Proximity-Labeling Reveals Novel Host and Parasite Proteins at the Toxoplasma Parasitophorous Vacuole Membrane

Toxoplasma is an intracellular pathogen which resides and replicates inside a membrane-bound vacuole in infected cells. This vacuole is modified by both parasite and host proteins which participate in a variety of host-parasite interactions at this interface, including nutrient exchange, effector transport, and immune modulation. ABSTRACT Toxoplasma gondii is a ubiquitous, intracellular parasite that envelops its parasitophorous vacuole with a protein-laden membrane (PVM). The PVM is critical for interactions with the infected host cell, such as nutrient transport and immune defense. Only a few parasite and host proteins have so far been identified on the host-cytosolic side of the Toxoplasma PVM. We report here the use of human foreskin fibroblasts expressing the proximity-labeling enzyme miniTurbo, fused to a domain that targets it to this face of the PVM, in combination with quantitative proteomics to specifically identify proteins present at this interface. Out of numerous human and parasite proteins with candidate PVM localization, we validate three parasite proteins (TGGT1_269950 [GRA61], TGGT1_215360 [GRA62], and TGGT1_217530 [GRA63]) and four new host proteins (PDCD6IP/ALIX, PDCD6, CC2D1A, and MOSPD2) as localized to the PVM in infected human cells through immunofluorescence microscopy. These results significantly expand our knowledge of proteins present at the Toxoplasma PVM and, given that three of the validated host proteins are components of the ESCRT (endosomal sorting complexes required for transport) machinery, they further suggest that novel biology is operating at this crucial host-pathogen interface. IMPORTANCE Toxoplasma is an intracellular pathogen which resides and replicates inside a membrane-bound vacuole in infected cells. This vacuole is modified by both parasite and host proteins which participate in a variety of host-parasite interactions at this interface, including nutrient exchange, effector transport, and immune modulation. Only a small number of parasite and host proteins present at the vacuolar membrane and exposed to the host cytosol have thus far been identified. Here, we report the identification of several novel parasite and host proteins present at the vacuolar membrane using enzyme-catalyzed proximity-labeling, significantly increasing our knowledge of the molecular players present and novel biology occurring at this crucial interface.

[1]  L. Weiss,et al.  Toxoplasma gondii subverts the host ESCRT machinery for parasite uptake of host cytosolic proteins , 2021, bioRxiv.

[2]  Musa A. Hassan,et al.  Genome-wide screens identify Toxoplasma gondii determinants of parasite fitness in IFNγ-activated murine macrophages , 2020, Nature Communications.

[3]  Oliver M. Crook,et al.  A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions , 2020, Cell host & microbe.

[4]  J. Boothroyd,et al.  Toxoplasma Uses GRA16 To Upregulate Host c-Myc , 2020, mSphere.

[5]  L. Weiss,et al.  The Toxoplasma gondii Cyst Wall Interactome , 2020, mBio.

[6]  Sarah E. Ewald,et al.  Automated Spatially Targeted Optical Micro Proteomics (autoSTOMP) to Determine Protein Complexity of Subcellular Structures. , 2019, Analytical chemistry.

[7]  J. Boothroyd,et al.  Translocation of effector proteins into host cells by Toxoplasma gondii. , 2019, Current opinion in microbiology.

[8]  H. Stenmark,et al.  The many functions of ESCRTs , 2019, Nature Reviews Molecular Cell Biology.

[9]  S. Sidik,et al.  In Vivo CRISPR Screen Identifies TgWIP as a Toxoplasma Modulator of Dendritic Cell Migration. , 2019, Cell host & microbe.

[10]  A. Stewart,et al.  A CRISPR platform for targeted in vivo screens identifies Toxoplasma gondii virulence factors in mice , 2019, Nature Communications.

[11]  Mark J. Miller,et al.  The secreted kinase ROP17 promotes Toxoplasma gondii dissemination by hijacking monocyte tissue migration , 2019, Nature Microbiology.

[12]  J. Vilo,et al.  g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) , 2019, Nucleic Acids Res..

[13]  J. Boothroyd,et al.  Translocation of Dense Granule Effectors across the Parasitophorous Vacuole Membrane in Toxoplasma-Infected Cells Requires the Activity of ROP17, a Rhoptry Protein Kinase , 2019, mSphere.

[14]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[15]  Jan Gorodkin,et al.  Cytoscape stringApp: Network analysis and visualization of proteomics data , 2018, bioRxiv.

