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Livneh I, Fabre B, Goldhirsh G, Lulu C, Zinger A, Shammai Vainer Y, Kaduri M, Dahan A, Ziv T, Schroeder A, Ben-Neriah Y, Zohar Y, Cohen-Kaplan V, Ciechanover A. Inhibition of nucleo-cytoplasmic proteasome translocation by the aromatic amino acids or silencing Sestrin3-their sensing mediator-is tumor suppressive. Cell Death Differ 2024:10.1038/s41418-024-01370-x. [PMID: 39266717 DOI: 10.1038/s41418-024-01370-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/11/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024] Open
Abstract
The proteasome, the catalytic arm of the ubiquitin system, is regulated via its dynamic compartmentation between the nucleus and the cytoplasm, among other mechanisms. Under amino acid shortage, the proteolytic complex is translocated to the cytoplasm, where it stimulates proteolysis to supplement recycled amino acids for essential protein synthesis. This response is mediated via the mTOR pathway and the lack of the three aromatic amino acids Tyr, Trp, and Phe (YWF). mTOR activation by supplementation of the triad inhibits proteasome translocation, leading to cell death. We now show that tumoral inherent stress conditions result in translocation of the proteasome from the nucleus to the cytosol. We further show that the modulation of the signaling cascade governed by YWF is applicable also to non-starved cells by using higher concentration of the triad to achieve a surplus relative to all other amino acids. Based on these two phenomena, we found that the modulation of stress signals via the administration of YWF leads to nuclear proteasome sequestration and inhibition of growth of xenograft, spontaneous, and metastatic mouse tumor models. In correlation with the observed effect of YWF on tumors, we found - using transcriptomic and proteomic analyses - that the triad affects various cellular processes related to cell proliferation, migration, and death. In addition, Sestrin3-a mediator of YWF sensing upstream of mTOR-is essential for proteasome translocation, and therefore plays a pro-tumorigenic role, positioning it as a potential oncogene. This newly identified approach for hijacking the cellular "satiety center" carries therefore potential therapeutic implications for cancer.
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Affiliation(s)
- Ido Livneh
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel.
- Institute of Pathology and Cytology, Rambam Health Care Campus, Haifa, Israel.
| | - Bertrand Fabre
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse 3, INP, CNRS, Auzeville-Tolosane, France
| | - Gilad Goldhirsh
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Chen Lulu
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adar Zinger
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yael Shammai Vainer
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Faculty of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maya Kaduri
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Faculty of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Aviva Dahan
- Institute of Pathology and Cytology, Rambam Health Care Campus, Haifa, Israel
| | - Tamar Ziv
- Smoler Proteomic Center, Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Avi Schroeder
- The Louis Family Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Faculty of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yaniv Zohar
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
- Institute of Pathology and Cytology, Rambam Health Care Campus, Haifa, Israel
| | - Victoria Cohen-Kaplan
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Aaron Ciechanover
- The Rappaport Technion Integrated Cancer Center (R-TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel.
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Campos-Chavez E, Paul S, Zhou Z, Alonso D, Verma AR, Fei J, Mondragón A. Translational T-box riboswitches bind tRNA by modulating conformational flexibility. Nat Commun 2024; 15:6592. [PMID: 39097611 PMCID: PMC11297988 DOI: 10.1038/s41467-024-50885-x] [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: 01/22/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024] Open
Abstract
T-box riboswitches are noncoding RNA elements involved in genetic regulation of most Gram-positive bacteria. They regulate amino acid metabolism by assessing the aminoacylation status of tRNA, subsequently affecting the transcription or translation of downstream amino acid metabolism-related genes. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a paradigmatic translational T-box. Results support a two-step binding model, where the tRNA anticodon is recognized first, followed by interactions with the NCCA sequence. Furthermore, after anticodon recognition, tRNA can transiently dock into the discriminator domain even in the absence of the tRNA NCCA-discriminator interactions. Establishment of the NCCA-discriminator interactions significantly stabilizes the fully bound state. Collectively, the data suggest high conformational flexibility in translational T-box riboswitches; and supports a conformational selection model for NCCA recognition. These findings provide a kinetic framework to understand how specific RNA elements underpin the binding affinity and specificity required for gene regulation.
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Affiliation(s)
- Eduardo Campos-Chavez
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Sneha Paul
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Institute of Molecular Sciences of Orsay, Paris-Saclay University, 91405, Orsay, France
| | - Zunwu Zhou
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Dulce Alonso
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Anjali R Verma
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
- Biophysics Program and Institute for Physical Sciences and Technology, University of Maryland, College Park, MD, 20742, USA
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
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3
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Zhang KH, Zhang FF, Zhang ZL, Fang KF, Sun WX, Kong N, Wu M, Liu HO, Liu Y, Li Z, Cai QQ, Wang Y, Wei QW, Lin PC, Lin Y, Xu W, Xu CJ, Yuan YY, Zhao SM. Follicle stimulating hormone controls granulosa cell glutamine synthesis to regulate ovulation. Protein Cell 2024; 15:512-529. [PMID: 38167949 PMCID: PMC11214834 DOI: 10.1093/procel/pwad065] [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: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Polycystic ovary syndrome (PCOS) is the leading cause of anovulatory infertility. Inadequate understanding of the ovulation drivers hinders PCOS intervention. Herein, we report that follicle stimulating hormone (FSH) controls follicular fluid (FF) glutamine levels to determine ovulation. Murine ovulation starts from FF-exposing granulosa cell (GC) apoptosis. FF glutamine, which decreases in pre-ovulation porcine FF, elevates in PCOS patients FF. High-glutamine chow to elevate FF glutamine inhibits mouse GC apoptosis and induces hormonal, metabolic, and morphologic PCOS traits. Mechanistically, follicle-development-driving FSH promotes GC glutamine synthesis to elevate FF glutamine, which maintain follicle wall integrity by inhibiting GC apoptosis through inactivating ASK1-JNK apoptotic pathway. FSH and glutamine inhibit the rapture of cultured murine follicles. Glutamine removal or ASK1-JNK pathway activation with metformin or AT-101 reversed PCOS traits in PCOS models that are induced with either glutamine or EsR1-KO. These suggest that glutamine, FSH, and ASK1-JNK pathway are targetable to alleviate PCOS.
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Affiliation(s)
- Kai-Hui Zhang
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
- Shanghai Key Laboratory of Metabolic Remodeling, and Children’s Hospital of Fudan University, Shanghai 200032, China
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan 250022, China
| | - Fei-Fei Zhang
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Zhi-Ling Zhang
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
- Shanghai Key Laboratory of Metabolic Remodeling, and Children’s Hospital of Fudan University, Shanghai 200032, China
- School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Ke-Fei Fang
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Wen-Xing Sun
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Na Kong
- Reproductive Medicine Center, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Min Wu
- Reproductive Medicine Center, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Hai-Ou Liu
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Yan Liu
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Zhi Li
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Qing-Qing Cai
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Yang Wang
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Quan-Wei Wei
- Department of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210014, China
| | - Peng-Cheng Lin
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, College of Pharmacy, Qinghai University for Nationalities, Xining 810007, China
| | - Yan Lin
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
- Shanghai Key Laboratory of Metabolic Remodeling, and Children’s Hospital of Fudan University, Shanghai 200032, China
| | - Wei Xu
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
- Shanghai Key Laboratory of Metabolic Remodeling, and Children’s Hospital of Fudan University, Shanghai 200032, China
- Shanghai Fifth People’s Hospital of Fudan University, Fudan University, Shanghai 200240, China
| | - Cong-Jian Xu
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
| | - Yi-Yuan Yuan
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
- Shanghai Key Laboratory of Metabolic Remodeling, and Children’s Hospital of Fudan University, Shanghai 200032, China
| | - Shi-Min Zhao
- The Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200090, China
- Shanghai Key Laboratory of Metabolic Remodeling, and Children’s Hospital of Fudan University, Shanghai 200032, China
- School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, College of Pharmacy, Qinghai University for Nationalities, Xining 810007, China
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4
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Tang T, Sun J, Li C. The role of Phafin proteins in cell signaling pathways and diseases. Open Life Sci 2024; 19:20220896. [PMID: 38947768 PMCID: PMC11211877 DOI: 10.1515/biol-2022-0896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Membrane-associated proteins are important membrane readers that mediate and facilitate the signaling and trafficking pathways in eukaryotic membrane-bound compartments. The protein members in the Phafin family are membrane readers containing two phosphoinositide recognition domains: the Pleckstrin Homology domain and the FYVE (Fab1, YOTB, Vac1, and early endosome antigen 1) domain. Phafin proteins, categorized into two subfamilies, Phafin1 and Phafin2, associate with cellular membranes through interactions involving membrane-embedded phosphoinositides and phosphoinositide-binding domains. These membrane-associated Phafin proteins play pivotal roles by recruiting binding partners and forming complexes, which contribute significantly to apoptotic, autophagic, and macropinocytotic pathways. Elevated expression levels of Phafin1 and Phafin2 are observed in various cancers. A recent study highlights a significant increase in Phafin1 protein levels in the lungs of idiopathic pulmonary fibrosis patients compared to normal subjects, suggesting a crucial role for Phafin1 in the pathogenesis of pulmonary fibrosis. Additionally, phosphatidylinositol-3-phosphate-binding 2 (Pib2), a close relative of the Phafin1 protein, functions as an amino acid sensor activating the TOCR1 pathway in yeasts. This review focuses on delineating the involvement of Phafin proteins in cellular signaling and their implications in diseases and briefly discusses the latest research findings concerning Pib2.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jing Sun
- Department of Biostatistics and Epidemiology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, Germany
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5
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Tang X, Liu H, Chang L, Wang X, Liu Q, Tang Z, Xia Q, Zhao P. A strategy for improving silk yield and organ size in silk-producing insects. FEBS J 2024. [PMID: 38923388 DOI: 10.1111/febs.17193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/24/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Insect silks possess excellent biodegradability, biocompatibility and mechanical properties, and have numerous applications in biomedicine and tissue engineering. However, the application of silk fiber is hindered by its limited supply, especially from non-domesticated insects. In the present study, the silk yield and organ size of Bombyx mori were significantly improved through genetic manipulation of the target of rapamycin complex 1 (TORC1) pathway components. Silk protein synthesis and silk gland size were decreased following rapamycin treatment, inhibiting the TORC1 signaling pathway both in vivo and ex vivo. The overexpression of posterior silk gland-specific Rheb and BmSLC7A5 improved silk protein synthesis and silk gland size by activating the TORC1 signaling pathway. Silk yield in BmSLC7A5-overexpression silkworms was significantly increased by approximately 25%. We have demonstrated that the TORC1 signaling pathway is involved in the transcription and translation of silk genes and transcriptional activators via phosphorylation of p70 S6 kinase 1 and 4E-binding protein 1. Our findings present a strategy for increasing silk yield and organ size in silk-producing insects.
