln1-/- mice, which mimic CLN1 disease, the mechanistic target of rapamycin complex-1 (mTORC1) kinase is hyperactivated. The activation of mTORC1 by nutrients requires its anchorage to lysosomal limiting membrane by Rag GTPases and Ragulator complex. These proteins form the lysosomal nutrient sensing scaffold to which mTORC1 must attach to activate. We found that in Cln1-/- mice, two constituent proteins of the Ragulator complex (vacuolar (H+)-ATPase and Lamtor1) require dynamic S-palmitoylation for endosomal trafficking to the lysosomal limiting membrane. Intriguingly, Ppt1 deficiency in Cln1-/- mice misrouted these proteins to the plasma membrane disrupting the lysosomal nutrient sensing scaffold. Despite this defect, mTORC1 was hyperactivated via the IGF1/PI3K/Akt-signaling pathway, which suppressed autophagy contributing to neuropathology. Importantly, pharmacological inhibition of PI3K/Akt suppressed mTORC1 activation, restored autophagy, and ameliorated neurodegeneration in Cln1-/- mice. Our findings reveal a previously unrecognized role of Cln1/Ppt1 in regulating mTORC1 activation and suggest that IGF1/PI3K/Akt may be a targetable pathway for CLN1 disease.
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Affiliation(s)
- Maria B Bagh
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Abhilash P Appu
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Tamal Sadhukhan
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Avisek Mondal
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Nisha Plavelil
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Mahadevan Raghavankutty
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Ajayan M Supran
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Sriparna Sadhukhan
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Aiyi Liu
- Biostatistics and Bioinformatics Branch (HNT72), Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Anil B Mukherjee
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA.
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10
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Wang X, Hu Z, Zhang W, Wu S, Hao Y, Xiao X, Li J, Yu X, Yang C, Wang J, Zhang H, Ma F, Shi W, Wang J, Lei X, Zhang X, He S. Inhibition of lysosome-tethered Ragulator-Rag-3D complex restricts the replication of Enterovirus 71 and Coxsackie A16. J Cell Biol 2023; 222:e202303108. [PMID: 37906052 PMCID: PMC10619577 DOI: 10.1083/jcb.202303108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/10/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
Enterovirus 71 (EV71) and Coxsackie A16 (CVA16) are two major causative agents of hand, foot, and mouth disease (HFMD) in young children. However, the mechanisms regulating the replication and pathogenesis of EV71/CVA16 remain incompletely understood. We performed a genome-wide CRISPR-Cas9 knockout screen and identified Ragulator as a mediator of EV71-induced apoptosis and pyroptosis. The Ragulator-Rag complex is required for EV71 and CVA16 replication. Upon infection, the Ragulator-Rag complex recruits viral 3D protein to the lysosomal surface through the interaction between 3D and RagB. Disruption of the lysosome-tethered Ragulator-Rag-3D complex significantly impairs the replication of EV71/CVA16. We discovered a novel EV71 inhibitor, ZHSI-1, which interacts with 3D and significantly reduces the lysosomal tethering of 3D. ZHSI-1 treatment significantly represses replication of EV71/CVA16 as well as virus-induced pyroptosis associated with viral pathogenesis. Importantly, ZHSI-1 treatment effectively protects against EV71 infection in neonatal and young mice. Thus, our study indicates that targeting lysosome-tethered Ragulator-Rag-3D may be an effective therapeutic strategy for HFMD.
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Affiliation(s)
- Xinhui Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Zhilin Hu
- Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Wei Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Shuwei Wu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Yongjin Hao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Xia Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingjing Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Xiaoliang Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Chengkui Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Jingfeng Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Huiying Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Feng Ma
- National Key Laboratory of Immunity and Inflammation, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaobo Lei
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaohu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Sudan He
- State Key Laboratory of Common Mechanism Research for Major Diseases, and Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
- Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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11
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Linde-Garelli KY, Rogala KB. Structural mechanisms of the mTOR pathway. Curr Opin Struct Biol 2023; 82:102663. [PMID: 37572585 DOI: 10.1016/j.sbi.2023.102663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/01/2023] [Accepted: 07/07/2023] [Indexed: 08/14/2023]
Abstract
The mTOR signaling pathway is essential for regulating cell growth and mammalian metabolism. The mTOR kinase forms two complexes, mTORC1 and mTORC2, which respond to external stimuli and regulate differential downstream targets. Cellular membrane-associated translocation mediates function and assembly of the mTOR complexes, and recent structural studies have begun uncovering the molecular basis by which the mTOR pathway (1) regulates signaling inputs, (2) recruits substrates, (3) localizes to biological membranes, and (4) becomes activated. Moreover, indications of dysregulated mTOR signaling are implicated in a wide range of diseases and an increasingly comprehensive understanding of structural mechanisms is driving novel translational development.
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Affiliation(s)
- Karen Y Linde-Garelli
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Tettoni SD, Egri SB, Doxsey DD, Veinotte K, Ouch C, Chang JY, Song K, Xu C, Shen K. Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing. Structure 2023; 31:1065-1076.e5. [PMID: 37453417 PMCID: PMC10529327 DOI: 10.1016/j.str.2023.06.012] [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: 03/02/2023] [Revised: 05/14/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream regulators. An important regulator is LAMTOR, which localizes Rag/Gtr on the lysosomal/vacuole membrane. In human cells, LAMTOR consists of five subunits, but in yeast, only three or four. Currently, it is not known how variation of the subunit stoichiometry may affect its structural organization and biochemical properties. Here, we report a 3.1 Å-resolution structural model of the Gtr-Lam complex in Schizosaccharomyces pombe. We found that SpGtr shares conserved architecture as HsRag, but the intersubunit communication that coordinates nucleotide loading on the two subunits differs. In contrast, SpLam contains distinctive structural features, but its GTP-specific GEF activity toward SpGtr is evolutionarily conserved. Our results revealed unique evolutionary paths of the protein components of the mTORC1 pathway.
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Affiliation(s)
- Steven D Tettoni
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Shawn B Egri
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Dylan D Doxsey
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Kristen Veinotte
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Christna Ouch
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jeng-Yih Chang
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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13
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Zhang H, Bernaleau L, Delacrétaz M, Hasanovic E, Drobek A, Eibel H, Rebsamen M. SLC15A4 controls endolysosomal TLR7-9 responses by recruiting the innate immune adaptor TASL. Cell Rep 2023; 42:112916. [PMID: 37527038 DOI: 10.1016/j.celrep.2023.112916] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023] Open
Abstract
Endolysosomal Toll-like receptors (TLRs) play crucial roles in immune responses to pathogens, while aberrant activation of these pathways is associated with autoimmune diseases, including systemic lupus erythematosus (SLE). The endolysosomal solute carrier family 15 member 4 (SLC15A4) is required for TLR7/8/9-induced responses and disease development in SLE models. SLC15A4 has been proposed to affect TLR7-9 activation through its transport activity, as well as by assembling an IRF5-activating complex with TASL, but the relative contribution of these functions remains unclear. Here, we show that the essential role of SLC15A4 is to recruit TASL to endolysosomes, while its transport activity is dispensable when TASL is tethered to this compartment. Endolysosomal-localized TASL rescues TLR7-9-induced IRF5 activation as well as interferon β and cytokine production in SLC15A4-deficient cells. SLC15A4 acts as signaling scaffold, and this function is essential to control TLR7-9-mediated inflammatory responses. These findings support targeting the SLC15A4-TASL complex as a potential therapeutic strategy for SLE and related diseases.
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Affiliation(s)
- Haobo Zhang
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Léa Bernaleau
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Maeva Delacrétaz
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Ed Hasanovic
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Ales Drobek
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Hermann Eibel
- Department of Rheumatology and Clinical Immunology, Medical Center and Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center and Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Manuele Rebsamen
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland.
