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Dutta M, Su Y, Plescia CB, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. J Biol Chem 2024; 300:107456. [PMID: 38866325 PMCID: PMC11298601 DOI: 10.1016/j.jbc.2024.107456] [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: 09/27/2023] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N), and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and the N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular, and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA; Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, Illinois, USA.
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
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2
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Herianto S, Subramani B, Chen BR, Chen CS. Recent advances in liposome development for studying protein-lipid interactions. Crit Rev Biotechnol 2024; 44:1-14. [PMID: 36170980 DOI: 10.1080/07388551.2022.2111294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/12/2022] [Accepted: 05/29/2022] [Indexed: 11/03/2022]
Abstract
Protein-lipid interactions are crucial for various cellular biological processes like intracellular signaling, membrane transport, and cytoskeletal dynamics. Therefore, studying these interactions is essential to understand and unravel their specific functions. Nevertheless, the interacting proteins of many lipids are poorly understood and still require systematic study. Liposomes are the most well-known and familiar biomimetic systems used to study protein-lipid interactions. Although liposomes have been widely used for studying protein-lipid interactions in classical methods such as the co-flotation assay (CFA), co-sedimentation assay (CSA), and flow cytometric assay (FCA), an overview of their current applications and developments in high-throughput methods is not yet available. Here, we summarize the liposome development in low and high-throughput methods to study protein-lipid interactions. Besides, a constructive comment for each platform is presented to stimulate the advancement of these technologies in the future.
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Affiliation(s)
- Samuel Herianto
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry (Chemical Biology Division), College of Science, National Taiwan University, Taipei, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Boopathi Subramani
- Institute of Food Science and Technology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bo-Ruei Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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3
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Leyland B, Novichkova E, Dolui AK, Jallet D, Daboussi F, Legeret B, Li Z, Li-Beisson Y, Boussiba S, Khozin-Goldberg I. Acyl-CoA binding protein is required for lipid droplet degradation in the diatom Phaeodactylum tricornutum. PLANT PHYSIOLOGY 2024; 194:958-981. [PMID: 37801606 DOI: 10.1093/plphys/kiad525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/28/2023] [Accepted: 07/15/2023] [Indexed: 10/08/2023]
Abstract
Diatoms (Bacillariophyceae) accumulate neutral storage lipids in lipid droplets during stress conditions, which can be rapidly degraded and recycled when optimal conditions resume. Since nutrient and light availability fluctuate in marine environments, storage lipid turnover is essential for diatom dominance of marine ecosystems. Diatoms have garnered attention for their potential to provide a sustainable source of omega-3 fatty acids. Several independent proteomic studies of lipid droplets isolated from the model oleaginous pennate diatom Phaeodactylum tricornutum have identified a previously uncharacterized protein with an acyl-CoA binding (ACB) domain, Phatrdraft_48778, here referred to as Phaeodactylum tricornutum acyl-CoA binding protein (PtACBP). We report the phenotypic effects of CRISPR-Cas9 targeted genome editing of PtACBP. ptacbp mutants were defective in lipid droplet and triacylglycerol degradation, as well as lipid and eicosapentaenoic acid synthesis, during recovery from nitrogen starvation. Transcription of genes responsible for peroxisomal β-oxidation, triacylglycerol lipolysis, and eicosapentaenoic acid synthesis was inhibited. A lipid-binding assay using a synthetic ACB domain from PtACBP indicated preferential binding specificity toward certain polar lipids. PtACBP fused to eGFP displayed an endomembrane-like pattern, which surrounded the periphery of lipid droplets. PtACBP is likely responsible for intracellular acyl transport, affecting cell division, development, photosynthesis, and stress response. A deeper understanding of the molecular mechanisms governing storage lipid turnover will be crucial for developing diatoms and other microalgae as biotechnological cell factories.
