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      The Toxoplasma micropore mediates endocytosis for selective nutrient salvage from host cell compartments

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          Abstract

          Apicomplexan parasite growth and replication relies on nutrient acquisition from host cells, in which intracellular multiplication occurs, yet the mechanisms that underlie the nutrient salvage remain elusive. Numerous ultrastructural studies have documented a plasma membrane invagination with a dense neck, termed the micropore, on the surface of intracellular parasites. However, the function of this structure remains unknown. Here we validate the micropore as an essential organelle for endocytosis of nutrients from the host cell cytosol and Golgi in the model apicomplexan Toxoplasma gondii. Detailed analyses demonstrated that Kelch13 is localized at the dense neck of the organelle and functions as a protein hub at the micropore for endocytic uptake. Intriguingly, maximal activity of the micropore requires the ceramide de novo synthesis pathway in the parasite. Thus, this study provides insights into the machinery underlying acquisition of host cell-derived nutrients by apicomplexan parasites that are otherwise sequestered from host cell compartments.

          Abstract

          Toxoplasma gondii acquires host cytosolic materials, yet the mechanism remains unknown. Wan et al. reveal the micropore as an essential organelle at the plasma membrane for endocytosis of host cytosolic proteins and biotin, and Golgi ceramide.

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          WGCNA: an R package for weighted correlation network analysis

          Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at .
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            Efficient proximity labeling in living cells and organisms with TurboID

            Protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. Enzyme-catalyzed proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, current PL methods require over 18 hour labeling times or utilize chemicals with limited cell permeability or high toxicity. We used yeast display-based directed evolution to engineer two promiscuous mutants of biotin ligase, TurboID and miniTurbo, which catalyze PL with much greater efficiency than BioID or BioID2, and enable 10-minute PL in cells with non-toxic and easily deliverable biotin. Furthermore, TurboID extends biotin-based PL to flies and worms.
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              Mechanisms of clathrin-mediated endocytosis

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                Author and article information

                Contributors
                LongS2018@163.com
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                22 February 2023
                22 February 2023
                2023
                : 14
                : 977
                Affiliations
                [1 ]GRID grid.22935.3f, ISNI 0000 0004 0530 8290, National Key Laboratory of Veterinary Public Health Security and School of Veterinary Medicine, , China Agricultural University, ; 100193 Beijing, China
                [2 ]GRID grid.12981.33, ISNI 0000 0001 2360 039X, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, , School of Life Sciences, Sun Yat-Sen University, ; Guangzhou, 510275 China
                [3 ]GRID grid.8752.8, ISNI 0000 0004 0460 5971, Biomedical Research and Innovation Centre and Environmental Research and Innovation Centre, , School of Science, Engineering and Environment, University of Salford, ; Salford, M5 4WT UK
                [4 ]GRID grid.412545.3, ISNI 0000 0004 1798 1300, College of Veterinary Medicine, , Shanxi Agricultural University, ; Taigu, 030801 Shanxi China
                [5 ]GRID grid.4367.6, ISNI 0000 0001 2355 7002, Department of Molecular Microbiology, , Washington University School of Medicine in Saint Louis, ; Saint Louis, MO 63110-1093 USA
                Author information
                http://orcid.org/0000-0001-8938-5530
                http://orcid.org/0000-0002-4709-1507
                http://orcid.org/0000-0002-2252-4855
                http://orcid.org/0000-0002-3608-0175
                http://orcid.org/0000-0002-5409-2831
                Article
                36571
                10.1038/s41467-023-36571-4
                9947163
                36813769
                426551d2-72b0-4101-9431-9dccd33f6452
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 2 May 2022
                : 3 February 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001809, National Natural Science Foundation of China (National Science Foundation of China);
                Award ID: 31772445
                Award ID: 31772445
                Award Recipient :
                Funded by: the National Key Research and Development Program of China (2021YFC2300802) and the Fund for Shanxi “1331 Project” (20211331-13) to X.Q. Z, and the University Startup Package to S.L..
                Categories
                Article
                Custom metadata
                © The Author(s) 2023

                Uncategorized
                parasite biology,parasite physiology,parasite host response
                Uncategorized
                parasite biology, parasite physiology, parasite host response

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