51
|
Thornton LB, Key M, Micchelli C, Stasic AJ, Kwain S, Floyd K, Moreno SN, Dominy BN, Whitehead DC, Dou Z. A cathepsin C-like protease mediates the post-translation modification of Toxoplasma gondii secretory proteins for optimal invasion and egress. mBio 2023; 14:e0017423. [PMID: 37326431 PMCID: PMC10470614 DOI: 10.1128/mbio.00174-23] [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: 01/19/2023] [Accepted: 05/01/2023] [Indexed: 06/17/2023] Open
Abstract
Microbial pathogens use proteases for their infections, such as digestion of proteins for nutrients and activation of their virulence factors. As an obligate intracellular parasite, Toxoplasma gondii must invade host cells to establish its intracellular propagation. To facilitate invasion, the parasites secrete invasion effectors from microneme and rhoptry, two unique organelles in apicomplexans. Previous work has shown that some micronemal invasion effectors experience a series of proteolytic cleavages within the parasite's secretion pathway for maturation, such as the aspartyl protease (TgASP3) and the cathepsin L-like protease (TgCPL), localized within the post-Golgi compartment and the endolysosomal system, respectively. Furthermore, it has been shown that the precise maturation of micronemal effectors is critical for Toxoplasma invasion and egress. Here, we show that an endosome-like compartment (ELC)-residing cathepsin C-like protease (TgCPC1) mediates the final trimming of some micronemal effectors, and its loss further results in defects in the steps of invasion, egress, and migration throughout the parasite's lytic cycle. Notably, the deletion of TgCPC1 completely blocks the activation of subtilisin-like protease 1 (TgSUB1) in the parasites, which globally impairs the surface-trimming of many key micronemal invasion and egress effectors. Additionally, we found that Toxoplasma is not efficiently inhibited by the chemical inhibitor targeting the malarial CPC ortholog, suggesting that these cathepsin C-like orthologs are structurally different within the apicomplexan phylum. Collectively, our findings identify a novel function of TgCPC1 in processing micronemal proteins within the Toxoplasma parasite's secretory pathway and expand the understanding of the roles of cathepsin C protease. IMPORTANCE Toxoplasma gondii is a microbial pathogen that is well adapted for disseminating infections. It can infect virtually all warm-blooded animals. Approximately one-third of the human population carries toxoplasmosis. During infection, the parasites sequentially secrete protein effectors from the microneme, rhoptry, and dense granule, three organelles exclusively found in apicomplexan parasites, to help establish their lytic cycle. Proteolytic cleavage of these secretory proteins is required for the parasite's optimal function. Previous work has revealed that two proteases residing within the parasite's secretory pathway cleave micronemal and rhoptry proteins, which mediate parasite invasion and egress. Here, we demonstrate that a cathepsin C-like protease (TgCPC1) is involved in processing several invasion and egress effectors. The genetic deletion of TgCPC1 prevented the complete maturation of some effectors in the parasites. Strikingly, the deletion led to a full inactivation of one surface-anchored protease, which globally impaired the trimming of some key micronemal proteins before secretion. Therefore, this finding represents a novel post-translational mechanism for the processing of virulence factors within microbial pathogens.
Collapse
Affiliation(s)
- L. Brock Thornton
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Melanie Key
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Chiara Micchelli
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Andrew J. Stasic
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Samuel Kwain
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Katherine Floyd
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Silvia N.J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Brian N. Dominy
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Daniel C. Whitehead
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, USA
| | - Zhicheng Dou
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, USA
| |
Collapse
|
52
|
Chan AW, Broncel M, Yifrach E, Haseley N, Chakladar S, Andree E, Herneisen AL, Shortt E, Treeck M, Lourido S. Analysis of CDPK1 targets identifies a trafficking adaptor complex that regulates microneme exocytosis in Toxoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523553. [PMID: 36712004 PMCID: PMC9882037 DOI: 10.1101/2023.01.11.523553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Apicomplexan parasites use Ca2+-regulated exocytosis to secrete essential virulence factors from specialized organelles called micronemes. Ca2+-dependent protein kinases (CDPKs) are required for microneme exocytosis; however, the molecular events that regulate trafficking and fusion of micronemes with the plasma membrane remain unresolved. Here, we combine sub-minute resolution phosphoproteomics and bio-orthogonal labeling of kinase substrates in Toxoplasma gondii to identify 163 proteins phosphorylated in a CDPK1-dependent manner. In addition to known regulators of secretion, we identify uncharacterized targets with predicted functions across signaling, gene expression, trafficking, metabolism, and ion homeostasis. One of the CDPK1 targets is a putative HOOK activating adaptor. In other eukaryotes, HOOK homologs form the FHF complex with FTS and FHIP to activate dynein-mediated trafficking of endosomes along microtubules. We show the FHF complex is partially conserved in T. gondii, consisting of HOOK, an FTS homolog, and two parasite-specific proteins (TGGT1_306920 and TGGT1_316650). CDPK1 kinase activity and HOOK are required for the rapid apical trafficking of micronemes as parasites initiate motility. Moreover, parasites lacking HOOK or FTS display impaired microneme protein secretion, leading to a block in the invasion of host cells. Taken together, our work provides a comprehensive catalog of CDPK1 targets and reveals how vesicular trafficking has been tuned to support a parasitic lifestyle.
Collapse
Affiliation(s)
- Alex W Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Malgorzata Broncel
- Signaling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
| | - Eden Yifrach
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Nicole Haseley
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Elena Andree
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Alice L Herneisen
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily Shortt
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Moritz Treeck
- Signaling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
53
|
Lis A, Baptista CG, Dahlgren K, Corvi MM, Blader IJ. Identification of Toxoplasma calcium-dependent protein kinase 3 as a stress-activated elongation factor 2 kinase. mSphere 2023; 8:e0015623. [PMID: 37272703 PMCID: PMC10449493 DOI: 10.1128/msphere.00156-23] [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: 03/24/2023] [Accepted: 04/19/2023] [Indexed: 06/06/2023] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite whose tachyzoite form causes disease via a lytic growth cycle. Its metabolic and cellular pathways are primarily designed to ensure parasite survival within a host cell. But during its lytic cycle, tachyzoites are exposed to the extracellular milieu and prolonged exposure requires activation of stress response pathways that include reprogramming the parasite proteome. Regulation of protein synthesis is therefore important for extracellular survival. We previously reported that in extracellularly stressed parasites, the elongation phase of protein synthesis is regulated by the Toxoplasma oxygen-sensing protein, PHYb. PHYb acts by promoting the activity of elongation factor eEF2, which is a GTPase that catalyzes the transfer of the peptidyl-tRNA from the A site to the P site of the ribosome. In the absence of PHYb, eEF2 is hyper-phosphorylated, which inhibits eEF2 from interacting with the ribosome. eEF2 kinases are atypical calcium-dependent kinases and BLAST analyses revealed the parasite kinase, CDPK3, as the most highly homologous to the Saccharomyces cerevisiae eEF2 kinase, RCK2. In parasites exposed to extracellular stress, loss of CDPK3 leads to decreased eEF2 phosphorylation and enhanced rates of elongation. Furthermore, co-immunoprecipitation studies revealed that CDPK3 and eEF2 interact in stressed parasites. Since CDPK3 and eEF2 normally localize to the plasma membrane and cytosol, respectively, we investigated how the two can interact. We report that under stress conditions, CDPK3 is not N-myristoylated likely leading to its cytoplasmic localization. In summary, we have identified a novel function for CDPK3 as the first protozoan extracellular stress-induced eEF2 kinase.IMPORTANCEAlthough it is an obligate intracellular parasite, Toxoplasma must be able to survive in the extracellular environment. Our previous work indicated that ensuring that elongation continues during protein synthesis is part of this stress response and that this is due to preventing phosphorylation of elongation factor 2. But the identity of the eEF2 kinase has remained unknown in Toxoplasma and other protozoan parasites. Here, we identify CDPK3 as the first protozoan eEF2 kinase and demonstrate that it is part of a stress response initiated when parasites are exposed to extracellular stress. We also demonstrate that CDPK3 engages eEF2 as a result of its relocalization from the plasma membrane to the cytosol.