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14
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Tsujimoto K, Takamatsu H, Kumanogoh A. The Ragulator complex: delving its multifunctional impact on metabolism and beyond. Inflamm Regen 2023; 43:28. [PMID: 37173755 PMCID: PMC10175929 DOI: 10.1186/s41232-023-00278-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Our understanding of lysosomes has undergone a significant transformation in recent years, from the view that they are static organelles primarily responsible for the disposal and recycling of cellular waste to their recognition as highly dynamic structures. Current research posits that lysosomes function as a signaling hub that integrates both extracellular and intracellular stimuli, thereby regulating cellular homeostasis. The dysregulation of lysosomal function has been linked to a wide range of diseases. Of note, lysosomes contribute to the activation of mammalian target of rapamycin complex 1 (mTORC1), a key regulator of cellular metabolism. The Ragulator complex, a protein complex anchored on the lysosomal membrane, was initially shown to tether the mTORC1 complex to lysosomes. Recent research has substantially expanded our understanding of the roles of the Ragulator complex in lysosomes, including roles in the regulation of metabolism, inflammation, cell death, cell migration, and the maintenance of homeostasis, via interactions with various proteins. This review summarizes our current knowledge on the diverse functions of the Ragulator complex, highlighting important protein interactions.
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Affiliation(s)
- Kohei Tsujimoto
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Osaka, Japan
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15
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Regulation of mTORC1 by the Rag GTPases. Biochem Soc Trans 2023; 51:655-664. [PMID: 36929165 DOI: 10.1042/bst20210038] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
The Rag GTPases are an evolutionarily conserved family that play a crucial role in amino acid sensing by the mammalian target of rapamycin complex 1 (mTORC1). mTORC1 is often referred to as the master regulator of cell growth. mTORC1 hyperactivation is observed in multiple diseases such as cancer, obesity, metabolic disorders, and neurodegeneration. The Rag GTPases sense amino acid levels and form heterodimers, where RagA or RagB binds to RagC or RagD, to recruit mTORC1 to the lysosome where it becomes activated. Here, we review amino acid signaling to mTORC1 through the Rag GTPases.
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16
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Xiao W, Yang Y, Chu C, Rung SA, Wang Z, Man Y, Lin J, Qu Y. Macrophage response mediated by extracellular matrix: recent progress. Biomed Mater 2023; 18. [PMID: 36595269 DOI: 10.1088/1748-605x/aca946] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Biomaterials are one of efficient treatment options for tissue defects in regenerative medicine. Compared to synthetic materials which tend to induce chronic inflammatory response and fibrous capsule, extracellular matrix (ECM) scaffold materials composed of biopolymers are thought to be capable of inducing a pro-regenerative immune microenvironment and facilitate wound healing. Immune cells are the first line of response to implanted biomaterials. In particular, macrophages greatly affect cell behavior and the ultimate treatment outcome based on multiple cell phenotypes with various functions. The macrophage polarization status is considered as a general reflection of the characteristics of the immune microenvironment. Since numerous reports has emphasized the limitation of classical M1/M2 nomenclature, high-resolution techniques such as single-cell sequencing has been applied to recognize distinct macrophage phenotypes involved in host responses to biomaterials. After reviewing latest literatures that explored the immune microenvironment mediated by ECM scaffolds, this paper describe the behaviors of highly heterogeneous and plastic macrophages subpopulations which affect the tissue regeneration. The mechanisms by which ECM scaffolds interact with macrophages are also discussed from the perspectives of the ECM ultrastructure along with the nucleic acid, protein, and proteoglycan compositions, in order to provide targets for potential therapeutic modulation in regenerative medicine.
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Affiliation(s)
- Wenlan Xiao
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Yang Yang
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Chenyu Chu
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Sheng-An Rung
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Zhanqi Wang
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Yi Man
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Jie Lin
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Yili Qu
- Department of Oral Implantology & Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
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17
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Tsujimoto K, Jo T, Nagira D, Konaka H, Park JH, Yoshimura S, Ninomiya A, Sugihara F, Hirayama T, Itotagawa E, Matsuzaki Y, Takaichi Y, Aoki W, Saita S, Nakamura S, Ballabio A, Nada S, Okada M, Takamatsu H, Kumanogoh A. The lysosomal Ragulator complex activates NLRP3 inflammasome in vivo via HDAC6. EMBO J 2023; 42:e111389. [PMID: 36444797 PMCID: PMC9811619 DOI: 10.15252/embj.2022111389] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/30/2022] Open
Abstract
The cellular activation of the NLRP3 inflammasome is spatiotemporally orchestrated by various organelles, but whether lysosomes contribute to this process remains unclear. Here, we show the vital role of the lysosomal membrane-tethered Ragulator complex in NLRP3 inflammasome activation. Deficiency of Lamtor1, an essential component of the Ragulator complex, abrogated NLRP3 inflammasome activation in murine macrophages and human monocytic cells. Myeloid-specific Lamtor1-deficient mice showed marked attenuation of NLRP3-associated inflammatory disease severity, including LPS-induced sepsis, alum-induced peritonitis, and monosodium urate (MSU)-induced arthritis. Mechanistically, Lamtor1 interacted with both NLRP3 and histone deacetylase 6 (HDAC6). HDAC6 enhances the interaction between Lamtor1 and NLRP3, resulting in NLRP3 inflammasome activation. DL-all-rac-α-tocopherol, a synthetic form of vitamin E, inhibited the Lamtor1-HDAC6 interaction, resulting in diminished NLRP3 inflammasome activation. Further, DL-all-rac-α-tocopherol alleviated acute gouty arthritis and MSU-induced peritonitis. These results provide novel insights into the role of lysosomes in the activation of NLRP3 inflammasomes by the Ragulator complex.
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Affiliation(s)
- Kohei Tsujimoto
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
| | - Tatsunori Jo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
| | - Daiki Nagira
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
| | - Hachiro Konaka
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
| | - Jeong Hoon Park
- Department of Internal MedicineDaini Osaka Police HospitalOsakaJapan
| | | | - Akinori Ninomiya
- Central Instrumentation Laboratory, Research Institute for Microbial DiseasesOsaka UniversityOsakaJapan
| | - Fuminori Sugihara
- Central Instrumentation Laboratory, Research Institute for Microbial DiseasesOsaka UniversityOsakaJapan
| | - Takehiro Hirayama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
| | - Eri Itotagawa
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
| | - Yusei Matsuzaki
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
- Division of Applied Life Sciences, Graduate School of AgricultureKyoto UniversityKyotoJapan
| | - Yuki Takaichi
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
- Division of Applied Life Sciences, Graduate School of AgricultureKyoto UniversityKyotoJapan
| | - Wataru Aoki
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
- Division of Applied Life Sciences, Graduate School of AgricultureKyoto UniversityKyotoJapan
| | - Shotaro Saita
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Institute for Advanced Co‐Creation StudiesOsaka UniversityOsakaJapan
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTXUSA
- Scuola Superiore Meridionale (SSM), School for Advanced StudiesFederico II UniversityNaplesItaly
| | - Shigeyuki Nada
- Department of Oncogene Research, Research Institute for Microbial DiseasesOsaka UniversityOsakaJapan
| | - Masato Okada
- Department of Oncogene Research, Research Institute for Microbial DiseasesOsaka UniversityOsakaJapan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Immunopathology, Immunology Frontier Research Center (iFReC)Osaka UniversityOsakaJapan
- The Japan Science and Technology – Core Research for Evolutional Science and Technology (JST–CREST)Osaka UniversityOsakaJapan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTIR)Osaka UniversityOsakaJapan
- Center for Advanced Modalities and DDS (CAMaD)Osaka UniversityOsakaJapan
- Center for Infectious Diseases for Education and Research (CiDER)Osaka UniversitySuitaJapan
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18
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Napolitano G, Di Malta C, Ballabio A. Non-canonical mTORC1 signaling at the lysosome. Trends Cell Biol 2022; 32:920-931. [PMID: 35654731 DOI: 10.1016/j.tcb.2022.04.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/21/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) signaling hub integrates multiple environmental cues to modulate cell growth and metabolism. Over the past decade considerable knowledge has been gained on the mechanisms modulating mTORC1 lysosomal recruitment and activation. However, whether and how mTORC1 is able to elicit selective responses to diverse signals has remained elusive until recently. We discuss emerging evidence for a 'non-canonical' mTORC1 signaling pathway that controls the function of microphthalmia/transcription factor E (MiT-TFE) transcription factors, key regulators of cell metabolism. This signaling pathway is mediated by a specific mechanism of substrate recruitment, and responds to stimuli that appear to converge on the lysosomal surface. We discuss the relevance of this pathway in physiological and disease conditions.