[16]  Junlong Zhao,et al.  Identification of Novel Dense-Granule Proteins in Toxoplasma gondii by Two Proximity-Based Biotinylation Approaches. , 2018, Journal of proteome research.

[17]  N. Perrimon,et al.  Efficient proximity labeling in living cells and organisms with TurboID , 2018, Nature Biotechnology.

[18]  G. Drin,et al.  Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites , 2018, EMBO Reports.

[19]  J. Boothroyd,et al.  Identification of a novel protein complex essential for effector translocation across the parasitophorous vacuole membrane of Toxoplasma gondii , 2018, PLoS pathogens.

[20]  D. Soldati-Favre,et al.  Efficient invasion by Toxoplasma depends on the subversion of host protein networks , 2017, Nature Microbiology.

[21]  B. Clough,et al.  The Toxoplasma Parasitophorous Vacuole: An Evolving Host-Parasite Frontier. , 2017, Trends in parasitology.

[22]  L. Sibley,et al.  Toxoplasma Effectors Targeting Host Signaling and Transcription , 2017, Clinical Microbiology Reviews.

[23]  Tim Wang,et al.  A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes , 2016, Cell.

[24]  M. Maki,et al.  Multifaceted Roles of ALG-2 in Ca2+-Regulated Membrane Trafficking , 2016, International journal of molecular sciences.

[25]  I. Coppens,et al.  In Vivo Biotinylation of the Toxoplasma Parasitophorous Vacuole Reveals Novel Dense Granule Proteins Important for Parasite Growth and Pathogenesis , 2016, mBio.

[26]  J. Wohlschlegel,et al.  The Rhoptry Pseudokinase ROP54 Modulates Toxoplasma gondii Virulence and Host GBP2 Loading , 2016, mSphere.

[27]  J. Boothroyd,et al.  A Novel Secreted Protein, MYR1, Is Central to Toxoplasma’s Manipulation of Host Cells , 2016, mBio.

[28]  Christopher J. Tonkin,et al.  An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell , 2015, eLife.

[29]  V. Doye,et al.  Probing nuclear pore complex architecture with proximity-dependent biotinylation , 2014, Proceedings of the National Academy of Sciences.

[30]  L. Sibley,et al.  The Toxoplasma pseudokinase ROP5 forms complexes with ROP18 and ROP17 kinases that synergize to control acute virulence in mice. , 2014, Cell host & microbe.

[31]  J. Boothroyd,et al.  GRA25 Is a Novel Virulence Factor of Toxoplasma gondii and Influences the Host Immune Response , 2014, Infection and Immunity.

[32]  Sarah E. Ewald,et al.  Toxoplasma Effector MAF1 Mediates Recruitment of Host Mitochondria and Impacts the Host Response , 2014, PLoS biology.

[33]  H. Furuoka,et al.  A novel dense granule protein, GRA22, is involved in regulating parasite egress in Toxoplasma gondii. , 2013, Molecular and biochemical parasitology.

[34]  A. Bougdour,et al.  Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression. , 2013, Cell host & microbe.

[35]  W. Weissenhorn,et al.  CC2D1A is a regulator of ESCRT-III CHMP4B. , 2012, Journal of molecular biology.

[36]  Brian Burke,et al.  A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells , 2012, The Journal of cell biology.

[37]  J. Boothroyd,et al.  A Helical Membrane‐Binding Domain Targets the Toxoplasma ROP2 Family to the Parasitophorous Vacuole , 2009, Traffic.

[38]  J. Gigley,et al.  Efficient Gene Replacements in Toxoplasma gondii Strains Deficient for Nonhomologous End Joining , 2009, Eukaryotic Cell.

[39]  J. Dubremetz,et al.  GRA12, a Toxoplasma dense granule protein associated with the intravacuolar membranous nanotubular network. , 2009, International journal for parasitology.

[40]  J. Dubremetz,et al.  Export of a Toxoplasma gondii Rhoptry Neck Protein Complex at the Host Cell Membrane to Form the Moving Junction during Invasion , 2009, PLoS pathogens.

[41]  A. Tripathi,et al.  Toxoplasma gondii actively remodels the microtubule network in host cells. , 2008, Microbes and infection.

[42]  J. Boothroyd,et al.  The Toxoplasma gondii Dense Granule Protein GRA7 Is Phosphorylated upon Invasion and Forms an Unexpected Association with the Rhoptry Proteins ROP2 and ROP4 , 2008, Infection and Immunity.