Collapse
Affiliation(s)
- Agnieszka Lis
- Department of Microbiology and Immunology, SUNY at Buffalo School of Medicine, Buffalo, New York, USA
| | - Carlos Gustavo Baptista
- Department of Microbiology and Immunology, SUNY at Buffalo School of Medicine, Buffalo, New York, USA
| | - Kelsey Dahlgren
- Department of Microbiology and Immunology, SUNY at Buffalo School of Medicine, Buffalo, New York, USA
| | - Maria M. Corvi
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Chascomús, Buenos Aires, Argentina
| | - Ira J. Blader
- Department of Microbiology and Immunology, SUNY at Buffalo School of Medicine, Buffalo, New York, USA
| |
Collapse
|
54
|
Ferrel A, Romano J, Panas MW, Coppens I, Boothroyd JC. Host MOSPD2 enrichment at the parasitophorous vacuole membrane varies between Toxoplasma strains and involves complex interactions. mSphere 2023; 8:e0067022. [PMID: 37341482 PMCID: PMC10449529 DOI: 10.1128/msphere.00670-22] [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: 12/22/2022] [Accepted: 04/25/2023] [Indexed: 06/22/2023] Open
Abstract
Toxoplasma gondii is an obligate, intracellular parasite. Infection of a cell produces a unique niche for the parasite named the parasitophorous vacuole (PV) initially composed of host plasma membrane invaginated during invasion. The PV and its membrane (parasitophorous vacuole membrane [PVM]) are subsequently decorated with a variety of parasite proteins allowing the parasite to optimally grow in addition to manipulate host processes. Recently, we reported a proximity-labeling screen at the PVM-host interface and identified host endoplasmic reticulum (ER)-resident motile sperm domain-containing protein 2 (MOSPD2) as being enriched at this location. Here we extend these findings in several important respects. First, we show that the extent and pattern of host MOSPD2 association with the PVM differ dramatically in cells infected with different strains of Toxoplasma. Second, in cells infected with Type I RH strain, the MOSPD2 staining is mutually exclusive with regions of the PVM that associate with mitochondria. Third, immunoprecipitation and liquid chromatography tandem mass spectrometry (LC-MS/MS) with epitope-tagged MOSPD2-expressing host cells reveal strong enrichment of several PVM-localized parasite proteins, although none appear to play an essential role in MOSPD2 association. Fourth, most MOSPD2 associating with the PVM is newly translated after infection of the cell and requires the major functional domains of MOSPD2, identified as the CRAL/TRIO domain and tail anchor, although these domains were not sufficient for PVM association. Lastly, ablation of MOSPD2 results in, at most, a modest impact on Toxoplasma growth in vitro. Collectively, these studies provide new insight into the molecular interactions involving MOSPD2 at the dynamic interface between the PVM and the host cytosol. IMPORTANCE Toxoplasma gondii is an intracellular pathogen that lives within a membranous vacuole inside of its host cell. This vacuole is decorated by a variety of parasite proteins that allow it to defend against host attack, acquire nutrients, and interact with the host cell. Recent work identified and validated host proteins enriched at this host-pathogen interface. Here, we follow up on one candidate named MOSPD2 shown to be enriched at the vacuolar membrane and describe it as having a dynamic interaction at this location depending on a variety of factors. Some of these include the presence of host mitochondria, intrinsic domains of the host protein, and whether translation is active. Importantly, we show that MOSPD2 enrichment at the vacuole membrane differs between strains indicating active involvement of the parasite with this phenotype. Altogether, these results shed light on the mechanism and role of protein associations in the host-pathogen interaction.
Collapse
Affiliation(s)
- Abel Ferrel
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
| | - Julia Romano
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael W. Panas
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - John C. Boothroyd
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, USA
| |
Collapse
|
55
|
Asady B, Sampels V, Romano JD, Levitskaya J, Lige B, Khare P, Le A, Coppens I. Function and regulation of a steroidogenic CYP450 enzyme in the mitochondrion of Toxoplasma gondii. PLoS Pathog 2023; 19:e1011566. [PMID: 37651449 PMCID: PMC10499268 DOI: 10.1371/journal.ppat.1011566] [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: 01/05/2023] [Revised: 09/13/2023] [Accepted: 07/19/2023] [Indexed: 09/02/2023] Open
Abstract
As an obligate intracellular parasite, Toxoplasma gondii must import essential nutrients from the host cell into the parasitophorous vacuole. We previously reported that the parasite scavenges cholesterol from host endocytic organelles for incorporation into membranes and storage as cholesteryl esters in lipid droplets. In this study, we have investigated whether Toxoplasma utilizes cholesterol as a precursor for the synthesis of metabolites, such as steroids. In mammalian cells, steroidogenesis occurs in mitochondria and involves membrane-bound type I cytochrome P450 oxidases that are activated through interaction with heme-binding proteins containing a cytochrome b5 domain, such as members of the membrane-associated progesterone receptor (MAPR) family. Our LC-MS targeted lipidomics detect selective classes of hormone steroids in Toxoplasma, with a predominance for anti-inflammatory hydroxypregnenolone species, deoxycorticosterone and dehydroepiandrosterone. The genome of Toxoplasma contains homologs encoding a single type I CYP450 enzyme (we named TgCYP450mt) and a single MAPR (we named TgMAPR). We showed that TgMAPR is a hemoprotein with conserved residues in a heme-binding cytochrome b5 domain. Both TgCYP450 and TgMAPR localize to the mitochondrion and show interactions in in situ proximity ligation assays. Genetic ablation of cyp450mt is not tolerated by Toxoplasma; we therefore engineered a conditional knockout strain and showed that iΔTgCYP450mt parasites exhibit growth impairment in cultured cells. Parasite strains deficient for mapr could be generated; however, ΔTgMAPR parasites suffer from poor global fitness, loss of plasma membrane integrity, aberrant mitochondrial cristae, and an abnormally long S-phase in their cell cycle. Compared to wild-type parasites, iΔTgCYP450mt and ΔTgMAPR lost virulence in mice and metabolomics studies reveal that both mutants have reduced levels of steroids. These observations point to a steroidogenic pathway operational in the mitochondrion of a protozoan that involves an evolutionary conserved TgCYP450mt enzyme and its binding partner TgMAPR.
Collapse
Affiliation(s)
- Beejan Asady
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Vera Sampels
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Julia D. Romano
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jelena Levitskaya
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Bao Lige
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Pratik Khare
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Anne Le
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| |
Collapse
|
56
|
van Strien J, Evers F, Lutikurti M, Berendsen SL, Garanto A, van Gemert GJ, Cabrera-Orefice A, Rodenburg RJ, Brandt U, Kooij TWA, Huynen MA. Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. PLoS Comput Biol 2023; 19:e1011090. [PMID: 37549177 PMCID: PMC10434966 DOI: 10.1371/journal.pcbi.1011090] [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: 04/06/2023] [Revised: 08/17/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Complexome profiling allows large-scale, untargeted, and comprehensive characterization of protein complexes in a biological sample using a combined approach of separating intact protein complexes e.g., by native gel electrophoresis, followed by mass spectrometric analysis of the proteins in the resulting fractions. Over the last decade, its application has resulted in a large collection of complexome profiling datasets. While computational methods have been developed for the analysis of individual datasets, methods for large-scale comparative analysis of complexomes from multiple species are lacking. Here, we present Comparative Clustering (CompaCt), that performs fully automated integrative analysis of complexome profiling data from multiple species, enabling systematic characterization and comparison of complexomes. CompaCt implements a novel method for leveraging orthology in comparative analysis to allow systematic identification of conserved as well as taxon-specific elements of the analyzed complexomes. We applied this method to a collection of 53 complexome profiles spanning the major branches of the eukaryotes. We demonstrate the ability of CompaCt to robustly identify the composition of protein complexes, and show that integrated analysis of multiple datasets improves characterization of complexes from specific complexome profiles when compared to separate analyses. We identified novel candidate interactors and complexes in a number of species from previously analyzed datasets, like the emp24, the V-ATPase and mitochondrial ATP synthase complexes. Lastly, we demonstrate the utility of CompaCt for the automated large-scale characterization of the complexome of the mosquito Anopheles stephensi shedding light on the evolution of metazoan protein complexes. CompaCt is available from https://github.com/cmbi/compact-bio.
Collapse
Affiliation(s)
- Joeri van Strien
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Felix Evers
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Madhurya Lutikurti
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stijn L. Berendsen
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alejandro Garanto
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Geert-Jan van Gemert
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard J. Rodenburg
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pediatrics, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, the Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Taco W. A. Kooij
- Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
57
|
Hildebrandt F, Mohammed M, Dziedziech A, Bhandage AK, Divne AM, Barrenäs F, Barragan A, Henriksson J, Ankarklev J. scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics. Front Immunol 2023; 14:1224591. [PMID: 37575232 PMCID: PMC10415529 DOI: 10.3389/fimmu.2023.1224591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Dendritic cells and macrophages are integral parts of the innate immune system and gatekeepers against infection. The protozoan pathogen, Toxoplasma gondii, is known to hijack host immune cells and modulate their immune response, making it a compelling model to study host-pathogen interactions. Here we utilize single cell Dual RNA-seq to parse out heterogeneous transcription of mouse bone marrow-derived dendritic cells (BMDCs) infected with two distinct genotypes of T. gondii parasites, over multiple time points post infection. We show that the BMDCs elicit differential responses towards T. gondii infection and that the two parasite lineages distinctly manipulate subpopulations of infected BMDCs. Co-expression networks define host and parasite genes, with implications for modulation of host immunity. Integrative analysis validates previously established immune pathways and additionally, suggests novel candidate genes involved in host-pathogen interactions. Altogether, this study provides a comprehensive resource for characterizing host-pathogen interplay at high-resolution.