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Affiliation(s)
- Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy.
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy.
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131 Naples, Italy; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
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19
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Shams R, Ito Y, Miyatake H. Development of an RHEB-Targeting Peptide To Inhibit mTORC1 Kinase Activity. ACS OMEGA 2022; 7:23479-23486. [PMID: 35847293 PMCID: PMC9280966 DOI: 10.1021/acsomega.2c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In cancer, the mechanistic/mammalian target of rapamycin complex-1 (mTORC1) is hyperactivated to promote survival under adverse conditions. The kinase activity of mTORC1 is activated by small-GTPase RHEB-GTP. Therefore, a new modality to inhibit mTORC1 activity has emerged, through intercepting RHEB. However, due to the relatively large contact area involved in the interaction between RHEB and mTORC1, facilitating this inhibition through small molecules has been challenging. Here, we report the development of a peptide that can inhibit the RHEB-mTORC1 interaction. The peptide, P1_WT, was designed based on the α-helix (aa 101-115) of the N-heat domain of mTOR to interact with switch II of RHEB. P1_WT bound to RHEB (K D = 0.14 μM) and inhibited RHEB-mTORN-heat interaction (IC50 = 0.33 μM) in vitro. Consequently, P1_WT inhibited mTORC1 activity at a sub-micromolar level (IC50 ∼ 0.3 μM). P1_WT was predicted to be cell-permeable due to the rich content of arginine (23%), enhancing the intracellular translocation. These results show that P1_WT is a potential compound to further develop inhibitors for mTORC1 by intercepting RHEB from mTORC1.
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Affiliation(s)
- Raef Shams
- Emergent
Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Wako, Saitama 351-0198, Japan
- Department
of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama 338-8570, Japan
| | - Yoshihiro Ito
- Emergent
Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Wako, Saitama 351-0198, Japan
- Nano
Medical Engineering Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hideyuki Miyatake
- Department
of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama 338-8570, Japan
- Nano
Medical Engineering Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
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20
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Yue S, Li G, He S, Li T. The central role of mTORC1 in amino acid sensing. Cancer Res 2022; 82:2964-2974. [PMID: 35749594 DOI: 10.1158/0008-5472.can-21-4403] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/28/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a master regulator of cell growth that controls cell homeostasis in response to nutrients, growth factors, and other environmental cues. Recent studies have emphasized the importance of lysosomes as a hub for nutrient sensing, especially amino acid sensing by mTORC1. This review highlights recent advances in understanding the amino acid-mTORC1 signaling axis and the role of mTORC1 in cancer.
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21
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Egri SB, Ouch C, Chou HT, Yu Z, Song K, Xu C, Shen K. Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism. Mol Cell 2022; 82:1836-1849.e5. [PMID: 35338845 PMCID: PMC9133170 DOI: 10.1016/j.molcel.2022.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 12/20/2022]
Abstract
mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process.
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Affiliation(s)
- Shawn B Egri
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA 01605, USA
| | - Christna Ouch
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Hui-Ting Chou
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation St, Worcester, MA 01605, USA.
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22
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Jain V, Bose S, Arya AK, Arif T. Lysosomes in Stem Cell Quiescence: A Potential Therapeutic Target in Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:1618. [PMID: 35406389 PMCID: PMC8996909 DOI: 10.3390/cancers14071618] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lysosomes are cellular organelles that regulate essential biological processes such as cellular homeostasis, development, and aging. They are primarily connected to the degradation/recycling of cellular macromolecules and participate in cellular trafficking, nutritional signaling, energy metabolism, and immune regulation. Therefore, lysosomes connect cellular metabolism and signaling pathways. Lysosome's involvement in the critical biological processes has rekindled clinical interest towards this organelle for treating various diseases, including cancer. Recent research advancements have demonstrated that lysosomes also regulate the maintenance and hemostasis of hematopoietic stem cells (HSCs), which play a critical role in the progression of acute myeloid leukemia (AML) and other types of cancer. Lysosomes regulate both HSCs' metabolic networks and identity transition. AML is a lethal type of blood cancer with a poor prognosis that is particularly associated with aging. Although the genetic landscape of AML has been extensively described, only a few targeted therapies have been produced, warranting the need for further research. This review summarizes the functions and importance of targeting lysosomes in AML, while highlighting the significance of lysosomes in HSCs maintenance.
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Affiliation(s)
- Vaibhav Jain
- Abramson Cancer Center, Department of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA;
| | - Swaroop Bose
- Department of Dermatology, Mount Sinai Icahn School of Medicine, New York, NY 10029, USA;
| | - Awadhesh K. Arya
- Department of Anesthesiology, Shock, Trauma and Anesthesiology Research Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Tasleem Arif
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai Icahn School of Medicine, New York, NY 10029, USA
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23
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Yue M, Xiao L, Yan R, Li X, Yang W. Pyroptosis in neurodegenerative diseases: What lies beneath the tip of the iceberg? Int Rev Immunol 2022:1-16. [PMID: 35312447 DOI: 10.1080/08830185.2022.2052064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Neurodegenerative diseases gradually receive attention with a rapidly aging global population. The hallmark of them is a progressive neuronal loss in the brain or peripheral nervous system due to complex reasons ranging from protein aggregation, immune dysregulation to abnormal cell death. The death style of nerve cell is no longer restricted to apoptosis, autophagy and necrosis as confirmed before. With the successive discoveries of the gasdermin (GSDM) protein family and key caspase molecules in the past several decades, pyroptosis emerges as a novel kind of programmed cell death. A substantial body of evidence has recognized the close connection between pyroptosis and the occurrence and development of neurodegenerative diseases. In this review, we summarize molecular mechanisms of pyroptosis, evidences for pyroptosis involvement in neurodegenerative diseases and finally we hope to provide a novel angle for clinical decision-making.
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Affiliation(s)
- Mengli Yue
- Department of Immunology, College of Basic Medical Sciences, JiLin University, Changchun City, Jilin Province, China
| | - Li Xiao
- Department of Immunology, College of Basic Medical Sciences, JiLin University, Changchun City, Jilin Province, China
| | - Rui Yan
- Department of Immunology, College of Basic Medical Sciences, JiLin University, Changchun City, Jilin Province, China
| | - Xinyi Li
- Department of Immunology, College of Basic Medical Sciences, JiLin University, Changchun City, Jilin Province, China
| | - Wei Yang
- Department of Immunology, College of Basic Medical Sciences, JiLin University, Changchun City, Jilin Province, China
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24
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Sun J, Liu Y, Hao X, Lin W, Su W, Chiang E, Baudry M, Bi X. LAMTOR1 inhibition of TRPML1‐dependent lysosomal calcium release regulates dendritic lysosome trafficking and hippocampal neuronal function. EMBO J 2022; 41:e108119. [PMID: 35099830 PMCID: PMC8886530 DOI: 10.15252/embj.2021108119] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 12/12/2021] [Accepted: 12/21/2021] [Indexed: 02/05/2023] Open
Abstract
Lysosomes function not only as degradatory compartments but also as dynamic intracellular calcium ion stores. The transient receptor potential mucolipin 1 (TRPML1) channel mediates lysosomal Ca2+ release, thereby participating in multiple cellular functions. The pentameric Ragulator complex, which plays a critical role in the activation of mTORC1, is also involved in lysosomal trafficking and is anchored to lysosomes through its LAMTOR1 subunit. Here, we report that the Ragulator restricts lysosomal trafficking in dendrites of hippocampal neurons via LAMTOR1‐mediated tonic inhibition of TRPML1 activity, independently of mTORC1. LAMTOR1 directly interacts with TRPML1 through its N‐terminal domain. Eliminating this inhibition in hippocampal neurons by LAMTOR1 deletion or by disrupting LAMTOR1‐TRPML1 binding increases TRPML1‐mediated Ca2+ release and facilitates dendritic lysosomal trafficking powered by dynein. LAMTOR1 deletion in the hippocampal CA1 region of adult mice results in alterations in synaptic plasticity, and in impaired object‐recognition memory and contextual fear conditioning, due to TRPML1 activation. Mechanistically, changes in synaptic plasticity are associated with increased GluA1 dephosphorylation by calcineurin and lysosomal degradation. Thus, LAMTOR1‐mediated inhibition of TRPML1 is critical for regulating dendritic lysosomal motility, synaptic plasticity, and learning.