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Affiliation(s)
- Ben Leyland
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus 84990, Israel
| | - Ekaterina Novichkova
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus 84990, Israel
| | - Achintya Kumar Dolui
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus 84990, Israel
| | - Denis Jallet
- Toulouse Biotechnology Institute Bio & Chemical Engineering, Institut National de la Recherche Agronomique, Institute National Des Sciences Appliquees, Le Centre national de la recherche scientifique, Toulouse 31077, France
| | - Fayza Daboussi
- Toulouse Biotechnology Institute Bio & Chemical Engineering, Institut National de la Recherche Agronomique, Institute National Des Sciences Appliquees, Le Centre national de la recherche scientifique, Toulouse 31077, France
| | - Bertrand Legeret
- Aix-Marseille University, CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, Saint Paul-Lez-Durance 13108, France
| | - Zhongze Li
- Aix-Marseille University, CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, Saint Paul-Lez-Durance 13108, France
| | - Yonghua Li-Beisson
- Aix-Marseille University, CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, Saint Paul-Lez-Durance 13108, France
| | - Sammy Boussiba
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus 84990, Israel
| | - Inna Khozin-Goldberg
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus 84990, Israel
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4
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Dutta M, Su Y, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557899. [PMID: 37745364 PMCID: PMC10516002 DOI: 10.1101/2023.09.15.557899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we find the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, lipid binding is shown to occur in the N protein C-terminal domain, which is supported by extensive in silico analysis. Anionic lipid binding occurs for both the free and N oligomeric forms suggesting N can associate with membranes in the nucleocapsid form. Herein we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to M assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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5
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Serwe G, Kachaner D, Gagnon J, Plutoni C, Lajoie D, Duramé E, Sahmi M, Garrido D, Lefrançois M, Arseneault G, Saba-El-Leil MK, Meloche S, Emery G, Therrien M. CNK2 promotes cancer cell motility by mediating ARF6 activation downstream of AXL signalling. Nat Commun 2023; 14:3560. [PMID: 37322019 PMCID: PMC10272126 DOI: 10.1038/s41467-023-39281-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Cell motility is a critical feature of invasive tumour cells that is governed by complex signal transduction events. Particularly, the underlying mechanisms that bridge extracellular stimuli to the molecular machinery driving motility remain partially understood. Here, we show that the scaffold protein CNK2 promotes cancer cell migration by coupling the pro-metastatic receptor tyrosine kinase AXL to downstream activation of ARF6 GTPase. Mechanistically, AXL signalling induces PI3K-dependent recruitment of CNK2 to the plasma membrane. In turn, CNK2 stimulates ARF6 by associating with cytohesin ARF GEFs and with a novel adaptor protein called SAMD12. ARF6-GTP then controls motile forces by coordinating the respective activation and inhibition of RAC1 and RHOA GTPases. Significantly, genetic ablation of CNK2 or SAMD12 reduces metastasis in a mouse xenograft model. Together, this work identifies CNK2 and its partner SAMD12 as key components of a novel pro-motility pathway in cancer cells, which could be targeted in metastasis.
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Affiliation(s)
- Guillaume Serwe
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - David Kachaner
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Jessica Gagnon
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Cédric Plutoni
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Driss Lajoie
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Eloïse Duramé
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Malha Sahmi
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Damien Garrido
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Martin Lefrançois
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Geneviève Arseneault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Marc K Saba-El-Leil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Gregory Emery
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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6
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Characterization of Protein-Membrane Interactions in Yeast Autophagy. Cells 2022; 11:cells11121876. [PMID: 35741004 PMCID: PMC9221364 DOI: 10.3390/cells11121876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Cells rely on autophagy to degrade cytosolic material and maintain homeostasis. During autophagy, content to be degraded is encapsulated in double membrane vesicles, termed autophagosomes, which fuse with the yeast vacuole for degradation. This conserved cellular process requires the dynamic rearrangement of membranes. As such, the process of autophagy requires many soluble proteins that bind to membranes to restructure, tether, or facilitate lipid transfer between membranes. Here, we review the methods that have been used to investigate membrane binding by the core autophagy machinery and additional accessory proteins involved in autophagy in yeast. We also review the key experiments demonstrating how each autophagy protein was shown to interact with membranes.