Collapse
Affiliation(s)
- Franziska Hildebrandt
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mubasher Mohammed
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
| | - Alexis Dziedziech
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
- Department of Global Health, Institut Pasteur, Paris, France
| | - Amol K. Bhandage
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anna-Maria Divne
- Microbial Single Cell Genomics Facility, SciLifeLab, Biomedical Center (BMC) Uppsala University, Uppsala, Sweden
| | - Fredrik Barrenäs
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
| | - Antonio Barragan
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
| | - Johan Henriksson
- Laboratory of Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Johan Ankarklev
- Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Stockholm, Sweden
- Microbial Single Cell Genomics Facility, SciLifeLab, Biomedical Center (BMC) Uppsala University, Uppsala, Sweden
| |
Collapse
|
58
|
Moloney NM, Barylyuk K, Tromer E, Crook OM, Breckels LM, Lilley KS, Waller RF, MacGregor P. Mapping diversity in African trypanosomes using high resolution spatial proteomics. Nat Commun 2023; 14:4401. [PMID: 37479728 PMCID: PMC10361982 DOI: 10.1038/s41467-023-40125-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
African trypanosomes are dixenous eukaryotic parasites that impose a significant human and veterinary disease burden on sub-Saharan Africa. Diversity between species and life-cycle stages is concomitant with distinct host and tissue tropisms within this group. Here, the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, are mapped across two life-stages. The four resulting datasets provide evidence of expression of approximately 5500 proteins per cell-type. Over 2500 proteins per cell-type are classified to specific subcellular compartments, providing four comprehensive spatial proteomes. Comparative analysis reveals key routes of parasitic adaptation to different biological niches and provides insight into the molecular basis for diversity within and between these pathogen species.
Collapse
Affiliation(s)
- Nicola M Moloney
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | | | - Eelco Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, Netherlands
| | - Oliver M Crook
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Lisa M Breckels
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Paula MacGregor
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
| |
Collapse
|
59
|
Abstract
The biology of a cell, whether it is a unicellular organism or part of a multicellular network, is influenced by cell type, temporal changes in cell state, and the cell's environment. Spatial cues play a critical role in the regulation of microbial pathogenesis strategies. Information about where the pathogen is-in a tissue or in proximity to a host cell-regulates gene expression and the compartmentalization of gene products in the microbe and the host. Our understanding of host and pathogen identity has bloomed with the accessibility of transcriptomics and proteomics techniques. A missing piece of the puzzle has been our ability to evaluate global transcript and protein expression in the context of the subcellular niche, primary cell, or native tissue environment during infection. This barrier is now lower with the advent of new spatial omics techniques to understand how location regulates cellular functions. This review will discuss how recent advances in spatial proteomics and transcriptomics approaches can address outstanding questions in microbial pathogenesis.
Collapse
Affiliation(s)
- Samantha Lempke
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Dana May
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Sarah E. Ewald
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| |
Collapse
|
60
|
Lockyer EJ, Torelli F, Butterworth S, Song OR, Howell S, Weston A, East P, Treeck M. A heterotrimeric complex of Toxoplasma proteins promotes parasite survival in interferon gamma-stimulated human cells. PLoS Biol 2023; 21:e3002202. [PMID: 37459303 PMCID: PMC10373997 DOI: 10.1371/journal.pbio.3002202] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/27/2023] [Accepted: 06/16/2023] [Indexed: 07/28/2023] Open
Abstract
Toxoplasma gondii secretes protein effectors to subvert the human immune system sufficiently to establish a chronic infection. Relative to murine infections, little is known about which parasite effectors disarm human immune responses. Here, we used targeted CRISPR screening to identify secreted protein effectors required for parasite survival in IFNγ-activated human cells. Independent screens were carried out using 2 Toxoplasma strains that differ in virulence in mice, leading to the identification of effectors required for survival in IFNγ-activated human cells. We identify the secreted protein GRA57 and 2 other proteins, GRA70 and GRA71, that together form a complex which enhances the ability of parasites to persist in IFNγ-activated human foreskin fibroblasts (HFFs). Components of the protein machinery required for export of Toxoplasma proteins into the host cell were also found to be important for parasite resistance to IFNγ in human cells, but these export components function independently of the identified protein complex. Host-mediated ubiquitination of the parasite vacuole has previously been associated with increased parasite clearance from human cells, but we find that vacuoles from GRA57, GRA70, and GRA71 knockout strains are surprisingly less ubiquitinated by the host cell. We hypothesise that this is likely a secondary consequence of deletion of the complex, unlinked to the IFNγ resistance mediated by these effectors.
Collapse
Affiliation(s)
- Eloise J Lockyer
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Francesca Torelli
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Simon Butterworth
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ok-Ryul Song
- High-Throughput Screening Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Anne Weston
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Philip East
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
- Cell Biology of Host-Pathogen Interaction Laboratory, Instituto Gulbenkian Ciência, Oeiras, Portugal
| |
Collapse
|
61
|
Tachibana Y, Hashizaki E, Sasai M, Yamamoto M. Host genetics highlights IFN-γ-dependent Toxoplasma genes encoding secreted and non-secreted virulence factors in in vivo CRISPR screens. Cell Rep 2023; 42:112592. [PMID: 37269286 DOI: 10.1016/j.celrep.2023.112592] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/25/2023] [Accepted: 05/17/2023] [Indexed: 06/05/2023] Open
Abstract
Secreted virulence factors of Toxoplasma to survive in immune-competent hosts have been extensively explored by classical genetics and in vivo CRISPR screen methods, whereas their requirements in immune-deficient hosts are incompletely understood. Those of non-secreted virulence factors are further enigmatic. Here we develop an in vivo CRISPR screen system to enrich not only secreted but also non-secreted virulence factors in virulent Toxoplasma-infected C57BL/6 mice. Notably, combined usage of immune-deficient Ifngr1-/- mice highlights genes encoding various non-secreted proteins as well as well-known effectors such as ROP5, ROP18, GRA12, and GRA45 as interferon-γ (IFN-γ)-dependent virulence genes. The screen results suggest a role of GRA72 for normal GRA17/GRA23 localization and the IFN-γ-dependent role of UFMylation-related genes. Collectively, our study demonstrates that host genetics can complement in vivo CRISPR screens to highlight genes encoding IFN-γ-dependent secreted and non-secreted virulence factors in Toxoplasma.
Collapse
Affiliation(s)
- Yuta Tachibana
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Emi Hashizaki
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
62
|
Li J, Xiao Q, Tan Q, Chen J, Sun L, Chen X, Chu Z, Wu H, Zhang Z, Li H, Zhao X, Zhang X. TgMORN2, a MORN Family Protein Involved in the Regulation of Endoplasmic Reticulum Stress in Toxoplasma gondii. Int J Mol Sci 2023; 24:10228. [PMID: 37373373 DOI: 10.3390/ijms241210228] [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: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
MORN proteins play a key role in the cytoskeletal structure of eukaryotes and are essential for the close arrangement of the endoplasmic reticulum and plasma membrane. A gene with nine MORN motifs (TGGT1_292120, named TgMORN2) was identified in the Toxoplasma gondii genome; it was presumed to belong to the MORN protein family and to have the function of forming the cytoskeleton, which affects the survival of T. gondii. However, the genetic deletion of MORN2 did not noticeably affect parasite growth and virulence. Using adjacent protein labeling techniques, we identified a network of TgMORN2 interactions, which mainly included endoplasmic reticulum stress (ER stress)-related proteins. In exploring these data, we found that the pathogenicity of the KO-TgMORN2 strain was significantly reduced in the case of tunicamycin-induced ER stress. Reticulon TgRTN (TGGT1_226430) and tubulin β-Tubulin were identified as interaction proteins of TgMORN2. Collectively, TgMORN2 plays a role in ER stress, which lays a foundation for further research on the function of the MORN protein in T. gondii.