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Affiliation(s)
- Jiandong Sun
- College of Osteopathic Medicine of the Pacific Western University of Health Sciences Pomona CA USA
| | - Yan Liu
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA USA
| | - Xiaoning Hao
- College of Osteopathic Medicine of the Pacific Western University of Health Sciences Pomona CA USA
| | - Weiju Lin
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA USA
| | - Wenyue Su
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA USA
| | - Emerald Chiang
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA USA
| | - Michel Baudry
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA USA
| | - Xiaoning Bi
- College of Osteopathic Medicine of the Pacific Western University of Health Sciences Pomona CA USA
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25
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Nuciferine protects against high-fat diet-induced hepatic steatosis and insulin resistance via activating TFEB-mediated autophagy–lysosomal pathway. Acta Pharm Sin B 2021; 12:2869-2886. [PMID: 35755273 PMCID: PMC9214335 DOI: 10.1016/j.apsb.2021.12.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 12/30/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is characterized by hepatic steatosis and insulin resistance and there are currently no approved drugs for its treatment. Hyperactivation of mTOR complex 1 (mTORC1) and subsequent impairment of the transcription factor EB (TFEB)-mediated autophagy–lysosomal pathway (ALP) are implicated in the development of NAFLD. Accordingly, agents that augment hepatic TFEB transcriptional activity may have therapeutic potential against NAFLD. The objective of this study was to investigate the effects of nuciferine, a major active component from lotus leaf, on NAFLD and its underlying mechanism of action. Here we show that nuciferine activated ALP and alleviated steatosis, insulin resistance in the livers of NAFLD mice and palmitic acid-challenged hepatocytes in a TFEB-dependent manner. Mechanistic investigation revealed that nuciferine interacts with the Ragulator subunit hepatitis B X-interacting protein and impairs the interaction of the Ragulator complex with Rag GTPases, thereby suppressing lysosomal localization and activity of mTORC1, which activates TFEB-mediated ALP and further ameliorates hepatic steatosis and insulin resistance. Our present results indicate that nuciferine may be a potential agent for treating NAFLD and that regulation of the mTORC1–TFEB–ALP axis could represent a novel pharmacological strategy to combat NAFLD.
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26
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Hesaka A, Tsukamoto Y, Nada S, Kawamura M, Ichimaru N, Sakai S, Nakane M, Mita M, Okuzaki D, Okada M, Isaka Y, Kimura T. d-Serine Mediates Cellular Proliferation for Kidney Remodeling. KIDNEY360 2021; 2:1611-1624. [PMID: 35372967 PMCID: PMC8785787 DOI: 10.34067/kid.0000832021] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/16/2021] [Indexed: 02/04/2023]
Abstract
Background d-serine, a long-term undetected enantiomer of serine, is a biomarker that reflects kidney function and disease activity. The physiologic functions of d-serine are unclear. Methods The dynamics of d-serine were assessed by measuring d-serine in human samples of living kidney donors using two-dimensional high-performance liquid chromatography, and by autoradiographic studies in mice. The effects of d-serine on the kidney were examined by gene expression profiling and metabolic studies using unilateral nephrectomy mice, and genetically modified cells. Results Unilateral nephrectomy in human living kidney donors decreases urinary excretion and thus increases the blood level of d-serine. d-serine is quickly and dominantly distributed to the kidney on injection in mice, suggesting the kidney is a main target organ. Treatment of d-serine at a low dose promotes the enlargement of remnant kidney in mouse model. Mechanistically, d-serine activates the cell cycle for tissue remodeling through an mTOR-related pathway. Conclusions d-serine is a physiologic molecule that promotes kidney remodeling. Besides its function as a biomarker, d-serine has a physiologic activity that influences kidney function.
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Affiliation(s)
- Atsushi Hesaka
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition,Reverse Translational Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition,Department of Nephrology, Osaka University Graduate School of Medicine
| | - Yusuke Tsukamoto
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition,Reverse Translational Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition
| | - Shigeyuki Nada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University
| | | | - Naotsugu Ichimaru
- Department of Urology, Osaka University Graduate School of Medicine,Department of Advanced Technology for Transplantation, Osaka University Graduate School of Medicine
| | - Shinsuke Sakai
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition,Reverse Translational Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition,Department of Nephrology, Osaka University Graduate School of Medicine
| | | | | | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Disease, Osaka University
| | - Masato Okada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine
| | - Tomonori Kimura
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition,Reverse Translational Project, Center for Rare Disease Research, National Institutes of Biomedical Innovation, Health and Nutrition,Department of Nephrology, Osaka University Graduate School of Medicine
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27
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Eskandari R, Ratnayake L, Lakin-Thomas PL. Shared Components of the FRQ-Less Oscillator and TOR Pathway Maintain Rhythmicity in Neurospora. J Biol Rhythms 2021; 36:329-345. [PMID: 33825541 PMCID: PMC8276340 DOI: 10.1177/0748730421999948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Molecular models for the endogenous oscillators that drive circadian rhythms in eukaryotes center on rhythmic transcription/translation of a small number of "clock genes." Although substantial evidence supports the concept that negative and positive transcription/translation feedback loops (TTFLs) are responsible for regulating the expression of these clock genes, certain rhythms in the filamentous fungus Neurospora crassa continue even when clock genes (frq, wc-1, and wc-2) are not rhythmically expressed. Identification of the rhythmic processes operating outside of the TTFL has been a major unresolved area in circadian biology. Our lab previously identified a mutation (vta) that abolishes FRQ-less rhythmicity of the conidiation rhythm and also affects rhythmicity when FRQ is functional. Further studies identified the vta gene product as a component of the TOR (Target of Rapamycin) nutrient-sensing pathway that is conserved in eukaryotes. We now report the discovery of TOR pathway components including GTR2 (homologous to the yeast protein Gtr2, and RAG C/D in mammals) as binding partners of VTA through co-immunoprecipitation (IP) and mass spectrometry analysis using a VTA-FLAG strain. Reciprocal IP with GTR2-FLAG found VTA as a binding partner. A Δgtr2 strain was deficient in growth responses to amino acids. Free-running conidiation rhythms in a FRQ-less strain were abolished in Δgtr2. Entrainment of a FRQ-less strain to cycles of heat pulses demonstrated that Δgtr2 is defective in entrainment. In all of these assays, Δgtr2 is similar to Δvta. In addition, expression of GTR2 protein was found to be rhythmic across two circadian cycles, and functional VTA was required for GTR2 rhythmicity. FRQ protein exhibited the expected rhythm in the presence of GTR2 but the rhythmic level of FRQ dampened in the absence of GTR2. These results establish association of VTA with GTR2, and their role in maintaining functional circadian rhythms through the TOR pathway.