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Affiliation(s)
- Xin Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of the Innovative Chinese Materia Medica & Health Intervention, Chongqing Academy of Chinese Materia Medica, China
| | - Huawei Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Li Chang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Institute for Brain Science and Disease, Chongqing Medical University, China
| | - Xin Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingsong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Zhangchen Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
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6
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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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7
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Farr E, Dimitrov D, Schmidt C, Turei D, Lobentanzer S, Dugourd A, Saez-Rodriguez J. MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions. Brief Bioinform 2024; 25:bbae347. [PMID: 39038934 PMCID: PMC11262834 DOI: 10.1093/bib/bbae347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/29/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
From the catalytic breakdown of nutrients to signaling, interactions between metabolites and proteins play an essential role in cellular function. An important case is cell-cell communication, where metabolites, secreted into the microenvironment, initiate signaling cascades by binding to intra- or extracellular receptors of neighboring cells. Protein-protein cell-cell communication interactions are routinely predicted from transcriptomic data. However, inferring metabolite-mediated intercellular signaling remains challenging, partially due to the limited size of intercellular prior knowledge resources focused on metabolites. Here, we leverage knowledge-graph infrastructure to integrate generalistic metabolite-protein with curated metabolite-receptor resources to create MetalinksDB. MetalinksDB is an order of magnitude larger than existing metabolite-receptor resources and can be tailored to specific biological contexts, such as diseases, pathways, or tissue/cellular locations. We demonstrate MetalinksDB's utility in identifying deregulated processes in renal cancer using multi-omics bulk data. Furthermore, we infer metabolite-driven intercellular signaling in acute kidney injury using spatial transcriptomics data. MetalinksDB is a comprehensive and customizable database of intercellular metabolite-protein interactions, accessible via a web interface (https://metalinks.omnipathdb.org/) and programmatically as a knowledge graph (https://github.com/biocypher/metalinks). We anticipate that by enabling diverse analyses tailored to specific biological contexts, MetalinksDB will facilitate the discovery of disease-relevant metabolite-mediated intercellular signaling processes.
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Affiliation(s)
- Elias Farr
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Daniel Dimitrov
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Christina Schmidt
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Denes Turei
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Sebastian Lobentanzer
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Aurelien Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
- EMBL European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
- EMBL European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
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8
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Dai X, Yan P, Wei W. Amino acid availability governs mTOR ubiquitination. Cell Res 2024; 34:335-336. [PMID: 38102197 PMCID: PMC11061116 DOI: 10.1038/s41422-023-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Affiliation(s)
- Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Peiqiang Yan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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9
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Xie M, Kaiser M, Gershtein Y, Schnyder D, Deviatiiarov R, Gazizova G, Shagimardanova E, Zikmund T, Kerckhofs G, Ivashkin E, Batkovskyte D, Newton PT, Andersson O, Fried K, Gusev O, Zeberg H, Kaiser J, Adameyko I, Chagin AS. The level of protein in the maternal murine diet modulates the facial appearance of the offspring via mTORC1 signaling. Nat Commun 2024; 15:2367. [PMID: 38531868 DOI: 10.1038/s41467-024-46030-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/09/2024] [Indexed: 03/28/2024] Open
Abstract
The development of craniofacial skeletal structures is fascinatingly complex and elucidation of the underlying mechanisms will not only provide novel scientific insights, but also help develop more effective clinical approaches to the treatment and/or prevention of the numerous congenital craniofacial malformations. To this end, we performed a genome-wide analysis of RNA transcription from non-coding regulatory elements by CAGE-sequencing of the facial mesenchyme of human embryos and cross-checked the active enhancers thus identified against genes, identified by GWAS for the normal range human facial appearance. Among the identified active cis-enhancers, several belonged to the components of the PI3/AKT/mTORC1/autophagy pathway. To assess the functional role of this pathway, we manipulated it both genetically and pharmacologically in mice and zebrafish. These experiments revealed that mTORC1 signaling modulates craniofacial shaping at the stage of skeletal mesenchymal condensations, with subsequent fine-tuning during clonal intercalation. This ability of mTORC1 pathway to modulate facial shaping, along with its evolutionary conservation and ability to sense external stimuli, in particular dietary amino acids, indicate that the mTORC1 pathway may play a role in facial phenotypic plasticity. Indeed, the level of protein in the diet of pregnant female mice influenced the activity of mTORC1 in fetal craniofacial structures and altered the size of skeletogenic clones, thus exerting an impact on the local geometry and craniofacial shaping. Overall, our findings indicate that the mTORC1 signaling pathway is involved in the effect of environmental conditions on the shaping of craniofacial structures.
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Affiliation(s)
- Meng Xie
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, Flemingsberg, Sweden
- School of Psychological and Cognitive Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Markéta Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Yaakov Gershtein
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Daniela Schnyder
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Kazan Federal University, Kazan, Russia
- Endocrinology Research Center, Moscow, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
- Intractable Disease Research Center, Juntendo University, Tokyo, Japan
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Kazan Federal University, Kazan, Russia
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Kazan Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Greet Kerckhofs
- Biomechanics Lab, Institute of Mechanics, Materials, and Civil Engineering (iMMC), UCLouvain, Louvain-la-Neuve, Belgium
- Pole of Morphology, Institute of Experimental and Clinical Research (IREC), UCLouvain, Woluwe, Belgium
- Department of Materials Engineering, KU Leuven, Leuven, Belgium
- Prometheus, Division for Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
| | - Evgeny Ivashkin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Department of Developmental and Comparative Physiology, N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dominyka Batkovskyte
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Phillip T Newton
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Astrid Lindgren Children's hospital, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kaj Fried
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Oleg Gusev
- Regulatory Genomics Research Center, Kazan Federal University, Kazan, Russia
- Endocrinology Research Center, Moscow, Russia
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
- Intractable Disease Research Center, Juntendo University, Tokyo, Japan
| | - Hugo Zeberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Andrei S Chagin
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
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10
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Yan M, Liu H, Su Y, Bi X, Yang N, Lin R, Lü G. Inhibition of AMPK activation in Echinococcus granulosus sensu stricto limits the parasite's glucose metabolism and survival. Antimicrob Agents Chemother 2024; 68:e0120223. [PMID: 38349157 PMCID: PMC10916388 DOI: 10.1128/aac.01202-23] [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: 09/23/2023] [Accepted: 01/04/2024] [Indexed: 03/07/2024] Open
Abstract
Cystic echinococcosis (CE) is a zoonotic parasitic disease caused by larvae of the Echinococcus granulosus sensu lato (s.l.) cluster. There is an urgent need to develop new drug targets and drug molecules to treat CE. Adenosine monophosphate (AMP)-activated protein kinase (AMPK), a serine/threonine protein kinase consisting of α, β, and γ subunits, plays a key role in the regulation of energy metabolism. However, the role of AMPK in regulating glucose metabolism in E. granulosus s.l. and its effects on parasite viability is unknown. In this study, we found that targeted knockdown of EgAMPKα or a small-molecule AMPK inhibitor inhibited the viability of E. granulosus sensu stricto (s.s.) and disrupted the ultrastructure. The results of in vivo experiments showed that the AMPK inhibitor had a significant therapeutic effect on E. granulosus s.s.-infected mice and resulted in the loss of cellular structures of the germinal layer. In addition, the inhibition of the EgAMPK/EgGLUT1 pathway limited glucose uptake and glucose metabolism functions in E. granulosus s.s.. Overall, our results suggest that EgAMPK can be a potential drug target for CE and that inhibition of EgAMPK activation is an effective strategy for the treatment of disease.
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Affiliation(s)
- Mingzhi Yan
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hui Liu
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yansen Su
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- Anhui University, Hefei, China
| | - Xiaojuan Bi
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Ning Yang
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Renyong Lin
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Basic Medical College, Xinjiang Medical University, Urumqi, China
| | - Guodong Lü
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- College of Pharmacy, Xinjiang Medical University, Urumqi, China
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11
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Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024; 71:108305. [PMID: 38215956 PMCID: PMC11182366 DOI: 10.1016/j.biotechadv.2023.108305] [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: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Cells execute biological functions to support phenotypes such as growth, migration, and secretion. Complementarily, each function of a cell has resource costs that constrain phenotype. Resource allocation by a cell allows it to manage these costs and optimize their phenotypes. In fact, the management of resource constraints (e.g., nutrient availability, bioenergetic capacity, and macromolecular machinery production) shape activity and ultimately impact phenotype. In mammalian systems, quantification of resource allocation provides important insights into higher-order multicellular functions; it shapes intercellular interactions and relays environmental cues for tissues to coordinate individual cells to overcome resource constraints and achieve population-level behavior. Furthermore, these constraints, objectives, and phenotypes are context-dependent, with cells adapting their behavior according to their microenvironment, resulting in distinct steady-states. This review will highlight the biological insights gained from probing resource allocation in mammalian cells and tissues.
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Affiliation(s)
- Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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12
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Law RC, Nurwono G, Park JO. A parallel glycolysis provides a selective advantage through rapid growth acceleration. Nat Chem Biol 2024; 20:314-322. [PMID: 37537378 PMCID: PMC10987256 DOI: 10.1038/s41589-023-01395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Glycolysis is a universal metabolic process that breaks down glucose to produce adenosine triphosphate (ATP) and biomass precursors. The Entner-Doudoroff (ED) pathway is a glycolytic pathway that parallels textbook glycolysis but yields half as much ATP. Accordingly, in organisms that possess both glycolytic pathways (for example, Escherichia coli), its raison d'être remains a mystery. In this study, we found that the ED pathway provides a selective advantage during growth acceleration. Upon carbon and nitrogen upshifts, E. coli accelerates growth faster with than without the ED pathway. Concurrent isotope tracing reveals that the ED pathway flux increases faster than that of textbook glycolysis. We attribute the fast response time of the ED pathway to its strong thermodynamic driving force and streamlining of glucose import. Intermittent nutrient supply manifests the evolutionary advantage of the parallel glycolysis; thus, the dynamic nature of an ostensibly redundant pathway's role in promoting rapid adaptation constitutes a metabolic design principle.