Collapse
Affiliation(s)
- Jinxuan Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Qianqian Xiao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Qianqian Tan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Junpeng Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Lingyu Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Ziyu Chu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Hongxia Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Zhenzhao Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Hongmei Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
| | - Xiaomin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
| |
Collapse
|
63
|
Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CM, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544849. [PMID: 37398106 PMCID: PMC10312741 DOI: 10.1101/2023.06.13.544849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of evolutionarily-related Babesia spp. ( B. bovis and B. divergens ). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species of Babesia, achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance in Babesia species. Highlights Use of two species for in vitro evolution identifies a high confidence locus associated with resistance Resistance mutation in phoD was validated using reverse genetics in B. divergens Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms Together, phoD is a novel resistance determinant in multiple Babesia spp .
Collapse
|
64
|
Wilde ML, Ruparel U, Klemm T, Lee VV, Calleja DJ, Komander D, Tonkin CJ. Characterisation of the OTU domain deubiquitinase complement of Toxoplasma gondii. Life Sci Alliance 2023; 6:e202201710. [PMID: 36958824 PMCID: PMC10038098 DOI: 10.26508/lsa.202201710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023] Open
Abstract
The phylum Apicomplexa contains several parasitic species of medical and agricultural importance. The ubiquitination machinery remains, for the most part, uncharacterised in apicomplexan parasites, despite the important roles that it plays in eukaryotic biology. Bioinformatic analysis of the ubiquitination machinery in apicomplexan parasites revealed an expanded ovarian tumour domain-containing (OTU) deubiquitinase (DUB) family in Toxoplasma, potentially reflecting functional importance in apicomplexan parasites. This study presents comprehensive characterisation of Toxoplasma OTU DUBs. AlphaFold-guided structural analysis not only confirmed functional orthologues found across eukaryotes, but also identified apicomplexan-specific enzymes, subsequently enabling discovery of a cryptic OTU DUB in Plasmodium species. Comprehensive biochemical characterisation of 11 Toxoplasma OTU DUBs revealed activity against ubiquitin- and NEDD8-based substrates and revealed ubiquitin linkage preferences for Lys6-, Lys11-, Lys48-, and Lys63-linked chain types. We show that accessory domains in Toxoplasma OTU DUBs impose linkage preferences, and in case of apicomplexan-specific TgOTU9, we discover a cryptic ubiquitin-binding domain that is essential for TgOTU9 activity. Using the auxin-inducible degron (AID) to generate knockdown parasite lines, TgOTUD6B was found to be important for Toxoplasma growth.
Collapse
Affiliation(s)
- Mary-Louise Wilde
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Ushma Ruparel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Theresa Klemm
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - V Vern Lee
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia; and Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, Australia
| | - Dale J Calleja
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Christopher J Tonkin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| |
Collapse
|
65
|
Thind AC, Mota CM, Gonçalves APN, Sha J, Wohlschlegel JA, Mineo TWP, Bradley PJ. The Toxoplasma gondii effector GRA83 modulates the host's innate immune response to regulate parasite infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543158. [PMID: 37398161 PMCID: PMC10312501 DOI: 10.1101/2023.05.31.543158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Toxoplasma gondii 's propensity to infect its host and cause disease is highly dependent on its ability to modulate host cell functions. One of the strategies the parasite uses to accomplish this is via the export of effector proteins from the secretory dense granules. Dense granule (GRA) proteins are known to play roles in nutrient acquisition, host cell cycle manipulation, and immune regulation. Here, we characterize a novel dense granule protein named GRA83, which localizes to the parasitophorous vacuole in tachyzoites and bradyzoites. Disruption of GRA83 results in increased virulence, weight loss, and parasitemia during the acute infection, as well as a marked increase in the cyst burden during the chronic infection. This increased parasitemia was associated with an accumulation of inflammatory infiltrates in tissues in both the acute and chronic infection. Murine macrophages infected with Δ gra83 tachyzoites produced less interleukin-12 (IL-12) in vitro , which was confirmed with reduced IL-12 and interferon gamma (IFN-γ) in vivo . This dysregulation of cytokines correlates with reduced nuclear translocation of the p65 subunit of the NF-κB complex. While GRA15 similarly regulates NF-κB, infection with Δ gra83/ Δ gra15 parasites did not further reduce p65 translocation to the host cell nucleus, suggesting these GRAs function in converging pathways. We also used proximity labelling experiments to reveal candidate GRA83 interacting T. gondii derived partners. Taken together, this work reveals a novel effector that stimulates the innate immune response, enabling the host to limit parasite burden. Importance Toxoplasma gondii poses a significant public health concern as it is recognized as one of the leading foodborne pathogens in the United States. Infection with the parasite can cause congenital defects in neonates, life-threatening complications in immunosuppressed patients, and ocular disease. Specialized secretory organelles, including the dense granules, play an important role in the parasite's ability to efficiently invade and regulate components of the host's infection response machinery to limit parasite clearance and establish an acute infection. Toxoplasma' s ability to avoid early clearance, while also successfully infecting the host long enough to establish a persistent chronic infection, is crucial in allowing for its transmission to a new host. While multiple GRAs directly modulate host signaling pathways, they do so in various ways highlighting the parasite's diverse arsenal of effectors that govern infection. Understanding how parasite-derived effectors harness host functions to evade defenses yet ensure a robust infection are important for understanding the complexity of the pathogen's tightly regulated infection. In this study, we characterize a novel secreted protein named GRA83 that stimulates the host cell's response to limit infection.
Collapse
|
66
|
Tandel J, Walzer KA, Byerly JH, Pinkston B, Beiting DP, Striepen B. Genetic Ablation of a Female-Specific Apetala 2 Transcription Factor Blocks Oocyst Shedding in Cryptosporidium parvum. mBio 2023; 14:e0326122. [PMID: 36786597 PMCID: PMC10233709 DOI: 10.1128/mbio.03261-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
The apicomplexan parasite Cryptosporidium is a leading global cause of diarrheal disease, and the infection poses a particularly grave threat to young children and those with weakened immune function. Infection occurs by ingestion of meiotic spores called oocysts, and transmission relies on fecal shedding of new oocysts. The entire life cycle thus occurs in a single host and features asexual as well as sexual forms of replication. Here, we identify and locus tag two Apetala 2-type (AP2) transcription factors and demonstrate that they are exclusively expressed in male and female gametes, respectively. To enable functional studies of essential genes in Cryptosporidium parvum, we develop and validate a small-molecule-inducible gene excision system, which we apply to the female factor AP2-F to achieve conditional gene knockout. Analyzing this mutant, we find the factor to be dispensable for asexual growth and early female fate determination in vitro but to be required for oocyst shedding in infected animals in vivo. Transcriptional analyses conducted in the presence or absence of AP2-F revealed that the factor controls the transcription of genes encoding crystalloid body proteins, which are exclusively expressed in female gametes. In C. parvum, the organelle is restricted to sporozoites, and its loss in other apicomplexan parasites leads to blocked transmission. Overall, our development of conditional gene ablation in C. parvum provides a robust method for genetic analysis in this parasite that enabled us to identify AP2-F as an essential regulator of transcription required for oocyst shedding and transmission. IMPORTANCE The parasite Cryptosporidium infects millions of people worldwide each year, leading to life-threatening diarrheal disease in young children and immunosuppressed individuals. There is no vaccine and only limited treatment. Transmission occurs via the fecal-oral route by an environmentally resilient spore-like oocyst. Infection takes place in the intestinal epithelium, where parasites initially propagate asexually before transitioning to male and female gametes, with sex leading to the formation of new oocysts. The essential role of sexual development for continuous infection and transmission makes it an attractive target for therapy and prevention. To study essential genes and potential drug targets across the life cycle, we established inducible gene excision for C. parvum. We determined that the female-specific transcription factor AP2-F is not required for asexual growth and early female development in vitro but is necessary for oocyst shedding in vivo. This work enhances the genetic tools available to study Cryptosporidium gene function.