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Affiliation(s)
- Rosa Eskandari
- Department of Biology, York University, Toronto, ON, Canada
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28
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The lysosomal Ragulator complex plays an essential role in leukocyte trafficking by activating myosin II. Nat Commun 2021; 12:3333. [PMID: 34099704 PMCID: PMC8184920 DOI: 10.1038/s41467-021-23654-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
Lysosomes are involved in nutrient sensing via the mechanistic target of rapamycin complex 1 (mTORC1). mTORC1 is tethered to lysosomes by the Ragulator complex, a heteropentamer in which Lamtor1 wraps around Lamtor2–5. Although the Ragulator complex is required for cell migration, the mechanisms by which it participates in cell motility remain unknown. Here, we show that lysosomes move to the uropod in motile cells, providing the platform where Lamtor1 interacts with the myosin phosphatase Rho-interacting protein (MPRIP) independently of mTORC1 and interferes with the interaction between MPRIP and MYPT1, a subunit of myosin light chain phosphatase (MLCP), thereby increasing myosin II–mediated actomyosin contraction. Additionally, formation of the complete Ragulator complex is required for leukocyte migration and pathophysiological immune responses. Together, our findings demonstrate that the lysosomal Ragulator complex plays an essential role in leukocyte migration by activating myosin II through interacting with MPRIP. Myosin II–mediated contractility is required for leukocyte migration. Here, authors show that lysosomes are involved in leukocyte migration by providing the platform where Ragulator complex interacts with the myosin phosphatase Rho-interacting protein (MPRIP) independently of mTORC1 and interferes with the interaction between MPRIP and a subunit of myosin light chain phosphatase (MLCP).
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29
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Lei HT, Mu X, Hattne J, Gonen T. A conformational change in the N terminus of SLC38A9 signals mTORC1 activation. Structure 2021; 29:426-432.e8. [PMID: 33296665 PMCID: PMC9994763 DOI: 10.1016/j.str.2020.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/20/2020] [Accepted: 11/16/2020] [Indexed: 11/28/2022]
Abstract
mTORC1 is a central hub that integrates environmental cues, such as cellular stresses and nutrient availability to modulate metabolism and cellular responses. Recently, SLC38A9, a lysosomal amino acid transporter, emerged as a sensor for luminal arginine and as an activator of mTORC1. The amino acid-mediated activation of mTORC1 is regulated by the N-terminal domain of SLC38A9. Here, we determined the crystal structure of zebrafish SLC38A9 (drSLC38A9) and found the N-terminal fragment inserted deep within the transporter, bound in the substrate-binding pocket where normally arginine would bind. This represents a significant conformational change of the N-terminal domain (N-plug) when compared with our recent arginine-bound structure of drSLC38A9. We propose a ball-and-chain model for mTORC1 activation, where N-plug insertion and Rag GTPase binding with SLC38A9 is regulated by luminal arginine levels. This work provides important insights into nutrient sensing by SLC38A9 to activate the mTORC1 pathways in response to dietary amino acids.
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Affiliation(s)
- Hsiang-Ting Lei
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xuelang Mu
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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30
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Nesterov SV, Yaguzhinsky LS, Podoprigora GI, Nartsissov YR. Amino Acids as Regulators of Cell Metabolism. BIOCHEMISTRY (MOSCOW) 2021; 85:393-408. [PMID: 32569548 DOI: 10.1134/s000629792004001x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review, we discuss the principles of regulation and synchronization of metabolic processes in mammalian cells using a two-component model of cell metabolism consisting of a controlling signaling system that regulates major enzymatic cascades and executive metabolic system that directly performs biosynthetic reactions. This approach has allowed us to distinguish two transitional metabolic states (from catabolism to anabolism and vice versa) accompanied by major rearrangements in the signaling system. The signaling system of natural amino acids was selected, because amino acids are involved in both signaling and executive metabolic subsystems of general cell metabolism. We have developed a graphical representation of metabolic events that allowed us to demonstrate the succession of processes occurring in both metabolic subsystems during complete metabolic cycle in a non-dividing cell. An important revealed feature of the amino acid signaling system is that the signaling properties of amino acid are determined not only by their molecular structure, but also by the location within the cell. Four major signaling groups of amino acids have been identified that localize to lysosomes, mitochondria, cytosol, and extracellular space adjacent to the plasma membrane. Although these amino acids groups are similar in the composition, they have different receptors. We also proposed a scheme for the metabolism regulation by amino acids signaling that can serve as a basis for developing more complete spatio-temporal picture of metabolic regulation involving a wide variety of intracellular signaling cascades.
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Affiliation(s)
- S V Nesterov
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - L S Yaguzhinsky
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - G I Podoprigora
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
| | - Ya R Nartsissov
- Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
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31
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Morozumi Y, Shiozaki K. Conserved and Divergent Mechanisms That Control TORC1 in Yeasts and Mammals. Genes (Basel) 2021; 12:genes12010088. [PMID: 33445779 PMCID: PMC7828246 DOI: 10.3390/genes12010088] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/23/2022] Open
Abstract
Target of rapamycin complex 1 (TORC1), a serine/threonine-protein kinase complex highly conserved among eukaryotes, coordinates cellular growth and metabolism with environmental cues, including nutrients and growth factors. Aberrant TORC1 signaling is associated with cancers and various human diseases, and TORC1 also plays a key role in ageing and lifespan, urging current active research on the mechanisms of TORC1 regulation in a variety of model organisms. Identification and characterization of the RAG small GTPases as well as their regulators, many of which are highly conserved from yeast to humans, led to a series of breakthroughs in understanding the molecular bases of TORC1 regulation. Recruitment of mammalian TORC1 (mTORC1) by RAGs to lysosomal membranes is a key step for mTORC1 activation. Interestingly, the RAG GTPases in fission yeast are primarily responsible for attenuation of TORC1 activity on vacuoles, the yeast equivalent of lysosomes. In this review, we summarize our current knowledge about the functions of TORC1 regulators on yeast vacuoles, and illustrate the conserved and divergent mechanisms of TORC1 regulation between yeasts and mammals.
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Affiliation(s)
- Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan;
- Correspondence: ; Tel.: +81-743-72-5543
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan;
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
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32
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Nada S, Okada M. Genetic dissection of Ragulator structure and function in amino acid-dependent regulation of mTORC1. J Biochem 2020; 168:621-632. [PMID: 32653916 DOI: 10.1093/jb/mvaa076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/12/2022] Open
Abstract
Ragulator is a heteropentameric protein complex consisting of two roadblock heterodimers wrapped by the membrane anchor p18/Lamtor1. The Ragulator complex functions as a lysosomal membrane scaffold for Rag GTPases to recruit and activate mechanistic target of rapamycin complex 1 (mTORC1). However, the roles of Ragulator structure in the regulation of mTORC1 function remain elusive. In this study, we disrupted Ragulator structure by directly anchoring RagC to lysosomes and monitored the effect on amino acid-dependent mTORC1 activation. Expression of lysosome-anchored RagC in p18-deficient cells resulted in constitutive lysosomal localization and amino acid-independent activation of mTORC1. Co-expression of Ragulator in this system restored the amino acid dependency of mTORC1 activation. Furthermore, ablation of Gator1, a suppressor of Rag GTPases, induced amino acid-independent activation of mTORC1 even in the presence of Ragulator. These results demonstrate that Ragulator structure is essential for amino acid-dependent regulation of Rag GTPases via Gator1. In addition, our genetic analyses revealed new roles of amino acids in the regulation of mTORC1 as follows: amino acids could activate a fraction of mTORC1 in a Rheb-independent manner, and could also drive negative-feedback regulation of mTORC1 signalling via protein phosphatases. These intriguing findings contribute to our overall understanding of the regulatory mechanisms of mTORC1 signalling.