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Affiliation(s)
- Richard C Law
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Glenn Nurwono
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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13
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Tang X, Liu H, Wang X, Chang L, Liu Q, Xia Q, Zhao P. BmSLC7A5 is essential for silk protein synthesis and larval development in Bombyx mori. INSECT SCIENCE 2024. [PMID: 38284747 DOI: 10.1111/1744-7917.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 01/30/2024]
Abstract
Insects produce silk to form cocoons, nests, and webs, which are important for their survival and reproduction. However, little is known about the molecular mechanism of silk protein synthesis at the translation level. The solute carrier family 7 (SLC7) genes are involved in activating the target of rapamycin complex 1 (TORC1) signaling pathway and protein translation process, but the physiological roles of SLC7 genes in silk-producing insects have not been reported. Here, we found that amino acid signaling regulates silk protein synthesis and larval development via the L-type amino acid transporter 1 (LAT1; also known as SLC7A5) in Bombyx mori. A total of 12 SLC7 homologs were identified in the silkworm genome, among which BmSLC7A5 was found to be a silk gland-enriched gene and may be involved in leucine transport. Bioinformatics analysis indicated that SLC7A5 displays high homology and a close phylogenetic relationship in silk-producing insects. Subsequently, we found that leucine treatment significantly increased silk protein synthesis by improving the transcription and protein levels of silk genes. Furthermore, systemic and silk gland-specific knockout of BmSLC7A5 led to decreased silk protein synthesis by inhibiting TORC1 signaling, and somatic mutation also resulted in arrested development from the 5th instar to the early pupal stage. Altogether, our study reveals that BmSLC7A5 is involved in regulating silk protein synthesis and larval development by affecting the TORC1 signaling pathway, which provides a new strategy and target for improving silk yield.
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Affiliation(s)
- Xin Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine & Health Science, Chongqing Academy of Chinese Materia Medica, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Huawei Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Xin Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Li Chang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingsong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
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14
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Zeng Q, Araki Y, Noda T. Pib2 is a cysteine sensor involved in TORC1 activation in Saccharomyces cerevisiae. Cell Rep 2024; 43:113599. [PMID: 38127619 DOI: 10.1016/j.celrep.2023.113599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/24/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) is a master regulator that monitors the availability of various amino acids to promote cell growth in Saccharomyces cerevisiae. It is activated via two distinct upstream pathways: the Gtr pathway, which corresponds to mammalian Rag, and the Pib2 pathway. This study shows that Ser3 was phosphorylated exclusively in a Pib2-dependent manner. Using Ser3 as an indicator of TORC1 activity, together with the established TORC1 substrate Sch9, we investigated which pathways were employed by individual amino acids. Different amino acids exhibited different dependencies on the Gtr and Pib2 pathways. Cysteine was most dependent on the Pib2 pathway and increased the interaction between TORC1 and Pib2 in vivo and in vitro. Moreover, cysteine directly bound to Pib2 via W632 and F635, two critical residues in the T(ail) motif that are necessary to activate TORC1. These results indicate that Pib2 functions as a sensor for cysteine in TORC1 regulation.
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Affiliation(s)
- Qingzhong Zeng
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Yasuhiro Araki
- Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
| | - Takeshi Noda
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan; Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
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15
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Bonfim IM, Paixão DA, Andrade MDO, Junior JM, Persinoti GF, de Giuseppe PO, Murakami MT. Plant structural and storage glucans trigger distinct transcriptional responses that modulate the motility of Xanthomonas pathogens. Microbiol Spectr 2023; 11:e0228023. [PMID: 37855631 PMCID: PMC10714752 DOI: 10.1128/spectrum.02280-23] [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: 06/04/2023] [Accepted: 09/05/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Pathogenic Xanthomonas bacteria can affect a variety of economically relevant crops causing losses in productivity, limiting commercialization and requiring phytosanitary measures. These plant pathogens exhibit high level of host and tissue specificity through multiple molecular strategies including several secretion systems, effector proteins, and a broad repertoire of carbohydrate-active enzymes (CAZymes). Many of these CAZymes act on the plant cell wall and storage carbohydrates, such as cellulose and starch, releasing products used as nutrients and modulators of transcriptional responses to support host colonization by mechanisms yet poorly understood. Here, we reveal that structural and storage β-glucans from the plant cell function as spatial markers, providing distinct chemical stimuli that modulate the transition between higher and lower motility states in Xanthomonas citri, a key virulence trait for many bacterial pathogens.
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Affiliation(s)
- Isabela Mendes Bonfim
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Molecular and Morphofunctional Biology, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Douglas Alvarez Paixão
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Maxuel de Oliveira Andrade
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Joaquim Martins Junior
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Mário Tyago Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
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16
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Goul C, Peruzzo R, Zoncu R. The molecular basis of nutrient sensing and signalling by mTORC1 in metabolism regulation and disease. Nat Rev Mol Cell Biol 2023; 24:857-875. [PMID: 37612414 DOI: 10.1038/s41580-023-00641-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 08/25/2023]
Abstract
The Ser/Thr kinase mechanistic target of rapamycin (mTOR) is a central regulator of cellular metabolism. As part of mTOR complex 1 (mTORC1), mTOR integrates signals such as the levels of nutrients, growth factors, energy sources and oxygen, and triggers responses that either boost anabolism or suppress catabolism. mTORC1 signalling has wide-ranging consequences for the growth and homeostasis of key tissues and organs, and its dysregulated activity promotes cancer, type 2 diabetes, neurodegeneration and other age-related disorders. How mTORC1 integrates numerous upstream cues and translates them into specific downstream responses is an outstanding question with major implications for our understanding of physiology and disease mechanisms. In this Review, we discuss recent structural and functional insights into the molecular architecture of mTORC1 and its lysosomal partners, which have greatly increased our mechanistic understanding of nutrient-dependent mTORC1 regulation. We also discuss the emerging involvement of aberrant nutrient-mTORC1 signalling in multiple diseases.
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Affiliation(s)
- Claire Goul
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Roberta Peruzzo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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17
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Hu J, Zhao C, Tan J, Lai S, Zhou Y, Dai L. Transcriptome analysis of Euwallacea interjectus reveals differentially expressed unigenes related to developmental stages and egg laying. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101100. [PMID: 37329642 DOI: 10.1016/j.cbd.2023.101100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/19/2023]
Abstract
Euwallacea interjectus (Curculionidae: Scolytinae) is an ambrosia beetle species in its early stages of research. Therefore, studying the related molecular mechanism associated with the development and egg laid is essential. Transcriptome sequencing was used in this study to compare the gene expression of the beetles at different developmental stages and female adults before and after oviposition. A total of 40,047 annotated unigenes were obtained. There were 4225 differentially expressed unigenes (DEUs) from larva to prepupa stage, 3651 DEUs between prepupa and pupa, 1675 DEUs generated from pupa to adult, and 4762 DEUs between females before and after oviposition. The most significant pathway differences between different development stages and before and after oviposition were selected through functional annotation of DEUs between different stages. Among them, there were many pathways related to protein metabolism including: neuroactive ligand-receptor interaction, endoplasmic reticulum and RNA transport. This study provides valuable information on the molecular regulation mechanism of development and the egg laid of E. interjectus.
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Affiliation(s)
- Jiafeng Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210036, China; College of Forestry, Nanjing Forestry University, Nanjing 210036, China
| | - Chen Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210036, China; College of Forestry, Nanjing Forestry University, Nanjing 210036, China
| | - Jiajin Tan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210036, China; College of Forestry, Nanjing Forestry University, Nanjing 210036, China
| | - Shengchang Lai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210036, China; College of Forestry, Nanjing Forestry University, Nanjing 210036, China
| | - Yang Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210036, China; College of Forestry, Nanjing Forestry University, Nanjing 210036, China
| | - Lulu Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210036, China; College of Forestry, Nanjing Forestry University, Nanjing 210036, China.
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18
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Barbier F, Fichtner F, Beveridge C. The strigolactone pathway plays a crucial role in integrating metabolic and nutritional signals in plants. NATURE PLANTS 2023; 9:1191-1200. [PMID: 37488268 DOI: 10.1038/s41477-023-01453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/24/2023] [Indexed: 07/26/2023]
Abstract
Strigolactones are rhizosphere signals and phytohormones that play crucial roles in plant development. They are also well known for their role in integrating nitrate and phosphate signals to regulate shoot and root development. More recently, sugars and citrate (an intermediate of the tricarboxylic acid cycle) were reported to inhibit the strigolactone response, with dramatic effects on shoot architecture. This Review summarizes the discoveries recently made concerning the mechanisms through which the strigolactone pathway integrates sugar, metabolite and nutrient signals. We highlight here that strigolactones and MAX2-dependent signalling play crucial roles in mediating the impacts of nutritional and metabolic cues on plant development and metabolism. We also discuss and speculate concerning the role of these interactions in plant evolution and adaptation to their environment.
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Affiliation(s)
- Francois Barbier
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, St Lucia, Queensland, Australia.
| | - Franziska Fichtner
- Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christine Beveridge
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, St Lucia, Queensland, Australia
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19
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Ryback B, Vorholt JA. Coenzyme biosynthesis in response to precursor availability reveals incorporation of β-alanine from pantothenate in prototrophic bacteria. J Biol Chem 2023; 299:104919. [PMID: 37315792 PMCID: PMC10393543 DOI: 10.1016/j.jbc.2023.104919] [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: 03/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023] Open
Abstract
Coenzymes are important for all classes of enzymatic reactions and essential for cellular metabolism. Most coenzymes are synthesized from dedicated precursors, also referred to as vitamins, which prototrophic bacteria can either produce themselves from simpler substrates or take up from the environment. The extent to which prototrophs use supplied vitamins and whether externally available vitamins affect the size of intracellular coenzyme pools and control endogenous vitamin synthesis is currently largely unknown. Here, we studied coenzyme pool sizes and vitamin incorporation into coenzymes during growth on different carbon sources and vitamin supplementation regimes using metabolomics approaches. We found that the model bacterium Escherichia coli incorporated pyridoxal, niacin, and pantothenate into pyridoxal 5'-phosphate, NAD, and coenzyme A (CoA), respectively. In contrast, riboflavin was not taken up and was produced exclusively endogenously. Coenzyme pools were mostly homeostatic and not affected by externally supplied precursors. Remarkably, we found that pantothenate is not incorporated into CoA as such but is first degraded to pantoate and β-alanine and then rebuilt. This pattern was conserved in various bacterial isolates, suggesting a preference for β-alanine over pantothenate utilization in CoA synthesis. Finally, we found that the endogenous synthesis of coenzyme precursors remains active when vitamins are supplied, which is consistent with described expression data of genes for enzymes involved in coenzyme biosynthesis under these conditions. Continued production of endogenous coenzymes may ensure rapid synthesis of the mature coenzyme under changing environmental conditions, protect against coenzyme limitation, and explain vitamin availability in naturally oligotrophic environments.