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7
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Lin HY, Pang MY, Feng MG, Ying SH. A peroxisomal sterol carrier protein 2 (Scp2) contributes to lipid trafficking in differentiation and virulence of the insect pathogenic fungus Beauveria bassiana. Fungal Genet Biol 2021; 158:103651. [PMID: 34906632 DOI: 10.1016/j.fgb.2021.103651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
Sterol carrier protein 2 (SCP2) represents a family of proteins binding a variety of lipids and plays essential roles in cellular physiology. However, its physiological roles are largely unknown in filamentous fungi. In this study, we functionally characterized an orthologous Scp2 gene in the filamentous insect pathogenic fungus Beauveria bassiana (BbScp2). BbScp2 was verified to be a peroxisomal protein and displayed different affinities to various lipids, with strong affinity to palmitic acid (PA) and ergosterol (ES). No significant binding activity was detected between protein and oleic acid (OA) or linoleic acid (LA). Ablation of BbScp2 did not cause significant effects on fungal growth on various carbon sources, but resulted in a modest reduction in conidial (49%) and blastospore yield (45%). In addition, exogenous lipids could recover the defectives in conidiation of ΔBbScp2 mutant strain. BbScp2 was required for the cytomembrane functionality in germlings, and its loss resulted in a more significant decrease in virulence indicated by cuticle infection assay than intrahemocoel injection assay. Our findings indicate that Scp2 links the lipid trafficking to the asexual differentiation and virulence of B. bassiana.
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Affiliation(s)
- Hai-Yan Lin
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meei-Yuan Pang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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8
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Rathod J, Yen HC, Liang B, Tseng YY, Chen CS, Wu WS. YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J 2021; 19:3692-3707. [PMID: 34285772 PMCID: PMC8261538 DOI: 10.1016/j.csbj.2021.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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Key Words
- ANTH, AP180 N-terminal Homology
- BAR, Bin-Amphiphysin-Rvs
- CAFA, Critical Assessment of Functional Annotation
- CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor
- Cvt, Cytoplasm-to-vacuole targeting
- ENTH, Epsin N-terminal Homology
- FDR, False Discovery Rate
- FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1
- GO, Gene Ontology
- ITC, Isothermal Titration Calorimetry
- LBD, Lipid-Binding Domain
- LMPD, LIPID MAPS Proteome Database
- LMSD, LIPID MAPS Structure Database
- LRD, Lipid-Related Domain
- Lipid-binding domain
- OMIM, Online Mendelian Inheritance in Man
- OSBP, Oxysterol-Binding Protein
- PH, Pleckstrin Homology
- PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate
- PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate
- PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate
- PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate
- PI-binding protein
- PI3P, phosphatidylinositol-3-phosphate
- PI4P, phosphatidylinositol-4-phosphate
- PI5P, phosphatidylinositol-5-phosphate
- PIs, Phosphoinositides
- PMID, PubMed ID
- PX, Phox Homology
- Phosphatidylinositol (PtdIns)
- Phosphoinositides (PIs)
- PtdIns, Phosphatidylinositol
- QCM, Quartz Crystal Microbalance
- S. cerevisiae
- SNX, Sorting Nexin
- SPR, Surface Plasmon Resonance
- YPIBP, Yeast Phosphoinositide-Binding Proteins
- Yeast
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Affiliation(s)
- Jagat Rathod
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Chen Yen
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Biqing Liang
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
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9