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Affiliation(s)
- Shigeyuki Nada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565, Japan
| | - Masato Okada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565, Japan
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33
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Fang X, Tan T, Gao B, Zhao Y, Liu T, Xia Q. Germacrone Regulates HBXIP-Mediated Cell Cycle, Apoptosis and Promotes the Formation of Autophagosomes to Inhibit the Proliferation of Gastric Cancer Cells. Front Oncol 2020; 10:537322. [PMID: 33244453 PMCID: PMC7683780 DOI: 10.3389/fonc.2020.537322] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
Germacrone, a monocyclic sesquiterpene, exerts marked antitumor effects in a variety of cancers, including hepatocellular carcinoma, gastric cancer, and breast cancer. However, the mechanism underlying the effects of germacrone on gastric cancer remains unclear. In this study, we show that germacrone inhibited gastric cancer cell proliferation in a dose-dependent manner, and induced G0/G1-phase cell cycle arrest and apoptosis in these cells. Moreover, germacrone increased the expression of LC3II/LC3I. And LC3II/LC3I was significant increased after germacrone treatment compared with germacrone and bafilomycin A1 (Baf A1) treatment, which suggested germacrone promoted the formation of autophagosomes. Proteomic analysis was then used to identify molecular targets of germacrone in gastric cancer. A total of 596 proteins were screened, and the top hit was identified as late endosomal/lysosomal adaptor and MAPK and MTOR activator 5 (LAMTOR5, also named HBXIP). Overexpression of HBXIP delayed the germacrone-induced cell cycle arrest, induction of apoptosis, and inhibition of autophagy. Combined, our results indicate that germacrone suppresses gastric cancer cell proliferation by inhibiting HBXIP, and this process is related to G0/G1-phase arrest and apoptosis.
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Affiliation(s)
- Xing Fang
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - TingFei Tan
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - BeiBei Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - YingLi Zhao
- Department of Pharmacy, The Second People's Hospital of Hefei, Hefei, China
| | - TingTing Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Pharmacy, The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, China
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Takahara T, Amemiya Y, Sugiyama R, Maki M, Shibata H. Amino acid-dependent control of mTORC1 signaling: a variety of regulatory modes. J Biomed Sci 2020; 27:87. [PMID: 32799865 PMCID: PMC7429791 DOI: 10.1186/s12929-020-00679-2] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/30/2020] [Indexed: 01/10/2023] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is an essential regulator of cell growth and metabolism through the modulation of protein and lipid synthesis, lysosome biogenesis, and autophagy. The activity of mTORC1 is dynamically regulated by several environmental cues, including amino acid availability, growth factors, energy levels, and stresses, to coordinate cellular status with environmental conditions. Dysregulation of mTORC1 activity is closely associated with various diseases, including diabetes, cancer, and neurodegenerative disorders. The discovery of Rag GTPases has greatly expanded our understanding of the regulation of mTORC1 activity by amino acids, especially leucine and arginine. In addition to Rag GTPases, other factors that also contribute to the modulation of mTORC1 activity have been identified. In this review, we discuss the mechanisms of regulation of mTORC1 activity by particular amino acids.
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Affiliation(s)
- Terunao Takahara
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
| | - Yuna Amemiya
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Risa Sugiyama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Masatoshi Maki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Hideki Shibata
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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35
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Nowosad A, Jeannot P, Callot C, Creff J, Perchey RT, Joffre C, Codogno P, Manenti S, Besson A. p27 controls Ragulator and mTOR activity in amino acid-deprived cells to regulate the autophagy-lysosomal pathway and coordinate cell cycle and cell growth. Nat Cell Biol 2020; 22:1076-1090. [PMID: 32807902 DOI: 10.1038/s41556-020-0554-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/06/2020] [Indexed: 01/31/2023]
Abstract
Autophagy is a catabolic process whereby cytoplasmic components are degraded within lysosomes, allowing cells to maintain energy homeostasis during nutrient depletion. Several studies reported that the CDK inhibitor p27Kip1 promotes starvation-induced autophagy by an unknown mechanism. Here we find that p27 controls autophagy via an mTORC1-dependent mechanism in amino acid-deprived cells. During prolonged starvation, a fraction of p27 is recruited to lysosomes, where it interacts with LAMTOR1, a component of the Ragulator complex required for mTORC1 activation. Binding of p27 to LAMTOR1 prevents Ragulator assembly and mTORC1 activation, promoting autophagy. Conversely, p27-/- cells exhibit elevated mTORC1 signalling as well as impaired lysosomal activity and autophagy. This is associated with cytoplasmic sequestration of TFEB, preventing induction of the lysosomal genes required for lysosome function. LAMTOR1 silencing or mTOR inhibition restores autophagy and induces apoptosis in p27-/- cells. Together, these results reveal a direct coordinated regulation between the cell cycle and cell growth machineries.
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Affiliation(s)
- Ada Nowosad
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.,UCL Cancer Institute, University College London, London, UK
| | - Pauline Jeannot
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Caroline Callot
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Justine Creff
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Renaud Thierry Perchey
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Joffre
- Cancer Research Center of Toulouse (CRCT), INSERM U1037, CNRS ERL5294, University of Toulouse, Toulouse, France
| | - Patrice Codogno
- Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Stephane Manenti
- Cancer Research Center of Toulouse (CRCT), INSERM U1037, CNRS ERL5294, University of Toulouse, Toulouse, France
| | - Arnaud Besson
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
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36
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de Martín Garrido N, Aylett CHS. Nutrient Signaling and Lysosome Positioning Crosstalk Through a Multifunctional Protein, Folliculin. Front Cell Dev Biol 2020; 8:108. [PMID: 32195250 PMCID: PMC7063858 DOI: 10.3389/fcell.2020.00108] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
FLCN was identified as the gene responsible for Birt-Hogg-Dubé (BHD) syndrome, a hereditary syndrome associated with the appearance of familiar renal oncocytomas. Most mutations affecting FLCN result in the truncation of the protein, and therefore loss of its associated functions, as typical for a tumor suppressor. FLCN encodes the protein folliculin (FLCN), which is involved in numerous biological processes; mutations affecting this protein thus lead to different phenotypes depending on the cellular context. FLCN forms complexes with two large interacting proteins, FNIP1 and FNIP2. Structural studies have shown that both FLCN and FNIPs contain longin and differentially expressed in normal versus neoplastic cells (DENN) domains, typically involved in the regulation of small GTPases. Accordingly, functional studies show that FLCN regulates both the Rag and the Rab GTPases depending on nutrient availability, which are respectively involved in the mTORC1 pathway and lysosomal positioning. Although recent structural studies shed light on the precise mechanism by which FLCN regulates the Rag GTPases, which in turn regulate mTORC1, how FLCN regulates membrane trafficking through the Rab GTPases or the significance of the intriguing FLCN-FNIP-AMPK complex formation are questions that still remain unanswered. We discuss the recent progress in our understanding of FLCN regulation of both growth signaling and lysosomal positioning, as well as future approaches to establish detailed mechanisms to explain the disparate phenotypes caused by the loss of FLCN function and the development of BHD-associated and other tumors.
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Affiliation(s)
| | - Christopher H. S. Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
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37
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Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to various environmental inputs, especially amino acids. In fact, the activity of mTORC1 is highly sensitive to changes in amino acid levels. Over past decades, a variety of proteins have been identified as participating in the mTORC1 pathway regulated by amino acids. Classically, the Rag guanosine triphosphatases (GTPases), which reside on the lysosome, transmit amino acid availability to the mTORC1 pathway and recruit mTORC1 to the lysosome upon amino acid sufficiency. Recently, several sensors of leucine, arginine, and S-adenosylmethionine for the amino acid-stimulated mTORC1 pathway have been coming to light. Characterization of these sensors is requisite for understanding how cells adjust amino acid sensing pathways to their different needs. In this review, we summarize recent advances in amino acid sensing mechanisms that regulate mTORC1 activity and highlight these identified sensors that accurately transmit specific amino acid signals to the mTORC1 pathway.