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20
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Liu LZ, Liu L, Shi ZH, Bian XL, Si ZR, Wang QQ, Xiang Y, Zhang Y. Amphibian pore-forming protein βγ-CAT drives extracellular nutrient scavenging under cell nutrient deficiency. iScience 2023; 26:106598. [PMID: 37128610 PMCID: PMC10148134 DOI: 10.1016/j.isci.2023.106598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/22/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
Nutrient acquisition is essential for animal cells. βγ-CAT is a pore-forming protein (PFP) and trefoil factor complex assembled under tight regulation identified in toad Bombina maxima. Here, we reported that B. maxima cells secreted βγ-CAT under glucose, glutamine, and pyruvate deficiency to scavenge extracellular proteins for their nutrient supply and survival. AMPK signaling positively regulated the expression and secretion of βγ-CAT. The PFP complex selectively bound extracellular proteins and promoted proteins uptake through endolysosomal pathways. Elevated intracellular amino acids, enhanced ATP production, and eventually prolonged cell survival were observed in the presence of βγ-CAT and extracellular proteins. Liposome assays indicated that high concentration of ATP negatively regulated the opening of βγ-CAT channels. Collectively, these results uncovered that βγ-CAT is an essential element in cell nutrient scavenging under cell nutrient deficiency by driving vesicular uptake of extracellular proteins, providing a new paradigm for PFPs in cell nutrient acquisition and metabolic flexibility.
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Affiliation(s)
- Ling-Zhen Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Long Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Zhi-Hong Shi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Xian-Ling Bian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Life Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zi-Ru Si
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Life Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qi-Quan Wang
- Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Yang Xiang
- Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
- Corresponding author
| | - Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Corresponding author
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21
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Ortega AD. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors. Biomolecules 2023; 13:biom13050765. [PMID: 37238635 DOI: 10.3390/biom13050765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
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Affiliation(s)
- Alvaro Darío Ortega
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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22
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Parker J. Pathophysiological Effects of Contemporary Lifestyle on Evolutionary-Conserved Survival Mechanisms in Polycystic Ovary Syndrome. Life (Basel) 2023; 13:life13041056. [PMID: 37109585 PMCID: PMC10145572 DOI: 10.3390/life13041056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is increasingly being characterized as an evolutionary mismatch disorder that presents with a complex mixture of metabolic and endocrine symptoms. The Evolutionary Model proposes that PCOS arises from a collection of inherited polymorphisms that have been consistently demonstrated in a variety of ethnic groups and races. In utero developmental programming of susceptible genomic variants are thought to predispose the offspring to develop PCOS. Postnatal exposure to lifestyle and environmental risk factors results in epigenetic activation of developmentally programmed genes and disturbance of the hallmarks of health. The resulting pathophysiological changes represent the consequences of poor-quality diet, sedentary behaviour, endocrine disrupting chemicals, stress, circadian disruption, and other lifestyle factors. Emerging evidence suggests that lifestyle-induced gastrointestinal dysbiosis plays a central role in the pathogenesis of PCOS. Lifestyle and environmental exposures initiate changes that result in disturbance of the gastrointestinal microbiome (dysbiosis), immune dysregulation (chronic inflammation), altered metabolism (insulin resistance), endocrine and reproductive imbalance (hyperandrogenism), and central nervous system dysfunction (neuroendocrine and autonomic nervous system). PCOS can be a progressive metabolic condition that leads to obesity, gestational diabetes, type two diabetes, metabolic-associated fatty liver disease, metabolic syndrome, cardiovascular disease, and cancer. This review explores the mechanisms that underpin the evolutionary mismatch between ancient survival pathways and contemporary lifestyle factors involved in the pathogenesis and pathophysiology of PCOS.
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Affiliation(s)
- Jim Parker
- School of Medicine, University of Wollongong, Wollongong, NSW 2522, Australia
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23
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Bian X, Si Z, Wang Q, Liu L, Shi Z, Tian C, Lee W, Zhang Y. IgG Fc-binding protein positively regulates the assembly of pore-forming protein complex βγ-CAT evolved to drive cell vesicular delivery and transport. J Biol Chem 2023; 299:104717. [PMID: 37068610 DOI: 10.1016/j.jbc.2023.104717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
Cell membranes form barriers for molecule exchange between the cytosol and the extracellular environments. βγ-CAT, a complex of pore-forming protein (PFP) BmALP1 (two βγ-crystallin domains with an aerolysin pore-forming domain) and the trefoil factor BmTFF3, has been identified in toad Bombina maxima. It plays pivotal roles, via inducing channel formation in various intra- or extra- cellular vesicles, as well as in nutrient acquisition, maintaining water balance, and antigen presentation. Thus, such a protein machine should be tightly regulated. Indeed, BmALP3 (a paralog of BmALP1) oxidizes BmALP1 to form a water-soluble polymer, leading to dissociation of the βγ-CAT complex and loss of biological activity. Here, we found that the B. maxima IgG Fc-binding protein (FCGBP), a well-conserved vertebrate mucin-like protein with unknown functions, acted as a positive regulator for βγ-CAT complex assembly. The interactions among FCGBP, BmALP1, and BmTFF3 were revealed by co-immunoprecipitation assays. Interestingly, FCGBP reversed the inhibitory effect of BmALP3 on the βγ-CAT complex. Furthermore, FCGBP reduced BmALP1 polymers and facilitated the assembly of βγ-CAT with the biological pore-forming activity in the presence of BmTFF3. Our findings define the role of FCGBP in mediating the assembly of a PFP machine evolved to drive cell vesicular delivery and transport.
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Affiliation(s)
- Xianling Bian
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ziru Si
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Qiquan Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Lingzhen Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhihong Shi
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Wenhui Lee
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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24
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Thoma V, Sakai S, Nagata K, Ishii Y, Maruyama S, Abe A, Kondo S, Kawata M, Hamada S, Deguchi R, Tanimoto H. On the origin of appetite: GLWamide in jellyfish represents an ancestral satiety neuropeptide. Proc Natl Acad Sci U S A 2023; 120:e2221493120. [PMID: 37011192 PMCID: PMC10104569 DOI: 10.1073/pnas.2221493120] [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: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 04/05/2023] Open
Abstract
Food intake is regulated by internal state. This function is mediated by hormones and neuropeptides, which are best characterized in popular model species. However, the evolutionary origins of such feeding-regulating neuropeptides are poorly understood. We used the jellyfish Cladonema to address this question. Our combined transcriptomic, behavioral, and anatomical approaches identified GLWamide as a feeding-suppressing peptide that selectively inhibits tentacle contraction in this jellyfish. In the fruit fly Drosophila, myoinhibitory peptide (MIP) is a related satiety peptide. Surprisingly, we found that GLWamide and MIP were fully interchangeable in these evolutionarily distant species for feeding suppression. Our results suggest that the satiety signaling systems of diverse animals share an ancient origin.
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Affiliation(s)
- Vladimiros Thoma
- Graduate School of Life Sciences, Tohoku University, Sendai980-8577, Japan
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai980-0845, Japan
| | - Shuhei Sakai
- Graduate School of Life Sciences, Tohoku University, Sendai980-8577, Japan
| | - Koki Nagata
- Graduate School of Life Sciences, Tohoku University, Sendai980-8577, Japan
| | - Yuu Ishii
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai980-0845, Japan
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobaku, Sendai980-8578, Japan
| | - Shinichiro Maruyama
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobaku, Sendai980-8578, Japan
- Department of Life Science, Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-ku, Tokyo112-8610, Japan
| | - Ayako Abe
- Graduate School of Life Sciences, Tohoku University, Sendai980-8577, Japan
| | - Shu Kondo
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Katsushika-ku, Tokyo125-8585, Japan
- Invertebrate Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
| | - Masakado Kawata
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobaku, Sendai980-8578, Japan
| | - Shun Hamada
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women’s University, Fukuoka813-8529, Japan
| | - Ryusaku Deguchi
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai980-0845, Japan
| | - Hiromu Tanimoto
- Graduate School of Life Sciences, Tohoku University, Sendai980-8577, Japan
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25
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Iskandaryan M, Blbulyan S, Sahakyan M, Vassilian A, Trchounian K, Poladyan A. L-amino acids affect the hydrogenase activity and growth of Ralstonia eutropha H16. AMB Express 2023; 13:33. [PMID: 36932299 PMCID: PMC10023824 DOI: 10.1186/s13568-023-01535-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023] Open
Abstract
Ralstonia eutropha H16 is a chemolithoautotrophic bacterium with O2-tolerant hydrogenase (Hyds) enzymes. Hyds are expressed in the presence of gas mixtures (H2, O2, CO2) or under energy limitation and stress conditions. O2-tolerant Hyds are promising candidates as anode biocatalysts in enzymatic fuel cells (EFCs). Supplementation of 0.5% (w/v) yeast extract to the fructose-nitrogen (FN) growth medium enhanced H2-oxidizing Hyd activity ~ sixfold. Our study aimed to identify key metabolites (L-amino acids (L-AAs) and vitamins) in yeast extract that are necessary for the increased synthesis and activity of Hyds. A decrease in pH and a reduction in ORP (from + 240 ± 5 mV to - 180 mV ± 10 mV values) after 24 h of growth in the presence of AAs were observed. Compared to the FN-medium control, supplementation of 7.0 μmol/ml of the L-AA mixture stimulated the growth of bacteria ~ 1.9 to 2.9 fold, after 72 h. The whole cells' H2-oxidizing Hyd activity was not observed in control samples, whereas the addition of L-AAs, mainly glycine resulted in a maximum of ~ 22 ± 0.5 and 15 ± 0.3 U, g CDW-1 activity after 24 h and 72 h, respectively. Our results suggest a correlation between ORP, pH, and function of Hyds in R. eutropha H16 in the presence of key L-AAs. L-AAs used in small amounts can be proposed as signaling molecules or key components of Hyd maturation. These results are important for the optimization of O2-tolerant Hyds production as anode biocatalysts.