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McLaughlin JE, Darwish NI, Garcia-Sanchez J, Tyagi N, Trick HN, McCormick S, Dill-Macky R, Tumer NE. A Lipid Transfer Protein has Antifungal and Antioxidant Activity and Suppresses Fusarium Head Blight Disease and DON Accumulation in Transgenic Wheat. PHYTOPATHOLOGY 2021; 111:671-683. [PMID: 32896217 DOI: 10.1094/phyto-04-20-0153-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Trichothecene mycotoxins such as deoxynivalenol (DON) are virulence factors of Fusarium graminearum, which causes Fusarium head blight, one of the most important diseases of small grain cereals. We previously identified a nonspecific lipid transfer protein (nsLTP) gene, AtLTP4.4, which was overexpressed in an activation-tagged Arabidopsis line resistant to trichothecin, a type B trichothecene in the same class as DON. Here we show that overexpression of AtLTP4.4 in transgenic wheat significantly reduced F. graminearum growth in 'Bobwhite' and 'RB07' lines in the greenhouse and reduced fungal lesion size in detached leaf assays. Hydrogen peroxide accumulation was attenuated on exposure of transgenic wheat plants to DON, indicating that AtLTP4.4 may confer resistance by inhibiting oxidative stress. Field testing indicated that disease severity was significantly reduced in two transgenic 'Bobwhite' lines expressing AtLTP4.4. DON accumulation was significantly reduced in four different transgenic 'Bobwhite' lines expressing AtLTP4.4 or a wheat nsLTP, TaLTP3, which was previously shown to have antioxidant activity. Recombinant AtLTP4.4 purified from Pichia pastoris exhibited potent antifungal activity against F. graminearum. These results demonstrate that overexpression of AtLTP4.4 in transgenic wheat suppresses DON accumulation in the field. Suppression of DON-induced reactive oxygen species by AtLTP4.4 might be the mechanism by which fungal spread and mycotoxin accumulation are inhibited in transgenic wheat plants.
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Affiliation(s)
- John E McLaughlin
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Noura I Darwish
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Jeffrey Garcia-Sanchez
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Neerja Tyagi
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Susan McCormick
- Mycotoxin Prevention and Applied Microbiology Unit, USDA-ARS-NCAUR, Peoria, IL 61604
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Nilgun E Tumer
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901
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10
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Abstract
The field of phosphoinositide signaling has expanded significantly in recent years. Phosphoinositides (also known as phosphatidylinositol phosphates or PIPs) are universal signaling molecules that directly interact with membrane proteins or with cytosolic proteins containing domains that directly bind phosphoinositides and are recruited to cell membranes. Through the activities of phosphoinositide kinases and phosphoinositide phosphatases, seven distinct phosphoinositide lipid molecules are formed from the parent molecule, phosphatidylinositol. PIP signals regulate a wide range of cellular functions, including cytoskeletal assembly, membrane budding and fusion, ciliogenesis, vesicular transport, and signal transduction. Given the many excellent reviews on phosphoinositide kinases, phosphoinositide phosphatases, and PIPs in general, in this review, we discuss recent studies and advances in PIP lipid signaling in the retina. We specifically focus on PIP lipids from vertebrate (e.g., bovine, rat, mouse, toad, and zebrafish) and invertebrate (e.g., Drosophila, horseshoe crab, and squid) retinas. We also discuss the importance of PIPs revealed from animal models and human diseases, and methods to study PIP levels both in vitro and in vivo. We propose that future studies should investigate the function and mechanism of activation of PIP-modifying enzymes/phosphatases and further unravel PIP regulation and function in the different cell types of the retina.
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Affiliation(s)
- Raju V S Rajala
- Departments of Ophthalmology, Physiology, and Cell Biology, and Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104.