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Affiliation(s)
- Xiu-Zhi Li
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan 430070, China
| | - Xiang-Hua Yan
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan 430070, China
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38
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Shen K, Rogala KB, Chou HT, Huang RK, Yu Z, Sabatini DM. Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex. Cell 2019; 179:1319-1329.e8. [PMID: 31704029 PMCID: PMC7008705 DOI: 10.1016/j.cell.2019.10.036] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/08/2019] [Accepted: 10/28/2019] [Indexed: 12/22/2022]
Abstract
mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway.
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Affiliation(s)
- Kuang Shen
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, USA
| | - Kacper B Rogala
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Hui-Ting Chou
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Rick K Huang
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
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39
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Abstract
The mechanistic target of rapamycin (mTOR) signaling pathway coordinates environmental and intracellular cues to control eukaryotic cell growth. As a pivot point between anabolic and catabolic processes, mTOR complex 1 (mTORC1) signaling has established roles in regulating metabolism, translation and autophagy. Hyperactivity of the mTOR pathway is associated with numerous human diseases, including diabetes, cancer and epilepsy. Pharmacological inhibition of the mTOR pathway can extend lifespan in a variety of model organisms. Given its broad control of essential cellular processes and clear relevance to human health, there is extensive interest in elucidating how upstream inputs regulate mTORC1 activation. In this Cell Science at a Glance article and accompanying poster, we summarize our understanding of how extracellular and intracellular signals feed into the mTOR pathway, how the lysosome acts as an mTOR signaling hub, and how downstream signaling controls autophagy and lysosome biogenesis.
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Affiliation(s)
- Kendall J Condon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute, Cambridge, MA 02142, USA.,The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA .,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute, Cambridge, MA 02142, USA.,The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
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40
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Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils ACP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM. Structural basis for the docking of mTORC1 on the lysosomal surface. Science 2019; 366:468-475. [PMID: 31601708 PMCID: PMC7176403 DOI: 10.1126/science.aay0166] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022]
Abstract
The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome.
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Affiliation(s)
- Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Gu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jibril F Kedir
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Laura F Bianchi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Rikke Dueholm
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anna Niehaus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daan Overwijn
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Sherry X Zhou
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daniel Leary
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nouf N Laqtom
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT.nano, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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41
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Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL. Architecture of human Rag GTPase heterodimers and their complex with mTORC1. Science 2019; 366:203-210. [PMID: 31601764 PMCID: PMC6795536 DOI: 10.1126/science.aax3939] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022]
Abstract
The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagAGTP/RagCGDP nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
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Affiliation(s)
| | - Glenn R Masson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Olga Perisic
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alex Berndt
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | | | - Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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42
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Phosphorylation of DEPDC5, a component of the GATOR1 complex, releases inhibition of mTORC1 and promotes tumor growth. Proc Natl Acad Sci U S A 2019; 116:20505-20510. [PMID: 31548394 DOI: 10.1073/pnas.1904774116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Pim and AKT serine/threonine protein kinases are implicated as drivers of cancer. Their regulation of tumor growth is closely tied to the ability of these enzymes to mainly stimulate protein synthesis by activating mTORC1 (mammalian target of rapamycin complex 1) signaling, although the exact mechanism is not completely understood. mTORC1 activity is normally suppressed by amino acid starvation through a cascade of multiple regulatory protein complexes, e.g., GATOR1, GATOR2, and KICSTOR, that reduce the activity of Rag GTPases. Bioinformatic analysis revealed that DEPDC5 (DEP domain containing protein 5), a component of GATOR1 complex, contains Pim and AKT protein kinase phosphorylation consensus sequences. DEPDC5 phosphorylation by Pim and AKT kinases was confirmed in cancer cells through the use of phospho-specific antibodies and transfection of phospho-inactive DEPDC5 mutants. Consistent with these findings, during amino acid starvation the elevated expression of Pim1 overcame the amino acid inhibitory protein cascade and activated mTORC1. In contrast, the knockout of DEPDC5 partially blocked the ability of small molecule inhibitors against Pim and AKT kinases both singly and in combination to suppress tumor growth and mTORC1 activity in vitro and in vivo. In animal experiments knocking in a glutamic acid (S1530E) in DEPDC5, a phospho mimic, in tumor cells induced a significant level of resistance to Pim and the combination of Pim and AKT inhibitors. Our results indicate a phosphorylation-dependent regulatory mechanism targeting DEPDC5 through which Pim1 and AKT act as upstream effectors of mTORC1 to facilitate proliferation and survival of cancer cells.
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43
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Zhang T, Péli-Gulli MP, Zhang Z, Tang X, Ye J, De Virgilio C, Ding J. Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases. SCIENCE ADVANCES 2019; 5:eaax8164. [PMID: 31579828 PMCID: PMC6760929 DOI: 10.1126/sciadv.aax8164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
The Rag/Gtr GTPases serve as a central module in the nutrient-sensing signaling network upstream of TORC1. In yeast, the anchoring of Gtr1-Gtr2 to membranes depends on the Ego1-Ego2-Ego3 ternary complex (EGO-TC), resulting in an EGO-TC-Gtr1-Gtr2 complex (EGOC). EGO-TC and human Ragulator share no obvious sequence similarities and also differ in their composition with respect to the number of known subunits, which raises the question of how the EGO-TC fulfills its function in recruiting Gtr1-Gtr2. Here, we report the structure of EGOC, in which Ego1 wraps around Ego2, Ego3, and Gtr1-Gtr2. In addition, Ego3 interacts with Gtr1-Gtr2 to stabilize the complex. The functional roles of key residues involved in the assembly are validated by in vivo assays. Our structural and functional data combined demonstrate that EGOC and Ragulator-Rag complex are structurally conserved and that EGO-TC is essential and sufficient to recruit Gtr1-Gtr2 to membranes to ensure appropriate TORC1 signaling.
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Affiliation(s)
- Tianlong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | | | - Zhen Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai 201210, China
| | - Xin Tang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai 201210, China
| | - Jie Ye
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai 201210, China
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44
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Rasheed N, Lima TB, Mercaldi GF, Nascimento AF, Silva AL, Righetto GL, Bar‐Peled L, Shen K, Sabatini DM, Gozzo FC, Aparicio R, Smetana JH. C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. FEBS Open Bio 2019; 9:1589-1602. [PMID: 31314152 PMCID: PMC6722880 DOI: 10.1002/2211-5463.12700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/28/2019] [Accepted: 07/15/2019] [Indexed: 01/09/2023] Open
Abstract
Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X-interacting protein (HBXIP; LAMTOR 1-5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, we present the crystal structure of human HBXIP-C7orf59 dimer (LAMTOR 4/5) at 2.9 Å and identify a phosphorylation site on C7orf59 which modulates its interaction with p18. Additionally, we demonstrate the requirement of HBXIP-C7orf59 to stabilize p18 and allow further binding of MP1-p14. The structure of the dimer revealed an unfolded N terminus in C7orf59 (residues 1-15) which was shown to be essential for p18 binding. Full-length p18 does not interact stably with MP1-p14 in the absence of HBXIP-C7orf59, but deletion of p18 residues 108-161 rescues MP1-p14 binding. C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro. C7orf59 Ser67 was phosphorylated in human embryonic kidney 293T cells. PKA activation with forskolin induced dissociation of p18 from C7orf59, which was prevented by the PKA inhibitor H-89. Our results highlight the essential role of HBXIP-C7orf59 dimer as a nucleator of pentameric Ragulator and support a sequential model of Ragulator assembly in which HBXIP-C7orf59 binds and stabilizes p18 which allows subsequent binding of MP1-p14.