Collapse
Affiliation(s)
- Jayesh Tandel
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Katelyn A. Walzer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica H. Byerly
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brittain Pinkston
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
67
|
Dubois DJ, Chehade S, Marq JB, Venugopal K, Maco B, Puig ATI, Soldati-Favre D, Marion S. Toxoplasma gondii HOOK-FTS-HIP Complex is Critical for Secretory Organelle Discharge during Motility, Invasion, and Egress. mBio 2023:e0045823. [PMID: 37093045 DOI: 10.1128/mbio.00458-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Members of the Apicomplexa phylum possess specialized secretory organelles that discharge, apically and in a timely regulated manner, key factors implicated in parasite motility, host cell invasion, egress and subversion of host cellular functions. The mechanisms regulating trafficking and apical docking of these secretory organelles are only partially elucidated. Here, we characterized two conserved endosomal trafficking regulators known to promote vesicle transport and/or fusion, HOOK and Fused Toes (FTS), in the context of organelle discharge in Toxoplasma gondii. TgHOOK and TgFTS form a complex with a coccidian-specific partner, named HOOK interacting partner (HIP). TgHOOK displays an apically enriched vesicular pattern and concentrates at the parasite apical tip where it colocalizes with TgFTS and TgHIP. Functional investigations revealed that TgHOOK is dispensable but fitness conferring. The protein regulates the apical positioning and secretion of micronemes and contributes to egress, motility, host cell attachment, and invasion. Conditional depletion of TgFTS or TgHIP impacted on the same processes but led to more severe phenotypes. This study provides evidence of endosomal trafficking regulators involved in the apical exocytosis of micronemes and possibly as a consequence or directly on the discharge of the rhoptries. IMPORTANCE Toxoplasma gondii affects between 30 and 80% of the human population, poses a life-threatening risk to immunocompromised individuals, and is a cause of abortion and birth defects following congenital transmission. T. gondii belongs to the phylum of Apicomplexa characterized by a set of unique apical secretory organelles called the micronemes and rhoptries. Upon host cell recognition, this obligatory intracellular parasite secretes specific effectors contained in micronemes and rhoptries to promote parasite invasion of host cells and subsequent persistence. Here, we identified novel T. gondii endosomal trafficking regulators and demonstrated that they regulate microneme organelle apical positioning and exocytosis, thereby strongly contributing to host cell invasion and parasite virulence.
Collapse
Affiliation(s)
- David J Dubois
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Sylia Chehade
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Baptiste Marq
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kannan Venugopal
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Bohumil Maco
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Albert Tell I Puig
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Sabrina Marion
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| |
Collapse
|
68
|
Koreny L, Mercado-Saavedra BN, Klinger CM, Barylyuk K, Butterworth S, Hirst J, Rivera-Cuevas Y, Zaccai NR, Holzer VJC, Klingl A, Dacks JB, Carruthers VB, Robinson MS, Gras S, Waller RF. Stable endocytic structures navigate the complex pellicle of apicomplexan parasites. Nat Commun 2023; 14:2167. [PMID: 37061511 PMCID: PMC10105704 DOI: 10.1038/s41467-023-37431-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/17/2023] [Indexed: 04/17/2023] Open
Abstract
Apicomplexan parasites have immense impacts on humanity, but their basic cellular processes are often poorly understood. Where endocytosis occurs in these cells, how conserved this process is with other eukaryotes, and what the functions of endocytosis are across this phylum are major unanswered questions. Using the apicomplexan model Toxoplasma, we identified the molecular composition and behavior of unusual, fixed endocytic structures. Here, stable complexes of endocytic proteins differ markedly from the dynamic assembly/disassembly of these machineries in other eukaryotes. We identify that these endocytic structures correspond to the 'micropore' that has been observed throughout the Apicomplexa. Moreover, conserved molecular adaptation of this structure is seen in apicomplexans including the kelch-domain protein K13 that is central to malarial drug-resistance. We determine that a dominant function of endocytosis in Toxoplasma is plasma membrane homeostasis, rather than parasite nutrition, and that these specialized endocytic structures originated early in infrakingdom Alveolata likely in response to the complex cell pellicle that defines this medically and ecologically important ancient eukaryotic lineage.
Collapse
Affiliation(s)
- Ludek Koreny
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | | | - Christen M Klinger
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | | | - Simon Butterworth
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Yolanda Rivera-Cuevas
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Nathan R Zaccai
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Victoria J C Holzer
- Plant Development, Ludwig-Maximilians-University Munich, Planegg-Martinsried, 82152, Germany
| | - Andreas Klingl
- Plant Development, Ludwig-Maximilians-University Munich, Planegg-Martinsried, 82152, Germany
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, T6G 2R3, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Simon Gras
- Experimental Parasitology, Department for Veterinary Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, 82152, Germany.
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| |
Collapse
|
69
|
Cao X, Huang M, Ma Y, Song X, Hu D. In vitro anti-Toxoplasma gondii effects of a coccidiostat dinitolmide. Vet Parasitol 2023; 316:109903. [PMID: 36871500 DOI: 10.1016/j.vetpar.2023.109903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Coccidiosis, caused by Eimeria species, results in huge economic losses to the animal industry. Dinitolmide, a veterinary-approved coccidiostat, has a wide anticoccidial spectrum with no effect on host immunity. However, the mechanism of its anticoccidial effects remains unclear. Here, we used an in vitro culture system of T. gondii to explore the anti-Toxoplasma effect of dinitolmide and its underlying mechanism against coccidia. We show that dinitolmide has potent in vitro anti-Toxoplasma activity with the half-maximal effective concentration (EC50) of 3.625 µg/ml. Dinitolmide treatment significantly inhibited the viability, invasion and proliferation of T. gondii tachyzoites. The recovery experiment showed that dinitolmide can completely kill T. gondii tachyzoites after 24 h of treatment. Morphologically abnormal parasites were observed after dinitolmide exposure, including asynchronous development of daughter cells and deficiency of parasite inner and outer membrane. Further electron microscopy results showed that the drug could damage the membrane structure of T. gondii. By comparative transcriptomic analysis, we found that genes related to cell apoptosis and nitric-oxide synthase were up-regulated after dinitolmide treatment, which might be responsible for parasite cell death. Meanwhile, many Sag-related sequence (srs) genes were down-regulated after treatment, which could be closely associated with the reduction of parasite invasion and proliferation capacity. Our study indicates that the coccidiostat dinitolmide has a potent inhibitory effect on T. gondii in vitro and provides insight into the mode of action of the drug.
Collapse
Affiliation(s)
- Xinru Cao
- Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mao Huang
- Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yazhen Ma
- Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xingju Song
- Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Dandan Hu
- Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China.
| |
Collapse
|
70
|
Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
Collapse
Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
| |
Collapse
|
71
|
Guérin A, Strelau KM, Barylyuk K, Wallbank BA, Berry L, Crook OM, Lilley KS, Waller RF, Striepen B. Cryptosporidium uses multiple distinct secretory organelles to interact with and modify its host cell. Cell Host Microbe 2023; 31:650-664.e6. [PMID: 36958336 DOI: 10.1016/j.chom.2023.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/09/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Cryptosporidium is a leading cause of diarrheal disease in children and an important contributor to early childhood mortality. The parasite invades and extensively remodels intestinal epithelial cells, building an elaborate interface structure. How this occurs at the molecular level and the contributing parasite factors are largely unknown. Here, we generated a whole-cell spatial proteome of the Cryptosporidium sporozoite and used genetic and cell biological experimentation to discover the Cryptosporidium-secreted effector proteome. These findings reveal multiple organelles, including an original secretory organelle, and generate numerous compartment markers by tagging native gene loci. We show that secreted proteins are delivered to the parasite-host interface, where they assemble into different structures including a ring that anchors the parasite into its unique epicellular niche. Cryptosporidium thus uses a complex set of secretion systems during and following invasion that act in concert to subjugate its host cell.
Collapse
Affiliation(s)
- Amandine Guérin
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine M Strelau
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Bethan A Wallbank
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laurence Berry
- LPHI, CNRS, Université de Montpellier, Montpellier 34095, France
| | - Oliver M Crook
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
72
|
Polino AJ, Hasan MM, Floyd K, Avila-Cruz Y, Yang Y, Goldberg DE. An essential endoplasmic reticulum-resident N-acetyltransferase ortholog in Plasmodium falciparum. J Cell Sci 2023; 136:286919. [PMID: 36744402 PMCID: PMC10038149 DOI: 10.1242/jcs.260551] [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: 08/19/2022] [Accepted: 01/27/2023] [Indexed: 02/07/2023] Open
Abstract
N-terminal acetylation is a common eukaryotic protein modification that involves the addition of an acetyl group to the N-terminus of a polypeptide. This modification is largely performed by cytosolic N-terminal acetyltransferases (NATs). Most associate with the ribosome, acetylating nascent polypeptides co-translationally. In the malaria parasite Plasmodium falciparum, exported effectors are thought to be translated into the endoplasmic reticulum (ER), processed by the aspartic protease plasmepsin V and then N-acetylated, despite having no clear access to cytosolic NATs. Here, we used inducible gene deletion and post-transcriptional knockdown to investigate the primary ER-resident NAT candidate, Pf3D7_1437000. We found that it localizes to the ER and is required for parasite growth. However, depletion of Pf3D7_1437000 had no effect on protein export or acetylation of the exported proteins HRP2 and HRP3. Despite this, Pf3D7_1437000 depletion impedes parasite development within the host red blood cell and prevents parasites from completing genome replication. Thus, this work provides further proof of N-terminal acetylation of secretory system proteins, a process unique to apicomplexan parasites, but strongly discounts a promising candidate for this post-translational modification.