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Affiliation(s)
- Meri Iskandaryan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia
| | - Syuzanna Blbulyan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia
| | - Mayramik Sahakyan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia
| | - Anait Vassilian
- Research Institute of Biology, Biology Faculty, YSU, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia.,Research Institute of Biology, Biology Faculty, YSU, Yerevan, Armenia
| | - Anna Poladyan
- Department of Biochemistry, Microbiology, and Biotechnology, Biology Faculty, YSU, Yerevan, Armenia. .,Research Institute of Biology, Biology Faculty, YSU, Yerevan, Armenia.
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26
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Liu Y, Birsoy K. Metabolic sensing and control in mitochondria. Mol Cell 2023; 83:877-889. [PMID: 36931256 PMCID: PMC10332353 DOI: 10.1016/j.molcel.2023.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are membrane-enclosed organelles with endosymbiotic origins, harboring independent genomes and a unique biochemical reaction network. To perform their critical functions, mitochondria must maintain a distinct biochemical environment and coordinate with the cytosolic metabolic networks of the host cell. This coordination requires them to sense and control metabolites and respond to metabolic stresses. Indeed, mitochondria adopt feedback or feedforward control strategies to restrain metabolic toxicity, enable metabolic conservation, ensure stable levels of key metabolites, allow metabolic plasticity, and prevent futile cycles. A diverse panel of metabolic sensors mediates these regulatory circuits whose malfunctioning leads to inborn errors of metabolism with mild to severe clinical manifestations. In this review, we discuss the logic and molecular basis of metabolic sensing and control in mitochondria. The past research outlined recurring patterns in mitochondrial metabolic sensing and control and highlighted key knowledge gaps in this organelle that are potentially addressable with emerging technological breakthroughs.
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Affiliation(s)
- Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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27
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Components of TOR and MAP kinase signaling control chemotropism and pathogenicity in the fungal pathogen Verticillium dahliae. Microbiol Res 2023; 271:127361. [PMID: 36921400 DOI: 10.1016/j.micres.2023.127361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Filamentous fungi can sense useful resources and hazards in their environment and direct growth of their hyphae accordingly. Chemotropism ensures access to nutrients, contact with other individuals (e.g., for mating), and interaction with hosts in the case of pathogens. Previous studies have revealed a complex chemotropic sensing landscape during host-pathogen interactions, but the underlying molecular machinery remains poorly characterized. Here we studied mechanisms controlling directed hyphal growth of the important plant-pathogenic fungus Verticillium dahliae towards different chemoattractants. We found that the homologs of the Rag GTPase Gtr1 and the GTPase-activating protein Tsc2, an activator and a repressor of the TOR kinase respectively, play important roles in hyphal chemotropism towards nutrients, plant-derived signals, and heterologous α-pheromone of Fusarium oxysporum. Furthermore, important roles of these regulators were identified in fungal development and pathogenicity. We also found that the mitogen-activated protein kinase (MAPK) Fus3 is required for chemotropism towards nutrients, while the G protein-coupled receptor (GPCR) Ste2 and the MAPK Slt2 control chemosensing of plant-derived signals and α-pheromone. Our study establishes V. dahliae as a suitable model system for the analysis of fungal chemotropism and discovers new components of chemotropic signaling during growth and host-pathogen interactions of V. dahliae.
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28
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Pirola CJ, Sookoian S. COVID-19 and non-alcoholic fatty liver disease: Biological insights from multi-omics data. Liver Int 2023; 43:580-587. [PMID: 36593576 DOI: 10.1111/liv.15509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
We explored the shared pathophysiological mechanisms between COVID-19 and non-alcoholic fatty liver disease (NAFLD) by integrating multi-omics data. We studied common genetic risk factors and underlying biological processes using functional enrichment analysis. To understand the sex-specific pathways involved in the clinical course of SARS-CoV-2 infection, we processed sex-stratified data from COVID-19 genome-wide association datasets. We further explored the transcriptional signature of the liver cells in healthy and COVID-19 tissue specimens. We also integrated genetic and metabolomic information. We found that COVID-19 and NAFLD share biological disease mechanisms, including pathways that regulate the inflammatory and lipopolysaccharide response. Single-cell transcriptomics revealed enrichment of complement-related pathways in Kupffer cells, syndecan-mediated signalling in plasma cells, and epithelial-to-mesenchymal transition in hepatic stellate cells. The strategy of pathway-level analysis of genomic and metabolomic data uncovered l-lactic acid, Krebs cycle intermediate compounds, arachidonic acid and cortisol among the most prominent shared metabolites.
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Affiliation(s)
- Carlos J Pirola
- Systems Biology of Complex Diseases, Centro de Altos Estudios en Ciencias Humanas y de la Salud (CAECIHS), Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Silvia Sookoian
- Clinical and Molecular Hepatology, Centro de Altos Estudios en Ciencias Humanas y de la Salud (CAECIHS), Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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29
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Kanaoka Y, Onodera K, Watanabe K, Hayashi Y, Usui T, Uemura T, Hattori Y. Inter-organ Wingless/Ror/Akt signaling regulates nutrient-dependent hyperarborization of somatosensory neurons. eLife 2023; 12:79461. [PMID: 36647607 PMCID: PMC9844989 DOI: 10.7554/elife.79461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/11/2022] [Indexed: 01/18/2023] Open
Abstract
Nutrition in early life has profound effects on an organism, altering processes such as organogenesis. However, little is known about how specific nutrients affect neuronal development. Dendrites of class IV dendritic arborization neurons in Drosophila larvae become more complex when the larvae are reared on a low-yeast diet compared to a high-yeast diet. Our systematic search for key nutrients revealed that the neurons increase their dendritic terminal densities in response to a combined deficiency in vitamins, metal ions, and cholesterol. The deficiency of these nutrients upregulates Wingless in a closely located tissue, body wall muscle. Muscle-derived Wingless activates Akt in the neurons through the receptor tyrosine kinase Ror, which promotes the dendrite branching. In larval muscles, the expression of wingless is regulated not only in this key nutrient-dependent manner, but also by the JAK/STAT signaling pathway. Additionally, the low-yeast diet blunts neuronal light responsiveness and light avoidance behavior, which may help larvae optimize their survival strategies under low-nutritional conditions. Together, our studies illustrate how the availability of specific nutrients affects neuronal development through inter-organ signaling.
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Affiliation(s)
| | - Koun Onodera
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Kaori Watanabe
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Yusaku Hayashi
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Tadao Usui
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Tadashi Uemura
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Research Center for Dynamic Living Systems, Kyoto UniversityKyotoJapan
- AMED-CRESTTokyoJapan
| | - Yukako Hattori
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- JST FORESTTokyoJapan
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30
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O'Neal MA, Gutierrez NR, Laing KL, Manoogian ENC, Panda S. Barriers to adherence in time-restricted eating clinical trials: An early preliminary review. Front Nutr 2023; 9:1075744. [PMID: 36712501 PMCID: PMC9877448 DOI: 10.3389/fnut.2022.1075744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Time-restricted eating (TRE) has shown potential benefits in optimizing the body's circadian rhythms and improving cardiometabolic health. However, as with all dietary interventions, a participant's ability to adhere to the protocol may be largely influenced by a variety of lifestyle factors. In TRE trials that reported participants' rates of adherence, the percentage of total days with successful adherence to TRE ranged from 47% to 95%. The purpose of this review is to (1) summarize findings of lifestyle factors affecting adherence to TRE clinical trials outside of the lab, and (2) explore a recommended set of behavioral intervention strategies for the application of TRE. A literature search on Pubmed was conducted to identify clinical TRE studies from 1988 to October 5, 2022, that investigated TRE as a dietary intervention. 21 studies included daily self-monitoring of adherence, though only 10 studies reported a combination of family, social, work, and miscellaneous barriers. To maximize participant adherence to TRE and increase the reliability of TRE clinical trials, future studies should monitor adherence, assess potential barriers, and consider incorporating a combination of behavioral intervention strategies in TRE protocols.
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31
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Davinelli S, Medoro A, Ali S, Passarella D, Intrieri M, Scapagnini G. Dietary Flavonoids and Adult Neurogenesis: Potential Implications for Brain Aging. Curr Neuropharmacol 2023; 21:651-668. [PMID: 36321225 PMCID: PMC10207917 DOI: 10.2174/1570159x21666221031103909] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/27/2022] [Accepted: 08/19/2022] [Indexed: 02/10/2023] Open
Abstract
Adult neurogenesis deficiency has been proposed to be a common hallmark in different age-related neurodegenerative diseases. The administration of flavonoids is currently reported as a potentially beneficial strategy for preventing brain aging alterations, including adult neurogenesis decline. Flavonoids are a class of plant-derived dietary polyphenols that have drawn attention for their neuroprotective and pro-cognitive effects. Although they undergo extensive metabolism and localize in the brain at low concentrations, flavonoids are now believed to improve cerebral vasculature and interact with signal transduction cascades involved in the regulation of adult neurogenesis. Furthermore, many dietary flavonoids have been shown to reduce oxidative stress and neuroinflammation, improving the neuronal microenvironment where adult neurogenesis occurs. The overall goal of this review is to summarize the evidence supporting the role of flavonoids in modulating adult neurogenesis as well as to highlight how these dietary agents may be promising candidates in restoring healthy brain function during physiological and pathological aging.
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Affiliation(s)
- Sergio Davinelli
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Alessandro Medoro
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Sawan Ali
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Daniela Passarella
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Mariano Intrieri
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Giovanni Scapagnini
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
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32
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Shi C, Murphy CT. piRNAs regulate a Hedgehog germline-to-soma pro-aging signal. NATURE AGING 2023; 3:47-63. [PMID: 37118518 PMCID: PMC10154208 DOI: 10.1038/s43587-022-00329-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2022] [Indexed: 04/30/2023]
Abstract
The reproductive system regulates somatic aging through competing anti- and pro-aging signals. Germline removal extends somatic lifespan through conserved pathways including insulin and mammalian target-of-rapamycin signaling, while germline hyperactivity shortens lifespan through unknown mechanisms. Here we show that mating-induced germline hyperactivity downregulates piRNAs, in turn desilencing their targets, including the Hedgehog-like ligand-encoding genes wrt-1 and wrt-10, ultimately causing somatic collapse and death. Germline-produced Hedgehog signals require PTR-6 and PTR-16 receptors for mating-induced shrinking and death. Our results reveal an unconventional role of the piRNA pathway in transcriptional regulation of Hedgehog signaling and a new role of Hedgehog signaling in the regulation of longevity and somatic maintenance: Hedgehog signaling is controlled by the tunable piRNA pathway to encode the previously unknown germline-to-soma pro-aging signal. Mating-induced piRNA downregulation in the germline and subsequent Hedgehog signaling to the soma enable the animal to tune somatic resource allocation to germline needs, optimizing reproductive timing and survival.