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Affiliation(s)
- Nadia Rasheed
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
- Institute of BiologyUniversity of CampinasBrazil
| | - Tatiani B. Lima
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
- Institute of ChemistryUniversity of CampinasBrazil
| | - Gustavo F. Mercaldi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | - Andrey F.Z. Nascimento
- Brazilian Synchrotron Light Laboratory (LNLS)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | - Ana L.S. Silva
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | - Germanna L. Righetto
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
| | | | - Kuang Shen
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Whitehead Institute for Biomedical ResearchCambridgeMAUSA
- Howard Hughes Medical InstituteCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of Harvard and Massachusetts Institute of TechnologyCambridgeMAUSA
| | - David M. Sabatini
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Whitehead Institute for Biomedical ResearchCambridgeMAUSA
- Howard Hughes Medical InstituteCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
- Broad Institute of Harvard and Massachusetts Institute of TechnologyCambridgeMAUSA
| | | | | | - Juliana H.C. Smetana
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasBrazil
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Inpanathan S, Botelho RJ. The Lysosome Signaling Platform: Adapting With the Times. Front Cell Dev Biol 2019; 7:113. [PMID: 31281815 PMCID: PMC6595708 DOI: 10.3389/fcell.2019.00113] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
Lysosomes are the terminal degradative compartment of autophagy, endocytosis and phagocytosis. What once was viewed as a simple acidic organelle in charge of macromolecular digestion has emerged as a dynamic organelle capable of integrating cellular signals and producing signal outputs. In this review, we focus on the concept that the lysosome surface serves as a platform to assemble major signaling hubs like mTORC1, AMPK, GSK3 and the inflammasome. These molecular assemblies integrate and facilitate cross-talk between signals such as amino acid and energy levels, membrane damage and infection, and ultimately enable responses such as autophagy, cell growth, membrane repair and microbe clearance. In particular, we review how molecular machinery like the vacuolar-ATPase proton pump, sestrins, the GATOR complexes, and the Ragulator, modulate mTORC1, AMPK, GSK3 and inflammation. We then elaborate how these signals control autophagy initiation and resolution, TFEB-mediated lysosome adaptation, lysosome remodeling, antigen presentation, inflammation, membrane damage repair and clearance. Overall, by being at the cross-roads for several membrane pathways, lysosomes have emerged as the ideal surveillance compartment to sense, integrate and elicit cellular behavior and adaptation in response to changing environmental and cellular conditions.
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Affiliation(s)
- Subothan Inpanathan
- Department of Chemistry and Biology, Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Roberto J Botelho
- Department of Chemistry and Biology, Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
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Sekiguchi T, Furuno N, Ishii T, Hirose E, Sekiguchi F, Wang Y, Kobayashi H. RagA, an mTORC1 activator, interacts with a hedgehog signaling protein, WDR35/IFT121. Genes Cells 2019; 24:151-161. [DOI: 10.1111/gtc.12663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Takeshi Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Nobuaki Furuno
- Laboratory for Amphibian Biology, Graduate School of Science Hiroshima University Higashihiroshima Japan
| | - Takashi Ishii
- Department of BiochemistryFukuoka Dental College Fukuoka Japan
| | - Eiji Hirose
- Faculty of Health Promotional Sciences Tokoha University Kitaku, Shizuoka Japan
| | - Fumiko Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Yonggang Wang
- Department of Molecular Biology, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Hideki Kobayashi
- Department of Human Nutrition, Faculty of Contemporary Life ScienceChugoku‐Gakuen University Okayama Japan
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Lamming DW, Bar-Peled L. Lysosome: The metabolic signaling hub. Traffic 2019; 20:27-38. [PMID: 30306667 PMCID: PMC6294686 DOI: 10.1111/tra.12617] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/17/2018] [Accepted: 10/07/2018] [Indexed: 12/27/2022]
Abstract
For the past five decades, the lysosome has been characterized as an unglamorous cellular recycling center. This notion has undergone a radical shift in the last 10 years, with new research revealing that this organelle serves as a major hub for metabolic signaling pathways. The discovery that master growth regulators, including the protein kinase mTOR (mechanistic target of rapamycin), make their home at the lysosomal surface has generated intense interest in the lysosome's key role in nutrient sensing and cellular homeostasis. The transcriptional networks required for lysosomal maintenance and function are just being unraveled and their connection to lysosome-based signaling pathways revealed. The catabolic and anabolic pathways that converge on the lysosome connect this organelle with multiple facets of cellular function; when these pathways are deregulated they underlie multiple human diseases, and promote cellular and organismal aging. Thus, understanding how lysosome-based signaling pathways function will not only illuminate the fascinating biology of this organelle but will also be critical in unlocking its therapeutic potentials.
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Affiliation(s)
- Dudley W. Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Liron Bar-Peled
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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Ragulator and SLC38A9 activate the Rag GTPases through noncanonical GEF mechanisms. Proc Natl Acad Sci U S A 2018; 115:9545-9550. [PMID: 30181260 DOI: 10.1073/pnas.1811727115] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) growth pathway detects nutrients through a variety of sensors and regulators that converge on the Rag GTPases, which form heterodimers consisting of RagA or RagB tightly bound to RagC or RagD and control the subcellular localization of mTORC1. The Rag heterodimer uses a unique "locking" mechanism to stabilize its active (GTPRagA-RagCGDP) or inactive (GDPRagA-RagCGTP) nucleotide states. The Ragulator complex tethers the Rag heterodimer to the lysosomal surface, and the SLC38A9 transmembrane protein is a lysosomal arginine sensor that upon activation stimulates mTORC1 activity through the Rag GTPases. How Ragulator and SLC38A9 control the nucleotide loading state of the Rag GTPases remains incompletely understood. Here we find that Ragulator and SLC38A9 are each unique guanine exchange factors (GEFs) that collectively push the Rag GTPases toward the active state. Ragulator triggers GTP release from RagC, thus resolving the locked inactivated state of the Rag GTPases. Upon arginine binding, SLC38A9 converts RagA from the GDP- to the GTP-loaded state, and therefore activates the Rag GTPase heterodimer. Altogether, Ragulator and SLC38A9 act on the Rag GTPases to activate the mTORC1 pathway in response to nutrient sufficiency.
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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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50
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Abstract
Background The protein kinase Target Of Rapamycin (TOR) is a nexus for the regulation of eukaryotic cell growth. TOR assembles into one of two distinct signalling complexes, TOR complex 1 (TORC1) and TORC2 (mTORC1/2 in mammals), with a set of largely non-overlapping protein partners. (m)TORC1 activation occurs in response to a series of stimuli relevant to cell growth, including nutrient availability, growth factor signals and stress, and regulates much of the cell's biosynthetic activity, from proteins to lipids, and recycling through autophagy. mTORC1 regulation is of great therapeutic significance, since in humans many of these signalling complexes, alongside subunits of mTORC1 itself, are implicated in a wide variety of pathophysiologies, including multiple types of cancer, neurological disorders, neurodegenerative diseases and metabolic disorders including diabetes. Methodology Recent years have seen numerous structures determined of (m)TOR, which have provided mechanistic insight into (m)TORC1 activation in particular, however the integration of cellular signals occurs upstream of the kinase and remains incompletely understood. Here we have collected and analysed in detail as many as possible of the molecular and structural studies which have shed light on (m)TORC1 repression, activation and signal integration. Conclusions A molecular understanding of this signal integration pathway is required to understand how (m)TORC1 activation is reconciled with the many diverse and contradictory stimuli affecting cell growth. We discuss the current level of molecular understanding of the upstream components of the (m)TORC1 signalling pathway, recent progress on this key biochemical frontier, and the future studies necessary to establish a mechanistic understanding of this master-switch for eukaryotic cell growth.
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Affiliation(s)
- Kailash Ramlaul
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
| | - Christopher H S Aylett
- Section of Structural Biology, Department of Medicine, Imperial College London, SW7 2AZ, UK
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