Collapse
Affiliation(s)
- Alexander J Polino
- Division of Infectious Diseases, Department of Medicine, and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Muhammad M Hasan
- Division of Infectious Diseases, Department of Medicine, and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Katherine Floyd
- Division of Infectious Diseases, Department of Medicine, and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Yolotzin Avila-Cruz
- Division of Infectious Diseases, Department of Medicine, and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Yujuan Yang
- Division of Infectious Diseases, Department of Medicine, and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| |
Collapse
|
73
|
Giuliano CJ, Wei KJ, Harling FM, Waldman BS, Farringer MA, Boydston EA, Lan TCT, Thomas RW, Herneisen AL, Sanderlin AG, Coppens I, Dvorin JD, Lourido S. Functional profiling of the Toxoplasma genome during acute mouse infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531216. [PMID: 36945434 PMCID: PMC10028831 DOI: 10.1101/2023.03.05.531216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Within a host, pathogens encounter a diverse and changing landscape of cell types, nutrients, and immune responses. Examining host-pathogen interactions in animal models can therefore reveal aspects of infection absent from cell culture. We use CRISPR-based screens to functionally profile the entire genome of the model apicomplexan parasite Toxoplasma gondii during mouse infection. Barcoded gRNAs were used to track mutant parasite lineages, enabling detection of bottlenecks and mapping of population structures. We uncovered over 300 genes that modulate parasite fitness in mice with previously unknown roles in infection. These candidates span multiple axes of host-parasite interaction, including determinants of tropism, host organelle remodeling, and metabolic rewiring. We mechanistically characterized three novel candidates, including GTP cyclohydrolase I, against which a small-molecule inhibitor could be repurposed as an antiparasitic compound. This compound exhibited antiparasitic activity against T. gondii and Plasmodium falciparum, the most lethal agent of malaria. Taken together, we present the first complete survey of an apicomplexan genome during infection of an animal host, and point to novel interfaces of host-parasite interaction that may offer new avenues for treatment.
Collapse
Affiliation(s)
| | - Kenneth J. Wei
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | - Faye M. Harling
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | | | - Madeline A. Farringer
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, Massachusetts, USA
- Biological Sciences in Public Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Raina W. Thomas
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | - Alice L. Herneisen
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | | | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Jeffrey D. Dvorin
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| |
Collapse
|
74
|
Munera López J, Alonso AM, Figueras MJ, Saldarriaga Cartagena AM, Hortua Triana MA, Diambra L, Vanagas L, Deng B, Moreno SNJ, Angel SO. Analysis of the Interactome of the Toxoplasma gondii Tgj1 HSP40 Chaperone. Proteomes 2023; 11:9. [PMID: 36976888 PMCID: PMC10056330 DOI: 10.3390/proteomes11010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/20/2023] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Toxoplasma gondii is an obligate intracellular apicomplexan that causes toxoplasmosis in humans and animals. Central to its dissemination and pathogenicity is the ability to rapidly divide in the tachyzoite stage and infect any type of nucleated cell. Adaptation to different cell contexts requires high plasticity in which heat shock proteins (Hsps) could play a fundamental role. Tgj1 is a type I Hsp40 of T. gondii, an ortholog of the DNAJA1 group, which is essential during the tachyzoite lytic cycle. Tgj1 consists of a J-domain, ZFD, and DNAJ_C domains with a CRQQ C-terminal motif, which is usually prone to lipidation. Tgj1 presented a mostly cytosolic subcellular localization overlapping partially with endoplasmic reticulum. Protein-protein Interaction (PPI) analysis showed that Tgj1 could be implicated in various biological pathways, mainly translation, protein folding, energy metabolism, membrane transport and protein translocation, invasion/pathogenesis, cell signaling, chromatin and transcription regulation, and cell redox homeostasis among others. The combination of Tgj1 and Hsp90 PPIs retrieved only 70 interactors linked to the Tgj1-Hsp90 axis, suggesting that Tgj1 would present specific functions in addition to those of the Hsp70/Hsp90 cycle, standing out invasion/pathogenesis, cell shape motility, and energy pathway. Within the Hsp70/Hsp90 cycle, translation-associated pathways, cell redox homeostasis, and protein folding were highly enriched in the Tgj1-Hsp90 axis. In conclusion, Tgj1 would interact with a wide range of proteins from different biological pathways, which could suggest a relevant role in them.
Collapse
Affiliation(s)
- Jonathan Munera López
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, Chascomús 7130, Argentina
| | - Andrés Mariano Alonso
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, Chascomús 7130, Argentina
| | - Maria Julia Figueras
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, Chascomús 7130, Argentina
| | - Ana María Saldarriaga Cartagena
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, Chascomús 7130, Argentina
| | - Miryam A. Hortua Triana
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Luis Diambra
- Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, Chascomús 7130, Argentina
| | - Bin Deng
- Department of Biology and VBRN, University of Vermont, Burlington, VT 05405, USA
| | - Silvia N. J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sergio Oscar Angel
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, Chascomús 7130, Argentina
| |
Collapse
|
75
|
Back PS, Moon AS, Pasquarelli RR, Bell HN, Torres JA, Chen AL, Sha J, Vashisht AA, Wohlschlegel JA, Bradley PJ. IMC29 Plays an Important Role in Toxoplasma Endodyogeny and Reveals New Components of the Daughter-Enriched IMC Proteome. mBio 2023; 14:e0304222. [PMID: 36622147 PMCID: PMC9973257 DOI: 10.1128/mbio.03042-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2023] Open
Abstract
The Toxoplasma inner membrane complex (IMC) is a unique organelle that plays critical roles in parasite motility, invasion, egress, and replication. The IMC is delineated into the apical, body, and basal regions, defined by proteins that localize to these distinct subcompartments. The IMC can be further segregated by proteins that localize specifically to the maternal IMC, the daughter bud IMC, or both. While the function of the maternal IMC has been better characterized, the precise roles of most daughter IMC components remain poorly understood. Here, we demonstrate that the daughter protein IMC29 plays an important role in parasite replication. We show that Δimc29 parasites exhibit severe replication defects, resulting in substantial growth defects and loss of virulence. Deletion analyses revealed that IMC29 localization is largely dependent on the N-terminal half of the protein containing four predicted coiled-coil domains while IMC29 function requires a short C-terminal helical region. Using proximity labeling, we identify eight novel IMC proteins enriched in daughter buds, significantly expanding the daughter IMC proteome. We additionally report four novel proteins with unique localizations to the interface between two parasites or to the outer face of the IMC, exposing new subregions of the organelle. Together, this work establishes IMC29 as an important early daughter bud component of replication and uncovers an array of new IMC proteins that provides important insights into this organelle. IMPORTANCE The inner membrane complex (IMC) is a conserved structure across the Apicomplexa phylum, which includes obligate intracellular parasites that cause toxoplasmosis, malaria, and cryptosporidiosis. The IMC is critical for the parasite to maintain its intracellular lifestyle, particularly in providing a scaffold for daughter bud formation during parasite replication. While many IMC proteins in the later stages of division have been identified, components of the early stages of division remain unknown. Here, we focus on the early daughter protein IMC29, demonstrating that it is crucial for faithful parasite replication and identifying specific regions of the protein that are important for its localization and function. We additionally use proximity labeling to reveal a suite of daughter-enriched IMC proteins, which represent promising candidates to further explore this IMC subcompartment.
Collapse
Affiliation(s)
- Peter S. Back
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Andy S. Moon
- Department of Molecular Microbiology and Immunology, University of California, Los Angeles, California, USA
| | | | - Hannah N. Bell
- Department of Molecular Microbiology and Immunology, University of California, Los Angeles, California, USA
| | - Juan A. Torres
- Department of Molecular Microbiology and Immunology, University of California, Los Angeles, California, USA
| | - Allan L. Chen
- Department of Molecular Microbiology and Immunology, University of California, Los Angeles, California, USA
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Peter J. Bradley
- Department of Molecular Microbiology and Immunology, University of California, Los Angeles, California, USA
| |
Collapse
|
76
|
Elsworth B, Keroack C, Rezvani Y, Paul A, Barazorda K, Tennessen J, Sack S, Moreira C, Gubbels MJ, Meyers M, Zarringhalam K, Duraisingh M. Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases. RESEARCH SQUARE 2023:rs.3.rs-2553721. [PMID: 36909484 PMCID: PMC10002801 DOI: 10.21203/rs.3.rs-2553721/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Apicomplexan egress from host cells is fundamental to the spread of infection and is poorly characterized in Babesia spp., parasites of veterinary importance and emerging zoonoses. Through the use of video microscopy, transcriptomics and chemical genetics, we have implicated signaling, proteases and gliding motility as key drivers of egress by Babesia divergens. We developed reverse genetics to perform a knockdown screen of putative mediators of egress, identifying kinases and proteases involved in distinct steps of egress (ASP3, PKG and CDPK4) and invasion (ASP2, ASP3 and PKG). Inhibition of egress leads to continued intracellular replication, indicating exit from the replication cycle is uncoupled from egress. Chemical genetics validated PKG, ASP2 and ASP3 as druggable targets in Babesia spp. All taken together, egress in B. divergens more closely resembles T. gondii than the more evolutionarily-related Plasmodium spp. We have established a molecular framework for biological and translational studies of B. divergens egress.