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Affiliation(s)
- Cheng Shi
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA.
| | - Coleen T Murphy
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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33
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Jamsheer K M, Awasthi P, Laxmi A. The social network of target of rapamycin complex 1 in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7026-7040. [PMID: 35781571 DOI: 10.1093/jxb/erac278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Target of rapamycin complex 1 (TORC1) is a highly conserved serine-threonine protein kinase crucial for coordinating growth according to nutrient availability in eukaryotes. It works as a central integrator of multiple nutrient inputs such as sugar, nitrogen, and phosphate and promotes growth and biomass accumulation in response to nutrient sufficiency. Studies, especially in the past decade, have identified the central role of TORC1 in regulating growth through interaction with hormones, photoreceptors, and stress signaling machinery in plants. In this review, we comprehensively analyse the interactome and phosphoproteome of the Arabidopsis TORC1 signaling network. Our analysis highlights the role of TORC1 as a central hub kinase communicating with the transcriptional and translational apparatus, ribosomes, chaperones, protein kinases, metabolic enzymes, and autophagy and stress response machinery to orchestrate growth in response to nutrient signals. This analysis also suggests that along with the conserved downstream components shared with other eukaryotic lineages, plant TORC1 signaling underwent several evolutionary innovations and co-opted many lineage-specific components during. Based on the protein-protein interaction and phosphoproteome data, we also discuss several uncharacterized and unexplored components of the TORC1 signaling network, highlighting potential links for future studies.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Institute of Genome Engineering, Amity University Uttar Pradesh, Noida 201313, India
| | - Prakhar Awasthi
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, New Delhi 110067, India
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López‐Haber C, Netting DJ, Hutchins Z, Ma X, Hamilton KE, Mantegazza AR. The phagosomal solute transporter SLC15A4 promotes inflammasome activity via mTORC1 signaling and autophagy restraint in dendritic cells. EMBO J 2022; 41:e111161. [PMID: 36031853 PMCID: PMC9574736 DOI: 10.15252/embj.2022111161] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 01/18/2023] Open
Abstract
Phagocytosis is the necessary first step to sense foreign microbes or particles and enables activation of innate immune pathways such as inflammasomes. However, the molecular mechanisms underlying how phagosomes modulate inflammasome activity are not fully understood. We show that in murine dendritic cells (DCs), the lysosomal histidine/peptide solute carrier transporter SLC15A4, associated with human inflammatory disorders, is recruited to phagosomes and is required for optimal inflammasome activity after infectious or sterile stimuli. Dextran sodium sulfate-treated SLC15A4-deficient mice exhibit decreased colon inflammation, reduced IL-1β production by intestinal DCs, and increased autophagy. Similarly, SLC15A4-deficient DCs infected with Salmonella typhimurium show reduced caspase-1 cleavage and IL-1β production. This correlates with peripheral NLRC4 inflammasome assembly and increased autophagy. Overexpression of constitutively active mTORC1 rescues decreased IL-1β levels and caspase1 cleavage, and restores perinuclear inflammasome positioning. Our findings support that SLC15A4 couples phagocytosis with inflammasome perinuclear assembly and inhibition of autophagy through phagosomal content sensing. Our data also reveal the previously unappreciated importance of mTORC1 signaling pathways to promote and sustain inflammasome activity.
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Affiliation(s)
- Cynthia López‐Haber
- Department of Pathology and Laboratory MedicineChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Present address:
Department of Microbiology and Immunology, Sidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Daniel J Netting
- Department of Microbiology and Immunology, Sidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Zachary Hutchins
- Department of Microbiology and Immunology, Sidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of PediatricsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Adriana R Mantegazza
- Department of Pathology and Laboratory MedicineChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Present address:
Department of Microbiology and Immunology, Sidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
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Wang Y, Guo K, Wang Q, Zhong G, Zhang W, Jiang Y, Mao X, Li X, Huang Z. Caenorhabditis elegans as an emerging model in food and nutrition research: importance of standardizing base diet. Crit Rev Food Sci Nutr 2022; 64:3167-3185. [PMID: 36200941 DOI: 10.1080/10408398.2022.2130875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As a model organism that has helped revolutionize life sciences, Caenorhabditis elegans has been increasingly used in nutrition research. Here we explore the tradeoffs between pros and cons of its use as a dietary model based primarily on literature review from the past decade. We first provide an overview of its experimental strengths as an animal model, focusing on lifespan and healthspan, behavioral and physiological phenotypes, and conservation of key nutritional pathways. We then summarize recent advances of its use in nutritional studies, e.g. food preference and feeding behavior, sugar status and metabolic reprogramming, lifetime and transgenerational nutrition tracking, and diet-microbiota-host interactions, highlighting cutting-edge technologies originated from or developed in C. elegans. We further review current challenges of using C. elegans as a nutritional model, followed by in-depth discussions on potential solutions. In particular, growth scales and throughputs, food uptake mode, and axenic culture of C. elegans are appraised in the context of food research. We also provide perspectives for future development of chemically defined nematode food ("NemaFood") for C. elegans, which is now widely accepted as a versatile and affordable in vivo model and has begun to show transformative potential to pioneer nutrition science.
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Affiliation(s)
- Yuqing Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Kaixin Guo
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Guohuan Zhong
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenjun Zhang
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiyi Jiang
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xinliang Mao
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xiaomin Li
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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Zhao WB, An JX, Hu YM, Li AP, Zhang SY, Zhang BQ, Zhang ZJ, Luo XF, Bian Q, Ma Y, Ding YY, Wang R, Liu YQ. Tavaborole-Induced Inhibition of the Aminoacyl-tRNA Biosynthesis Pathway against Botrytis cinerea Contributes to Disease Control and Fruit Quality Preservation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12297-12309. [PMID: 36149871 DOI: 10.1021/acs.jafc.2c03441] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The inhibitory effect of tavaborole on the invasion of Botrytis cinerea in grapes and tomatoes, as well as the potential mechanism involved, was discovered in this study. Our findings showed that tavaborole inhibited Botrytis cinerea spore germination and mycelial expansion in vitro and that the control efficiency in vivo on fruit decay was dose-dependent, which was effective in reducing disease severity and maintaining the organoleptic quality of the fruit, such as reducing weight loss and retaining fruit hardness and titratable acid contents during storage. Furthermore, the precise mechanism of action was investigated further. Propidium iodide staining revealed that Botrytis cinerea treated with tavaborole lost membrane integrity. For further validation, cytoplasmic malondialdehyde accumulation and leakage of cytoplasmic constituents were determined. Notably, the inhibitory effect was also dependent on inhibiting the activities of aminoacyl-tRNA synthetases involved in the aminoacyl-tRNA biosynthesis pathway in Botrytis cinerea. The above findings concluded that tavaborole was effective against Botrytis cinerea infection in postharvest fruit, and a related mechanism was also discussed, which may provide references for the drug repurposing of tavaborole as a postharvest fungicide.
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Affiliation(s)
- Wen-Bin Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jun-Xia An
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yong-Mei Hu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - An-Ping Li
- Gansu Institute for Drug Control, Lanzhou 730000, P. R. China
| | - Shao-Yong Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Bao-Qi Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhi-Jun Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Xiong-Fei Luo
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Qiang Bian
- National Pesticide Engineering Research Center (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yue Ma
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yan-Yan Ding
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Rui Wang
- Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong Province, Weifang University, Weifang 261061, China
| | - Ying-Qian Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou 730000, China
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Shin HR, Citron YR, Wang L, Tribouillard L, Goul CS, Stipp R, Sugasawa Y, Jain A, Samson N, Lim CY, Davis OB, Castaneda-Carpio D, Qian M, Nomura DK, Perera RM, Park E, Covey DF, Laplante M, Evers AS, Zoncu R. Lysosomal GPCR-like protein LYCHOS signals cholesterol sufficiency to mTORC1. Science 2022; 377:1290-1298. [PMID: 36007018 PMCID: PMC10023259 DOI: 10.1126/science.abg6621] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lysosomes coordinate cellular metabolism and growth upon sensing of essential nutrients, including cholesterol. Through bioinformatic analysis of lysosomal proteomes, we identified lysosomal cholesterol signaling (LYCHOS, previously annotated as G protein-coupled receptor 155), a multidomain transmembrane protein that enables cholesterol-dependent activation of the master growth regulator, the protein kinase mechanistic target of rapamycin complex 1 (mTORC1). Cholesterol bound to the amino-terminal permease-like region of LYCHOS, and mutating this site impaired mTORC1 activation. At high cholesterol concentrations, LYCHOS bound to the GATOR1 complex, a guanosine triphosphatase (GTPase)-activating protein for the Rag GTPases, through a conserved cytoplasm-facing loop. By sequestering GATOR1, LYCHOS promotes cholesterol- and Rag-dependent recruitment of mTORC1 to lysosomes. Thus, LYCHOS functions in a lysosomal pathway for cholesterol sensing and couples cholesterol concentrations to mTORC1-dependent anabolic signaling.
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Affiliation(s)
- Hijai R. Shin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Y. Rose Citron
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lei Wang
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Laura Tribouillard
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Claire S. Goul
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robin Stipp
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yusuke Sugasawa
- Department of Anesthesiology and Pain Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Aakriti Jain
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nolwenn Samson
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Chun-Yan Lim
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Oliver B. Davis
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - David Castaneda-Carpio
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mingxing Qian
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Daniel K. Nomura
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Rushika M. Perera
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Douglas F. Covey
- Department of Developmental Biology and Biochemistry, Washington University School of Medicine, St Louis, MO 63110, USA
- The Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Mathieu Laplante
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Alex S. Evers
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
- Department of Developmental Biology and Biochemistry, Washington University School of Medicine, St Louis, MO 63110, USA
- The Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
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Penugurti V, Mishra YG, Manavathi B. AMPK: An odyssey of a metabolic regulator, a tumor suppressor, and now a contextual oncogene. Biochim Biophys Acta Rev Cancer 2022; 1877:188785. [PMID: 36031088 DOI: 10.1016/j.bbcan.2022.188785] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Metabolic reprogramming is a unique but complex biochemical adaptation that allows solid tumors to tolerate various stresses that challenge cancer cells for survival. Under conditions of metabolic stress, mammalian cells employ adenosine monophosphate (AMP)-activated protein kinase (AMPK) to regulate energy homeostasis by controlling cellular metabolism. AMPK has been described as a cellular energy sensor that communicates with various metabolic pathways and networks to maintain energy balance. Earlier studies characterized AMPK as a tumor suppressor in the context of cancer. Later, a paradigm shift occurred in support of the oncogenic nature of AMPK, considering it a contextual oncogene. In support of this, various cellular and mouse models of tumorigenesis and clinicopathological studies demonstrated increased AMPK activity in various cancers. This review will describe AMPK's pro-tumorigenic activity in various malignancies and explain the rationale and context for using AMPK inhibitors in combination with anti-metabolite drugs to treat AMPK-driven cancers.
