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      Toxoplasma gondii PPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export

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          Abstract

          The intracellular parasite Toxoplasma gondii infects a large proportion of humans worldwide and can cause adverse complications in the settings of immune-compromise and pregnancy. T. gondii thrives within many different cell types due in part to its residence within a specialized and heavily modified compartment in which the parasite divides, termed the parasitophorous vacuole. Within this vacuole, numerous proteins optimize intracellular survival following their secretion by the parasite. We investigated the contribution of one of these proteins, TgPPM3C, predicted to contain a PP2C-class serine/threonine phosphatase domain and previously shown to interact with the protein MYR1, an essential component of a putative vacuolar translocon that mediates effector export into the host cell. Parasites lacking the TgPPM3C gene exhibit a minor growth defect in vitro, are avirulent during acute infection in mice, and form fewer cysts in mouse brain during chronic infection. Phosphoproteomic assessment of TgPPM3C deleted parasite cultures demonstrated alterations in the phosphorylation status of many secreted vacuolar proteins including two exported effector proteins, GRA16 and GRA28, as well as MYR1. Parasites lacking TgPPM3C are defective in GRA16 and GRA28 export, but not in the export of other MYR1-dependant effectors. Phosphomimetic mutation of two GRA16 serine residues results in export defects, suggesting that de-phosphorylation is a critical step in the process of GRA16 export. These findings provide another example of the emerging role of phosphatases in regulating the complex environment of the T. gondii parasitophorous vacuole and influencing the export of specific effector proteins from the vacuolar lumen into the host cell.

          Author summary

          The flexible life cycle of the intracellular parasite Toxoplasma gondii allows it to infect many different types of warm-blooded hosts, as well as diverse cell types once inside the host organism. This formidable achievement is partly mediated by the establishment of a unique compartment following host cell invasion, termed the parasitophorous vacuole. While advancements have been made in cataloguing Toxoplasma secreted proteins that reside within this vacuole, the specific functions and contributions of many of these secreted parasite “tools” remain elusive. Here, we assessed the contribution of a parasite vacuolar protein called TgPPM3C, predicted to function as an enzyme that dephosphorylates other proteins. We found that deleting the TgPPM3C gene in the parasite results in a profound virulence defect during infection in mice, likely due to the dysregulated phosphorylation status of many vacuolar proteins detected by phosphoproteomic analysis of TgPPM3C-deleted parasites. We found that the phosphorylation status of one such protein, GRA16, influences its ability to cross the parasitophorous vacuole membrane and enter the host cell, where it is known to induce host transcriptional changes that benefit parasite growth. These findings illustrate the emerging role of Toxoplasma vacuolar phosphatases in regulating host-parasite interactions during infection.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            The EMBL-EBI search and sequence analysis tools APIs in 2019

            Abstract The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.
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              Toxoplasmosis.

              Toxoplasma gondii is a protozoan parasite that infects up to a third of the world's population. Infection is mainly acquired by ingestion of food or water that is contaminated with oocysts shed by cats or by eating undercooked or raw meat containing tissue cysts. Primary infection is usually subclinical but in some patients cervical lymphadenopathy or ocular disease can be present. Infection acquired during pregnancy may cause severe damage to the fetus. In immunocompromised patients, reactivation of latent disease can cause life-threatening encephalitis. Diagnosis of toxoplasmosis can be established by direct detection of the parasite or by serological techniques. The most commonly used therapeutic regimen, and probably the most effective, is the combination of pyrimethamine with sulfadiazine and folinic acid. This Seminar provides an overview and update on management of patients with acute infection, pregnant women who acquire infection during gestation, fetuses or infants who are congenitally infected, those with ocular disease, and immunocompromised individuals. Controversy about the effectiveness of primary and secondary prevention in pregnant women is discussed. Important topics of current and future research are presented.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Resources
                Role: Investigation
                Role: InvestigationRole: Methodology
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                28 December 2020
                December 2020
                : 16
                : 12
                : e1008771
                Affiliations
                [1 ] Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
                [2 ] Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
                [3 ] Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
                University at Buffalo, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0003-0859-2226
                https://orcid.org/0000-0001-8809-3333
                https://orcid.org/0000-0002-0221-354X
                https://orcid.org/0000-0001-9073-6641
                https://orcid.org/0000-0002-0357-7396
                Article
                PPATHOGENS-D-20-01418
                10.1371/journal.ppat.1008771
                7793252
                33370417
                4d1662bb-553c-42e5-b341-468b08751eb3
                © 2020 Mayoral et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 30 June 2020
                : 23 November 2020
                Page count
                Figures: 5, Tables: 1, Pages: 29
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: R01AI134753
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: F31AI136401
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: T32GM007288
                Award Recipient :
                Funded by: Einstein Analytical Imaging Facility
                Award ID: P30CA013330, SIG #1S10OD016214-01A1, SIG #1S10OD019961-01
                R01AI134753 (LMW) and F31AI136401 (J.M.) National Institutes of Health/National Institute of Allergy and Infectious Diseases https://www.niaid.nih.gov/ T32GM007288 (JM) National Institutes of Health/National Institute of General Medical Sciences https://www.nigms.nih.gov/. This work was also supported by P30CA013330, SIG #1S10OD016214-01A1, and SIG #1S10OD019961-01 (Einstein Analytical Imaging Facility) The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Medicine and Health Sciences
                Medical Conditions
                Parasitic Diseases
                Biology and Life Sciences
                Parasitology
                Parasite Physiology
                Parasitophorous Vacuole
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Phosphatases
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Phosphatases
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Vacuoles
                Biology and Life Sciences
                Parasitology
                Parasite Groups
                Apicomplexa
                Tachyzoites
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Transmission and Infection
                Host Cells
                Biology and Life Sciences
                Biochemistry
                Proteins
                Post-Translational Modification
                Phosphorylation
                Biology and Life Sciences
                Parasitology
                Parasite Replication
                Custom metadata
                vor-update-to-uncorrected-proof
                2021-01-08
                Proteomic data has been deposited into the mass spectrometry open access repository Chorus under Project ID 1695. The proteomic data was also deposited in ToxoDB (EuPathDb).

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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