Collapse
|
77
|
Functional Characterization of 15 Novel Dense Granule Proteins in Toxoplasma gondii Using the CRISPR-Cas9 System. Microbiol Spectr 2023; 11:e0307822. [PMID: 36515555 PMCID: PMC9927372 DOI: 10.1128/spectrum.03078-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The analysis of the subcellular localization and function of dense granule proteins (GRAs) is of central importance for the understanding of host-parasite interaction and pathogenesis of Toxoplasma gondii infection. Here, we identified 15 novel GRAs and used C-terminal endogenous gene tagging to determine their localization at the intravacuolar network (IVN), parasitophorous vacuole (PV), or PV membrane (PVM) in the tachyzoites and at the periphery of the bradyzoites-containing cysts. The functions of the 15 gra genes were examined in type I RH strain and 5 of these gra genes were also evaluated in the cyst-forming type II Pru strain. The 15 novel gra genes were successfully disrupted by using CRISPR-Cas9 mediated homologous recombination and the results showed that 13 gra genes were not individually essential for T. gondii replication in vitro or virulence in mice during acute and chronic infection. Intriguingly, deletion of TGME49_266410 and TGME49_315910 in both RH and Pru strains decreased the parasite replication in vitro and attenuated its virulence, and also reduced the cyst-forming ability of the Pru strain in mice during chronic infection. Comparison of the transcriptomic profiles of the 15 gra genes suggests that they may play roles in other life cycle stages and genotypes of T. gondii. Taken together, our findings improve the understanding of T. gondii pathogenesis and demonstrate the involvement of two novel GRAs, TGME49_266410 and TGME49_315910, in the parasite replication and virulence. IMPORTANCE Dense granule proteins (GRAs) play important roles in Toxoplasma gondii pathogenicity. However, the functions of many putative GRAs have not been elucidated. Here, we found that 15 novel GRAs are secreted into intravacuolar network (IVN), parasitophorous vacuole (PV), or PV membrane (PVM) in tachyzoites and are located at the periphery of the bradyzoite-containing cysts. TGME49_266410 and TGME49_315910 were crucial to the growth of RH and Pru strains in vitro. Deletion of TGME49_266410 and TGME49_315910 attenuated the parasite virulence in mice. However, disruption of other 13 gra genes did not have a significant impact on the proliferation and pathogenicity of T. gondii in vitro or in vivo. The marked effects of the two novel GRAs (TGME49_266410 and TGME49_315910) on the in vitro growth and virulence of T. gondii are notable and warrant further elucidation of the temporal and spatial dynamics of translocation of these two novel GRAs and how do they interfere with host cell functions.
Collapse
|
78
|
Thornton LB, Key M, Micchelli C, Stasic AJ, Kwain S, Floyd K, Moreno SNJ, Dominy BN, Whitehead DC, Dou Z. A cathepsin C-like protease post-translationally modifies Toxoplasma gondii secretory proteins for optimal invasion and egress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.21.525043. [PMID: 36712013 PMCID: PMC9882377 DOI: 10.1101/2023.01.21.525043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial pathogens use proteases for their infections, such as digestion of proteins for nutrients and activation of their virulence factors. As an obligate intracellular parasite, Toxoplasma gondii must invade host cells to establish its intracellular propagation. To facilitate invasion, the parasites secrete invasion effectors from microneme and rhoptry, two unique organelles in apicomplexans. Previous work has shown that some micronemal invasion effectors experience a series of proteolytic cleavages within the parasite's secretion pathway for maturation, such as the aspartyl protease (TgASP3) and the cathepsin L-like protease (TgCPL), localized within the post-Golgi compartment (1) and the endolysosomal system (2), respectively. Furthermore, it has been shown that the precise maturation of micronemal effectors is critical for Toxoplasma invasion and egress (1). Here, we show that an endosome-like compartment (ELC)-residing cathepsin C-like protease (TgCPC1) mediates the final trimming of some micronemal effectors, and its loss further results in defects in the steps of invasion, egress, and migration throughout the parasite's lytic cycle. Notably, the deletion of TgCPC1 completely blocks the activation of subtilisin-like protease 1 (TgSUB1) in the parasites, which globally impairs the surface-trimming of many key micronemal invasion and egress effectors. Additionally, we found that TgCPC1 was not efficiently inhibited by the chemical inhibitor targeting its malarial ortholog, suggesting that these cathepsin C-like orthologs are structurally different within the apicomplexan phylum. Taken together, our findings identify a novel function of TgCPC1 in the processing of micronemal proteins within the secretory pathway of Toxoplasma parasites and expand the understanding of the roles of cathepsin C protease. IMPORTANCE Toxoplasma gondii is a microbial pathogen that is well adapted for disseminating infections. It can infect virtually all warm-blooded animals. Approximately one-third of the human population carries toxoplasmosis. During infection, the parasites sequentially secrete protein effectors from the microneme, rhoptry, and dense granule, three organelles exclusively found in apicomplexan parasites, to help establish their lytic cycle. Proteolytic cleavage of these secretory proteins is required for the parasite's optimal function. Previous work has revealed that two proteases residing within the parasite's secretory pathway cleave micronemal and rhoptry proteins, which mediate parasite invasion and egress. Here, we demonstrate that a cathepsin C-like protease (TgCPC1) is involved in processing several invasion and egress effectors. The genetic deletion of TgCPC1 prevented the complete maturation of some effectors in the parasites. Strikingly, the deletion led to a full inactivation of one surface-anchored protease, which globally impaired the trimming of some key micronemal proteins before secretion. Therefore, this finding represents a novel post-translational mechanism for the processing of virulence factors within microbial pathogens.
Collapse
Affiliation(s)
- L. Brock Thornton
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Melanie Key
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Chiara Micchelli
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Andrew J. Stasic
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Samuel Kwain
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Katherine Floyd
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Silvia N. J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Brian N. Dominy
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Daniel C. Whitehead
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Zhicheng Dou
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| |
Collapse
|
79
|
Kimmel J, Schmitt M, Sinner A, Jansen PWTC, Mainye S, Ramón-Zamorano G, Toenhake CG, Wichers-Misterek JS, Cronshagen J, Sabitzki R, Mesén-Ramírez P, Behrens HM, Bártfai R, Spielmann T. Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3. Cell Syst 2023; 14:9-23.e7. [PMID: 36657393 DOI: 10.1016/j.cels.2022.12.001] [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: 07/22/2022] [Revised: 10/07/2022] [Accepted: 12/08/2022] [Indexed: 01/19/2023]
Abstract
Taxon-specific proteins are key determinants defining the biology of all organisms and represent prime drug targets in pathogens. However, lacking comparability with proteins in other lineages makes them particularly difficult to study. In malaria parasites, this is exacerbated by technical limitations. Here, we analyzed the cellular location, essentiality, function, and, in selected cases, interactome of all unknown non-secretory proteins encoded on an entire P. falciparum chromosome. The nucleus was the most common localization, indicating that it is a hotspot of parasite-specific biology. More in-depth functional studies with four proteins revealed essential roles in DNA replication and mitosis. The mitosis proteins defined a possible orphan complex and a highly diverged complex needed for spindle-kinetochore connection. Structure-function comparisons indicated that the taxon-specific proteins evolved by different mechanisms. This work demonstrates the feasibility of gene-by-gene screens to elucidate the biology of malaria parasites and reveal critical parasite-specific processes of interest as drug targets.