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11
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Abstract
Numerous cell death-controlling genes have been identified in fungi, especially in the context of conspecific nonself discrimination (allorecognition). However, our understanding of the molecular mechanisms by which these genes trigger programmed cell death (PCD) is limited, as is our knowledge about their relation to PCD pathways in other major eukaryotic kingdoms. Here, we show that the cell death-inducing RCD-1 protein from Neurospora crassa is related to the cytotoxic N-terminal domain of gasdermin, which is the executioner of inflammatory cell death reaction in mammals termed pyroptosis. Our work documents an evolutionary transkingdom relationship of cell death execution proteins between fungi and animals. Programmed cell death (PCD) in filamentous fungi prevents cytoplasmic mixing following fusion between conspecific genetically distinct individuals (allorecognition) and serves as a defense mechanism against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (i.e., senescence plasmids). Recently, we identified regulatorof cell death-1 (rcd-1), a gene controlling PCD in germinated asexual spores in the filamentous fungus Neurospora crassa. rcd-1 alleles are highly polymorphic and fall into two haplogroups in N. crassa populations. Coexpression of alleles from the two haplogroups, rcd-1–1 and rcd-1–2, is necessary and sufficient to trigger a cell death reaction. Here, we investigated the molecular bases of rcd-1-dependent cell death. Based on in silico analyses, we found that RCD-1 is a remote homolog of the N-terminal pore-forming domain of gasdermin, the executioner protein of a highly inflammatory cell death reaction termed pyroptosis, which plays a key role in mammalian innate immunity. We show that RCD-1 localizes to the cell periphery and that cellular localization of RCD-1 was correlated with conserved positively charged residues on predicted amphipathic α-helices, as shown for murine gasdermin-D. Similar to gasdermin, RCD-1 binds acidic phospholipids in vitro, notably, cardiolipin and phosphatidylserine, and interacts with liposomes containing such lipids. The RCD-1 incompatibility system was reconstituted in human 293T cells, where coexpression of incompatible rcd-1–1/rcd-1–2 alleles triggered pyroptotic-like cell death. Oligomers of RCD-1 were associated with the cell death reaction, further supporting the evolutionary relationship between gasdermin and rcd-1. This report documents an ancient transkingdom relationship of cell death execution modules involved in organismal defense.
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12
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Pimm ML, Hotaling J, Henty-Ridilla JL. Profilin choreographs actin and microtubules in cells and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 355:155-204. [PMID: 32859370 PMCID: PMC7461721 DOI: 10.1016/bs.ircmb.2020.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Actin and microtubules play essential roles in aberrant cell processes that define and converge in cancer including: signaling, morphology, motility, and division. Actin and microtubules do not directly interact, however shared regulators coordinate these polymers. While many of the individual proteins important for regulating and choreographing actin and microtubule behaviors have been identified, the way these molecules collaborate or fail in normal or disease contexts is not fully understood. Decades of research focus on Profilin as a signaling molecule, lipid-binding protein, and canonical regulator of actin assembly. Recent reports demonstrate that Profilin also regulates microtubule dynamics and polymerization. Thus, Profilin can coordinate both actin and microtubule polymer systems. Here we reconsider the biochemical and cellular roles for Profilin with a focus on the essential cytoskeletal-based cell processes that go awry in cancer. We also explore how the use of model organisms has helped to elucidate mechanisms that underlie the regulatory essence of Profilin in vivo and in the context of disease.
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Affiliation(s)
- Morgan L Pimm
- Department of Cell and Developmental Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Jessica Hotaling
- Department of Cell and Developmental Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Jessica L Henty-Ridilla
- Department of Cell and Developmental Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States; Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States.