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Affiliation(s)
- Vasudevarao Penugurti
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Yasaswi Gayatri Mishra
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Bramanandam Manavathi
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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Dinh H, Lundbäck I, Kumar S, Than AT, Morimoto J, Ponton F. Sugar-rich larval diet promotes lower adult pathogen load and higher survival after infection in a polyphagous fly. J Exp Biol 2022; 225:276376. [PMID: 35904096 DOI: 10.1242/jeb.243910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022]
Abstract
Nutrition is a central factor influencing immunity and resistance to infection, but the extent to which nutrition during development affects adult responses to infections is poorly understood. Our study investigated how the nutritional composition of the larval diet affects the survival, pathogen load, and food intake of adult fruit flies, Bactrocera tryoni, after septic bacterial infection. We found a sex-specific effect of larval diet composition on survival post-infection: survival rate was higher and bacterial load was lower for infected females fed sugar-rich larval diet compared with females fed protein-rich larval diet, an effect that was absent in males. Both males and females were heavier when fed a balanced larval diet compared to protein- or sugar-rich diet, while body lipid reserves were higher in the sugar-rich larval diet compared with other diets. Body protein reserve was lower for sugar-rich larval diets compared to other diets in males, but not females. Both females and males shifted their nutrient intake to ingest a sugar-rich diet when infected compared with sham-infected flies without any effect of the larval diet, suggesting that sugar-rich diets can be beneficial to fight off bacterial infection as shown in previous literature. Overall, our findings show that nutrition during early life can shape individual fitness in adulthood.
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Affiliation(s)
- Hue Dinh
- School of Natural Sciences, Macquarie University, Australia
| | - Ida Lundbäck
- School of Natural Sciences, Macquarie University, Australia
| | - Sheemal Kumar
- School of Natural Sciences, Macquarie University, Australia
| | - Anh The Than
- School of Natural Sciences, Macquarie University, Australia.,Department of Entomology, Vietnam National University of Agriculture, Vietnam
| | - Juliano Morimoto
- School of Natural Sciences, Macquarie University, Australia.,School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Ave, Aberdeen AB24 2TZ, UK.,Programa de Pós-graduação em Ecologia e Conservação, Universidade Federal do Paraná, Curitiba, 82590-300, Brazil
| | - Fleur Ponton
- School of Natural Sciences, Macquarie University, Australia
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Jiao Y, Gong X, Qi K, Xie Z, Wang Y, Yuan K, Pan Q, Zhang S, Shiratake K, Khanizadeh S, Tao S. Transcriptome analysis provides new ideas for studying the regulation of glucose-induced lignin biosynthesis in pear calli. BMC PLANT BIOLOGY 2022; 22:310. [PMID: 35754039 PMCID: PMC9235211 DOI: 10.1186/s12870-022-03658-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Glucose can be involved in metabolic activities as a structural substance or signaling molecule and plays an important regulatory role in fruit development. Glucose metabolism is closely related to the phenylpropanoid pathway, but the specific role of glucose in regulating lignin biosynthesis in pear fruit is still unclear. The transcriptome of pear calli generated from fruit and treated with glucose was analyzed to investigate the role of glucose in lignin biosynthesis. RESULTS The treatment of exogenous glucose significantly enhanced the accumulation of lignin in pear calli. A total of 6566 differentially expressed genes were obtained by transcriptome sequencing. Glycolysis was found to be the pathway with significant changes. Many differentially expressed genes were enriched in secondary metabolic pathways, especially the phenylpropanoid pathway. Expression of structural genes (PbPAL, PbHCT, PbCOMT, PbPRX) in lignin biosynthesis was up-regulated after glucose treatment. In addition, glucose might regulate lignin biosynthesis through interactions with ABA, GA, and SA signaling. Several candidate MYB transcription factors involved in glucose-induced lignin biosynthesis have also been revealed. The qRT-PCR analyses showed that the expression pattern of PbPFP at early developmental stage in 'Dangshansuli' fruits was consistent with the trend of lignin content. Transient expression of PbPFP resulted in a significant increase of lignin content in 'Dangshansuli' fruits at 35 days after full bloom (DAB) and tobacco leaves, indicating that PbPFP (Pbr015118.1) might be associated with the enhancement of lignin biosynthesis in response to glucose treatment. CONCLUSIONS PbPFP plays a positive role in regulating lignin biosynthesis in response to glucose treatment. This study may reveal the regulatory pathway related to lignin accumulation in pear calli induced by glucose.
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Affiliation(s)
- Yuru Jiao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xin Gong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihua Xie
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yanling Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kaili Yuan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Qi Pan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | | | | | - Shutian Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Wang K, Peng X, Yang A, Huang Y, Tan Y, Qian Y, Lv F, Si H. Effects of Diets With Different Protein Levels on Lipid Metabolism and Gut Microbes in the Host of Different Genders. Front Nutr 2022; 9:940217. [PMID: 35782952 PMCID: PMC9240812 DOI: 10.3389/fnut.2022.940217] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/30/2022] [Indexed: 12/21/2022] Open
Abstract
The purpose of this experiment was to investigate the effects of different protein levels on lipid metabolism and gut microbes in mice of different genders. A total of 60 mice (30 female and 30 male) were randomly assigned to six groups and fed female mice with low protein diet (FLP), basal protein diet (FBD), and high protein diet (FHP). Similarly, the male mice fed with low protein diet (MLP), basal protein diet (MBD), and high protein diet (MHP). The low protein diet contained 14% CP, the basal diet contained 20% CP, and the high protein diet contained 26% CP. The results of the study showed that both basal and high protein diets significantly reduced the perirenal adipose tissues (PEAT) index in male mice compared to low protein diet (p < 0.05). For the gut, the FHP significantly increased the relative gut weight compared to the FBD and FLP (p < 0.05). At the same time, the FHP also significantly increased the relative gut length compared with the FBD and FLP (p < 0.05). The MHP significantly increased TC concentration compared with the MLP (p < 0.05), and the MBD tended to increase TC concentration compared with the MLP in serum (p = 0.084). The histomorphology result of the jejunum and ileum showed that a low protein diet was beneficial to the digestion and absorption of nutrients in the small intestine of mice. While different protein levels had no effect on the total number of fecal microbial species in mice, different protein levels had a significant effect on certain fecal microbes in mice, the absolute abundance of Verrucomicrobia in the feces of male mice was significantly higher in both high and basal protein diets than in the low protein diet (p < 0.05). The high protein diet significantly reduced the absolute abundance of Patescibacteria in the feces of female mice compared to both the basal and low protein diets (p < 0.05). The absolute abundance of Patescibacteria in male feces was not affected by dietary protein levels (p > 0.05). Taken together, our results suggest that a low protein diet can alter fat deposition and lipid metabolism in mice, and that it benefited small intestinal epithelial structure and microbes.
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Affiliation(s)
- Kaijun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaomin Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Anqi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yiqin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yuxiao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yajing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Feifei Lv
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongbin Si
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- *Correspondence: Hongbin Si,
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Rai M, Curley M, Coleman Z, Demontis F. Contribution of proteases to the hallmarks of aging and to age-related neurodegeneration. Aging Cell 2022; 21:e13603. [PMID: 35349763 PMCID: PMC9124314 DOI: 10.1111/acel.13603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 12/20/2022] Open
Abstract
Protein quality control ensures the degradation of damaged and misfolded proteins. Derangement of proteostasis is a primary cause of aging and age-associated diseases. The ubiquitin-proteasome and autophagy-lysosome play key roles in proteostasis but, in addition to these systems, the human genome encodes for ~600 proteases, also known as peptidases. Here, we examine the role of proteases in aging and age-related neurodegeneration. Proteases are present across cell compartments, including the extracellular space, and their substrates encompass cellular constituents, proteins with signaling functions, and misfolded proteins. Proteolytic processing by proteases can lead to changes in the activity and localization of substrates or to their degradation. Proteases cooperate with the autophagy-lysosome and ubiquitin-proteasome systems but also have independent proteolytic roles that impact all hallmarks of cellular aging. Specifically, proteases regulate mitochondrial function, DNA damage repair, cellular senescence, nutrient sensing, stem cell properties and regeneration, protein quality control and stress responses, and intercellular signaling. The capacity of proteases to regulate cellular functions translates into important roles in preserving tissue homeostasis during aging. Consequently, proteases influence the onset and progression of age-related pathologies and are important determinants of health span. Specifically, we examine how certain proteases promote the progression of Alzheimer's, Huntington's, and/or Parkinson's disease whereas other proteases protect from neurodegeneration. Mechanistically, cleavage by proteases can lead to the degradation of a pathogenic protein and hence impede disease pathogenesis. Alternatively, proteases can generate substrate byproducts with increased toxicity, which promote disease progression. Altogether, these studies indicate the importance of proteases in aging and age-related neurodegeneration.
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Affiliation(s)
- Mamta Rai
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Michelle Curley
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Zane Coleman
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | - Fabio Demontis
- Department of Developmental NeurobiologySt. Jude Children’s Research HospitalMemphisTennesseeUSA
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Abstract
The mechanistic target of rapamycin (mTOR) regulates numerous extracellular and intracellular signals involved in the maintenan-ce of cellular homeostasis and cell growth. mTOR also functions as an endogenous inhibitor of autophagy. Under nutrient-rich conditions, mTOR complex 1 (mTORC1) phosphorylates the ULK1 complex, preventing its activation and subsequent autophagosome formation, while inhibition of mTORC1 using either rapamycin or nutrient deprivation induces autophagy. Autophagy and proteasomal proteolysis provide amino acids necessary for protein translation. Although the connection between mTORC1 and autophagy is well characterized, the association of mTORC1 inhibition with proteasome biogenesis and activity has not been fully elucidated yet. Proteasomes are long-lived cellular organelles. Their spatiotemporal rather than homeostatic regulation could be another adaptive cellular mechanism to respond to starvation. Here, we reviewed several published reports and the latest research from our group to examine the connection between mTORC1 and proteasome. We have also investigated and described the effect of mTORC1 inhibition on proteasome activity using purified proteasomes. Since mTORC1 inhibitors are currently evaluated as treatments for several human diseases, a better understanding of the link between mTORC1 activity and proteasome function is of utmost importance.