[43]  I. Coppens,et al.  New host nuclear functions are not required for the modifications of the parasitophorous vacuole of Toxoplasma , 2007, Cellular microbiology.

[44]  Erik L. L. Sonnhammer,et al.  Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..

[45]  H. Vial,et al.  Inverted topology of the Toxoplasma gondii ROP5 rhoptry protein provides new insights into the association of the ROP2 protein family with the parasitophorous vacuole membrane , 2007, Cellular microbiology.

[46]  J. Ajioka,et al.  Polymorphic Secreted Kinases Are Key Virulence Factors in Toxoplasmosis , 2006, Science.

[47]  Peter J Bradley,et al.  Proteomic Analysis of Rhoptry Organelles Reveals Many Novel Constituents for Host-Parasite Interactions in Toxoplasma gondii* , 2005, Journal of Biological Chemistry.

[48]  D. Hill,et al.  Biology and epidemiology of Toxoplasma gondii in man and animals , 2005, Animal Health Research Reviews.

[49]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[50]  S. Parmley,et al.  Toxoplasma gondii MAG1 protein expression. , 2002, Trends in parasitology.

[51]  John D. Storey A direct approach to false discovery rates , 2002 .

[52]  A. Hehl,et al.  Success and Virulence in Toxoplasma as the Result of Sexual Recombination Between Two Distinct Ancestries , 2001, Science.

[53]  L. Sibley,et al.  Toxoplasma evacuoles: a two‐step process of secretion and fusion forms the parasitophorous vacuole , 2001, The EMBO journal.

[54]  R. Haselkorn,et al.  Subcellular localization of acetyl-CoA carboxylase in the apicomplexan parasite Toxoplasma gondii , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[55]  I. Coppens,et al.  Toxoplasma gondii Exploits Host Low-Density Lipoprotein Receptor-Mediated Endocytosis for Cholesterol Acquisition , 2000, The Journal of cell biology.

[56]  G. Ward,et al.  Identification and molecular characterization of GRA8, a novel, proline-rich, dense granule protein of Toxoplasma gondii. , 2000, Molecular and biochemical parasitology.

[57]  L. Sibley,et al.  Differential membrane targeting of the secretory proteins GRA4 and GRA6 within the parasitophorous vacuole formed by Toxoplasma gondii. , 1999, Molecular and biochemical parasitology.

[58]  L. Sibley,et al.  Transmembrane insertion of the Toxoplasma gondii GRA5 protein occurs after soluble secretion into the host cell. , 1999, Molecular biology of the cell.

[59]  Dimier,et al.  Interferon‐γ‐activated primary enterocytes inhibit Toxoplasma gondii replication: a role for intracellular iron , 1998, Immunology.

[60]  K. Joiner,et al.  Association of host cell endoplasmic reticulum and mitochondria with the Toxoplasma gondii parasitophorous vacuole membrane: a high affinity interaction. , 1997, Journal of cell science.

[61]  Mark Fricker,et al.  Interphase Nuclei of Many Mammalian Cell Types Contain Deep, Dynamic, Tubular Membrane-bound Invaginations of the Nuclear Envelope , 1997, The Journal of cell biology.

[62]  S. Parmley,et al.  Regulated secretion of multi-lamellar vesicles leads to formation of a tubulo-vesicular network in host-cell vacuoles occupied by Toxoplasma gondii. , 1995, Journal of cell science.

[63]  A. Capron,et al.  Molecular structure of a Toxoplasma gondii dense granule antigen (GRA 5) associated with the parasitophorous vacuole membrane. , 1993, Molecular and biochemical parasitology.

[64]  J. Schwartzman,et al.  Localization of a Toxoplasma gondii rhoptry protein by immunoelectron microscopy during and after host cell penetration. , 1992, The Journal of protozoology.

[65]  E. Pfefferkorn Interferon gamma blocks the growth of Toxoplasma gondii in human fibroblasts by inducing the host cells to degrade tryptophan. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[66]  J. G. Hirsch,et al.  THE INTERACTION BETWEEN TOXOPLASMA GONDII AND MAMMALIAN CELLS , 1972, The Journal of experimental medicine.

[67]  H. Stenmark,et al.  Cellular Functions and Molecular Mechanisms of the ESCRT Membrane-Scission Machinery. , 2017, Trends in biochemical sciences.

[68]  T. M. Carvalho,et al.  Behaviour of microtubules in cells infected with Toxoplasma gondii. , 2001, Biocell : official journal of the Sociedades Latinoamericanas de Microscopia Electronica ... et. al.