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13
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Wang Q, Corey RA, Hedger G, Aryal P, Grieben M, Nasrallah C, Baronina A, Pike ACW, Shi J, Carpenter EP, Sansom MSP. Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2. Structure 2019; 28:169-184.e5. [PMID: 31806353 PMCID: PMC7001106 DOI: 10.1016/j.str.2019.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/04/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023]
Abstract
Polycystin-2 (PC2) is a transient receptor potential (TRP) channel present in ciliary membranes of the kidney. PC2 shares a transmembrane fold with other TRP channels, in addition to an extracellular domain found in TRPP and TRPML channels. Using molecular dynamics (MD) simulations and cryoelectron microscopy we identify and characterize PIP2 and cholesterol interactions with PC2. PC2 is revealed to have a PIP binding site close to the equivalent vanilloid/lipid binding site in the TRPV1 channel. A 3.0-Å structure reveals a binding site for cholesterol on PC2. Cholesterol interactions with the channel at this site are characterized by MD simulations. The two classes of lipid binding sites are compared with sites observed in other TRPs and in Kv channels. These findings suggest PC2, in common with other ion channels, may be modulated by both PIPs and cholesterol, and position PC2 within an emerging model of the roles of lipids in the regulation and organization of ciliary membranes. Lipid interactions of PC2 channels have been explored by MD simulation and cryo-EM PIP2 binds to a site corresponding to the vanilloid/lipid binding site of TRPV1 Cholesterol binds between the S3 and S4 helices and S6 of the adjacent subunit PC2, in common with other channels, may be modulated by PIPs and cholesterol
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Affiliation(s)
- Qinrui Wang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - George Hedger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Prafulla Aryal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mariana Grieben
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Chady Nasrallah
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Agnese Baronina
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough SL1 3WE, UK
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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14
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de la Ballina LR, Munson MJ, Simonsen A. Lipids and Lipid-Binding Proteins in Selective Autophagy. J Mol Biol 2019; 432:135-159. [PMID: 31202884 DOI: 10.1016/j.jmb.2019.05.051] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells have the capacity to degrade intracellular components through a lysosomal degradation pathway called macroautophagy (henceforth referred to as autophagy) in which superfluous or damaged cytosolic entities are engulfed and separated from the rest of the cell constituents into double membraned vesicles known as autophagosomes. Autophagosomes then fuse with endosomes and lysosomes, where cargo is broken down into basic building blocks that are released to the cytoplasm for the cell to reuse. Autophagic degradation can target either cytoplasmic material in bulk (non-selective autophagy) or particular cargo in what is called selective autophagy. Proper autophagic turnover requires the orchestrated participation of several players that need to be tightly and temporally coordinated. Whereas a large number of autophagy-related (ATG) proteins have been identified and their functions and regulation are starting to be understood, there is substantially less knowledge regarding the specific lipids constituting the autophagic membranes as well as their role in initiating, enabling or regulating the autophagic process. This review focuses on lipids and their corresponding binding proteins that are crucial in the process of selective autophagy.
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Affiliation(s)
- Laura R de la Ballina
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Michael J Munson
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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15
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Ebrahimzadeh Z, Mukherjee A, Crochetière MÈ, Sergerie A, Amiar S, Thompson LA, Gagnon D, Gaumond D, Stahelin RV, Dacks JB, Richard D. A pan-apicomplexan phosphoinositide-binding protein acts in malarial microneme exocytosis. EMBO Rep 2019; 20:e47102. [PMID: 31097469 PMCID: PMC6549027 DOI: 10.15252/embr.201847102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/28/2019] [Accepted: 04/12/2019] [Indexed: 11/09/2022] Open
Abstract
Invasion of human red blood cells by the malaria parasite Plasmodium falciparum is an essential step in the development of the disease. Consequently, the molecular players involved in host cell invasion represent important targets for inhibitor design and vaccine development. The process of merozoite invasion is a succession of steps underlined by the sequential secretion of the organelles of the apical complex. However, little is known with regard to how their contents are exocytosed. Here, we identify a phosphoinositide-binding protein conserved in apicomplexan parasites and show that it is important for the attachment and subsequent invasion of the erythrocyte by the merozoite. Critically, removing the protein from its site of action by knock sideways preferentially prevents the secretion of certain types of micronemes. Our results therefore provide evidence for a role of phosphoinositide lipids in the malaria invasion process and provide further insight into the secretion of microneme organelle populations, which is potentially applicable to diverse apicomplexan parasites.
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Affiliation(s)
- Zeinab Ebrahimzadeh
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
| | - Angana Mukherjee
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
| | - Marie-Ève Crochetière
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
| | - Audrey Sergerie
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
| | - Souad Amiar
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - L Alexa Thompson
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Dominic Gagnon
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
| | - David Gaumond
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Dave Richard
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Québec, QC, Canada
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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