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Affiliation(s)
- Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Won Hoon Choi
- BK21 FOUR Biomedical Science Program, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
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44
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Mishra R, Gupta Y, Ghaley G, Bhowmick NA. Functional Diversity of Macropinocytosis. Subcell Biochem 2022; 98:3-14. [PMID: 35378700 DOI: 10.1007/978-3-030-94004-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Eukaryotic cells are capable of internalizing different types of cargo by plasma membrane ruffling and forming vesicles in a process known as endocytosis. The most extensively characterized endocytic pathways are clathrin-coated pits, lipid raft/caveolae-mediated endocytosis, phagocytosis, and macropinocytosis. Macropinocytosis is unique among all the endocytic processes due to its nonselective internalization of extracellular fluid, solutes, and membrane in large endocytic vesicles known as macropinosomes with unique susceptibility toward Na+/H+ exchanger inhibitors. Range of cell types capable of macropinocytosis and known to play important role in different physiological processes, which include antigen presentation, nutrient sensing, migration, and signaling. Understanding the physiological function of macropinocytosis will be helpful in filling the gaps in our knowledge and which can be exploited to develop novel therapeutic targets. In this chapter, we discuss the different molecular mechanisms that initiate the process of macropinocytosis with special emphasis on proteins involved and their diversified role in different cell types.
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Affiliation(s)
- Rajeev Mishra
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, India.
| | - Yamini Gupta
- Cancer Research Laboratory, Department of Biosciences, Manipal University, Jaipur, Rajasthan, India
| | - Garima Ghaley
- Department of Biosciences, Manipal University, Jaipur, Rajasthan, India
| | - Neil A Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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45
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Abstract
Macropinocytosis is an evolutionarily conserved endocytic pathway that mediates non-selective uptake of extracellular fluid in bulk. Macropinocytosis is initiated by localized polymerization of the actin cytoskeleton, which generates plasma membrane protrusions that enclose part of the environment into large endocytic vesicles. From amoebae to mammalian cells, the actin dynamics that drive macropinosome formation are regulated by a conserved set of intracellular signaling proteins including Ras superfamily GTPases and PI3-kinases. In mammalian cells, multiple upstream signaling pathways control activity of these core regulators in response to cell-extrinsic and cell-intrinsic stimuli. Growth factor signaling pathways play a central role in macropinocytosis induction. In addition, an increasing number of functionally diverse processes has been identified as macropinocytosis regulators, including several nutrient-sensing and developmental signaling pathways. Many of these signaling pathways have proto-oncogenic properties, and their dysregulation drives the high macropinocytic activity that is commonly observed in cancer cells. These regulatory principles illustrate how macropinocytosis is controlled by complex upstream inputs to exert diverse cellular functions in physiological and pathological contexts.
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46
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Tripathi R, Aggarwal T, Lindberg FA, Klemm AH, Fredriksson R. SLC38A10 Regulate Glutamate Homeostasis and Modulate the AKT/TSC2/mTOR Pathway in Mouse Primary Cortex Cells. Front Cell Dev Biol 2022; 10:854397. [PMID: 35450293 PMCID: PMC9017388 DOI: 10.3389/fcell.2022.854397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Glutamate acts as a critical regulator of neurotransmitter balance, recycling, synaptic function and homeostasis in the brain and glutamate transporters control glutamate levels in the brain. SLC38A10 is a member of the SLC38 family and regulates protein synthesis and cellular stress responses. Here, we uncover the role of SLC38A10 as a transceptor involved in glutamate-sensing signaling pathways that control both the glutamate homeostasis and mTOR-signaling. The culture of primary cortex cells from SLC38A10 knockout mice had increased intracellular glutamate. In addition, under nutrient starvation, KO cells had an impaired response in amino acid-dependent mTORC1 signaling. Combined studies from transcriptomics, protein arrays and metabolomics established that SLC38A10 is involved in mTOR signaling and that SLC38A10 deficient primary cortex cells have increased protein synthesis. Metabolomic data showed decreased cholesterol levels, changed fatty acid synthesis, and altered levels of fumaric acid, citrate, 2-oxoglutarate and succinate in the TCA cycle. These data suggests that SLC38A10 may act as a modulator of glutamate homeostasis, and mTOR-sensing and loss of this transceptor result in lower cholesterol, which could have implications in neurodegenerative diseases.
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Affiliation(s)
- Rekha Tripathi
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
- *Correspondence: Rekha Tripathi,
| | - Tanya Aggarwal
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Frida A. Lindberg
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Anna H. Klemm
- BioImage Informatics Facility, SciLifeLab, Division of Visual Information and Interaction, Department of Information Technology, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Bioscience, Unit of Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
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47
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Yu JSL, Correia-Melo C, Zorrilla F, Herrera-Dominguez L, Wu MY, Hartl J, Campbell K, Blasche S, Kreidl M, Egger AS, Messner CB, Demichev V, Freiwald A, Mülleder M, Howell M, Berman J, Patil KR, Alam MT, Ralser M. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance. Nat Microbiol 2022; 7:542-555. [PMID: 35314781 PMCID: PMC8975748 DOI: 10.1038/s41564-022-01072-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic–prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically. Using microbiome data analysis and a self-establishing metabolically cooperating yeast community model, the authors show that the presence of auxotrophs in a microbial community increases metabolic interactions between cells and fosters antimicrobial drug tolerance.
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Affiliation(s)
- Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Francisco Zorrilla
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucia Herrera-Dominguez
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Mary Y Wu
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Johannes Hartl
- Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marco Kreidl
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vadim Demichev
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité University Medicine, Berlin, Germany.,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Howell
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Kiran R Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE. .,Warwick Medical School, University of Warwick, Coventry, UK.
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK. .,Department of Biochemistry, Charité University Medicine, Berlin, Germany. .,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany.
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48
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Lu V, Roy IJ, Torres A, Joly JH, Ahsan FM, Graham NA, Teitell MA. Glutamine-dependent signaling controls pluripotent stem cell fate. Dev Cell 2022; 57:610-623.e8. [PMID: 35216682 PMCID: PMC8930616 DOI: 10.1016/j.devcel.2022.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/01/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
Abstract
Human pluripotent stem cells (hPSCs) can self-renew indefinitely or can be induced to differentiate. We previously showed that exogenous glutamine (Gln) withdrawal biased hPSC differentiation toward ectoderm and away from mesoderm. We revealed that, although all three germ lineages are capable of de novo Gln synthesis, only ectoderm generates sufficient Gln to sustain cell viability and differentiation, and this finding clarifies lineage fate restrictions under Gln withdrawal. Furthermore, we found that Gln acts as a signaling molecule for ectoderm that supersedes lineage-specifying cytokine induction. In contrast, Gln in mesoderm and endoderm is the preferred precursor of α-ketoglutarate without a direct signaling role. Our work raises a question about whether the nutrient environment functions directly in cell differentiation during development. Interestingly, transcriptome analysis of a gastrulation-stage human embryo shows that unique Gln enzyme-encoding gene expression patterns may also distinguish germ lineages in vivo. Together, our study suggests that intracellular Gln may help coordinate differentiation of the three germ layers.
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Affiliation(s)
- Vivian Lu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Irena J Roy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Alejandro Torres
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - James H Joly
- Mork Family Department of Chemical Engineering and Materials Science, Los Angeles, CA 90089, USA
| | - Fasih M Ahsan
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael A Teitell
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA; Department of Bioengineering, Department of Pediatrics, California NanoSystems Institute, and Broad Center for Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
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49
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Gumerov VM, Andrianova EP, Matilla MA, Page KM, Monteagudo-Cascales E, Dolphin AC, Krell T, Zhulin IB. Amino acid sensor conserved from bacteria to humans. Proc Natl Acad Sci U S A 2022; 119:e2110415119. [PMID: 35238638 PMCID: PMC8915833 DOI: 10.1073/pnas.2110415119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/10/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceAmino acids are the building blocks of life and important signaling molecules. Despite their common structure, no universal mechanism for amino acid recognition by cellular receptors is currently known. We discovered a simple motif, which binds amino acids in various receptor proteins from all major life-forms. In humans, this motif is found in subunits of calcium channels that are implicated in pain and neurodevelopmental disorders. Our findings suggest that γ-aminobutyric acid-derived drugs bind to the same motif in human proteins that binds natural ligands in bacterial receptors, thus enabling future improvement of important drugs.
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Affiliation(s)
- Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
| | - Ekaterina P. Andrianova
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
| | - Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain
| | - Karen M. Page
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain
| | - Annette C. Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
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50
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Li S, Kim HE. Implications of Sphingolipids on Aging and Age-Related Diseases. FRONTIERS IN AGING 2022; 2:797320. [PMID: 35822041 PMCID: PMC9261390 DOI: 10.3389/fragi.2021.797320] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/31/2021] [Indexed: 01/14/2023]
Abstract
Aging is a process leading to a progressive loss of physiological integrity and homeostasis, and a primary risk factor for many late-onset chronic diseases. The mechanisms underlying aging have long piqued the curiosity of scientists. However, the idea that aging is a biological process susceptible to genetic manipulation was not well established until the discovery that the inhibition of insulin/IGF-1 signaling extended the lifespan of C. elegans. Although aging is a complex multisystem process, López-Otín et al. described aging in reference to nine hallmarks of aging. These nine hallmarks include: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. Due to recent advances in lipidomic, investigation into the role of lipids in biological aging has intensified, particularly the role of sphingolipids (SL). SLs are a diverse group of lipids originating from the Endoplasmic Reticulum (ER) and can be modified to create a vastly diverse group of bioactive metabolites that regulate almost every major cellular process, including cell cycle regulation, senescence, proliferation, and apoptosis. Although SL biology reaches all nine hallmarks of aging, its contribution to each hallmark is disproportionate. In this review, we will discuss in detail the major contributions of SLs to the hallmarks of aging and age-related diseases while also summarizing the importance of their other minor but integral contributions.
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Affiliation(s)
- Shengxin Li
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, TX, United States
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Hyun-Eui Kim
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, TX, United States
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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