Collapse
Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Marius Schmitt
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Alexej Sinner
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | | | - Sheila Mainye
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Gala Ramón-Zamorano
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Christa Geeke Toenhake
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, the Netherlands
| | | | - Jakob Cronshagen
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ricarda Sabitzki
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Paolo Mesén-Ramírez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Hannah Michaela Behrens
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| |
Collapse
|
80
|
Singer M, Simon K, Forné I, Meissner M. A central CRMP complex essential for invasion in Toxoplasma gondii. PLoS Biol 2023; 21:e3001937. [PMID: 36602948 PMCID: PMC9815656 DOI: 10.1371/journal.pbio.3001937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Apicomplexa are obligate intracellular parasites. While most species are restricted to specific hosts and cell types, Toxoplasma gondii can invade every nucleated cell derived from warm-blooded animals. This broad host range suggests that this parasite can recognize multiple host cell ligands or structures, leading to the activation of a central protein complex, which should be conserved in all apicomplexans. During invasion, the unique secretory organelles (micronemes and rhoptries) are sequentially released and several micronemal proteins have been suggested to be required for host cell recognition and invasion. However, to date, only few micronemal proteins have been demonstrated to be essential for invasion, suggesting functional redundancy that might allow such a broad host range. Cysteine Repeat Modular Proteins (CRMPs) are a family of apicomplexan-specific proteins. In T. gondii, two CRMPs are present in the genome, CRMPA (TGGT1_261080) and CRMPB (TGGT1_292020). Here, we demonstrate that both proteins form a complex that contains the additional proteins MIC15 and the thrombospondin type 1 domain-containing protein (TSP1). Disruption of this complex results in a block of rhoptry secretion and parasites being unable to invade the host cell. In conclusion, this complex is a central invasion complex conserved in all apicomplexans.
Collapse
Affiliation(s)
- Mirko Singer
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig-Maximilians-University (LMU) Munich, Germany
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
- * E-mail: (MS); (MM)
| | - Kathrin Simon
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig-Maximilians-University (LMU) Munich, Germany
| | - Ignasi Forné
- Faculty of Medicine, Protein Analysis Unit, Biomedical Center (BMC), Ludwig-Maximilians-University (LMU) Munich, Martinsried, Germany
| | - Markus Meissner
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig-Maximilians-University (LMU) Munich, Germany
- * E-mail: (MS); (MM)
| |
Collapse
|
81
|
Mathur V, Salomaki ED, Wakeman KC, Na I, Kwong WK, Kolisko M, Keeling PJ. Reconstruction of Plastid Proteomes of Apicomplexans and Close Relatives Reveals the Major Evolutionary Outcomes of Cryptic Plastids. Mol Biol Evol 2023; 40:6969433. [PMID: 36610734 PMCID: PMC9847631 DOI: 10.1093/molbev/msad002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Apicomplexans and related lineages comprise many obligate symbionts of animals; some of which cause notorious diseases such as malaria. They evolved from photosynthetic ancestors and transitioned into a symbiotic lifestyle several times, giving rise to species with diverse non-photosynthetic plastids. Here, we sought to reconstruct the evolution of the cryptic plastids in the apicomplexans, chrompodellids, and squirmids (ACS clade) by generating five new single-cell transcriptomes from understudied gregarine lineages, constructing a robust phylogenomic tree incorporating all ACS clade sequencing datasets available, and using these to examine in detail, the evolutionary distribution of all 162 proteins recently shown to be in the apicoplast by spatial proteomics in Toxoplasma. This expanded homology-based reconstruction of plastid proteins found in the ACS clade confirms earlier work showing convergence in the overall metabolic pathways retained once photosynthesis is lost, but also reveals differences in the degrees of plastid reduction in specific lineages. We show that the loss of the plastid genome is common and unexpectedly find many lineage- and species-specific plastid proteins, suggesting the presence of evolutionary innovations and neofunctionalizations that may confer new functional and metabolic capabilities that are yet to be discovered in these enigmatic organelles.
Collapse
Affiliation(s)
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Ina Na
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Waldan K Kwong
- Present address: Instituto Gulbenkian de Ciência (IGC) Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| |
Collapse
|
82
|
Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei. Nat Microbiol 2023; 8:533-547. [PMID: 36804636 PMCID: PMC9981465 DOI: 10.1038/s41564-022-01295-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/21/2022] [Indexed: 02/22/2023]
Abstract
Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive 'cartographic' analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.
Collapse
|
83
|
Huet D, Moreno SNJ. Interorganellar Communication Through Membrane Contact Sites in Toxoplasma Gondii. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231189064. [PMID: 37560622 PMCID: PMC10408353 DOI: 10.1177/25152564231189064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/11/2023]
Abstract
Apicomplexan parasites are a group of protists that cause disease in humans and include pathogens like Plasmodium spp., the causative agent of malaria, and Toxoplasma gondii, the etiological agent of toxoplasmosis and one of the most ubiquitous human parasites in the world. Membrane contact sites (MCSs) are widespread structures within eukaryotic cells but their characterization in apicomplexan parasites is only in its very beginnings. Basic biological features of the T. gondii parasitic cycle support numerous organellar interactions, including the transfer of Ca2+ and metabolites between different compartments. In T. gondii, Ca2+ signals precede a series of interrelated molecular processes occurring in a coordinated manner that culminate in the stimulation of key steps of the parasite life cycle. Calcium transfer from the endoplasmic reticulum to other organelles via MCSs would explain the precision, speed, and efficiency that is needed during the lytic cycle of T. gondii. In this short review, we discuss the implications of these structures in cellular signaling, with an emphasis on their potential role in Ca2+ signaling.
Collapse
Affiliation(s)
- Diego Huet
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Silvia N. J. Moreno
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| |
Collapse
|
84
|
Toxoplasma Shelph, a Phosphatase Located in the Parasite Endoplasmic Reticulum, Is Required for Parasite Virulence. mSphere 2022; 7:e0035022. [PMID: 36326242 PMCID: PMC9769683 DOI: 10.1128/msphere.00350-22] [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] [Indexed: 11/06/2022] Open
Abstract
Toxoplasma gondii is a single-celled parasitic eukaryote that evolved to successfully propagate in any nucleated cell. As with any other eukaryote, its life cycle is regulated by signaling pathways controlled by kinases and phosphatases. T. gondii encodes an atypical bacterial-like phosphatase absent from mammalian genomes, named Shelph, after its first identification in the psychrophilic bacterium Schewanella sp. Here, we demonstrate that Toxoplasma Shelph is an active phosphatase localized in the parasite endoplasmic reticulum. The phenotyping of a shelph knockout (KO) line showed a minor impairment in invasion on human fibroblasts, while the other steps of the parasite lytic cycle were not affected. In contrast with Plasmodium ortholog Shelph1, this invasion deficiency was not correlated with any default in the biogenesis of secretory organelles. However, Shelph-KO parasites displayed a much-pronounced defect in virulence in vivo. These phenotypes could be rescued by genetic complementation, thus supporting an important function for Shelph in the context of a natural infection. IMPORTANCE Toxoplasma gondii belongs to the Apicomplexa phylum, which comprises more than 5,000 species, among which is Plasmodium falciparum, the notorious agent of human malaria. Intriguingly, the Apicomplexa genomes encode at least one phosphatase closely related to the bacterial Schewanella phosphatase, or Shelph. To better understand the importance of these atypical bacterial enzymes in eukaryotic parasites, we undertook the functional characterization of T. gondii Shelph. Our results uncovered its subcellular localization and its enzymatic activity, revealed its subtle involvement during the tachyzoite invasion step of the lytic cycle, and more importantly, highlighted a critical requirement of this phosphatase for parasite propagation in mice. Overall, this study revealed an unexpected role for T. gondii Shelph in the maintenance of parasite virulence in vivo.
Collapse
|
85
|
Mou M, Pan Z, Lu M, Sun H, Wang Y, Luo Y, Zhu F. Application of Machine Learning in Spatial Proteomics. J Chem Inf Model 2022; 62:5875-5895. [PMID: 36378082 DOI: 10.1021/acs.jcim.2c01161] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years, especially the subcellular proteomics. Numerous evidence indicate that the subcellular localization of proteins is associated with various cellular processes and disease progression. Mass spectrometry (MS)-based and imaging-based experimental approaches have been developed to acquire large-scale spatial proteomic data. To allow the reliable analysis of increasingly complex spatial proteomics data, machine learning (ML) methods have been widely used in both MS-based and imaging-based spatial proteomic data analysis pipelines. Here, we comprehensively survey the applications of ML in spatial proteomics from following aspects: (1) data resources for spatial proteome are comprehensively introduced; (2) the roles of different ML algorithms in data analysis pipelines are elaborated; (3) successful applications of spatial proteomics and several analytical tools integrating ML methods are presented; (4) challenges existing in modern ML-based spatial proteomics studies are discussed. This review provides guidelines for researchers seeking to apply ML methods to analyze spatial proteomic data and can facilitate insightful understanding of cell biology as well as the future research in medical and drug discovery communities.
Collapse
Affiliation(s)
- Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
86
|
Wang JL, Li TT, Elsheikha HM, Liang QL, Zhang ZW, Wang M, Sibley LD, Zhu XQ. The protein phosphatase 2A holoenzyme is a key regulator of starch metabolism and bradyzoite differentiation in Toxoplasma gondii. Nat Commun 2022; 13:7560. [PMID: 36476594 PMCID: PMC9729606 DOI: 10.1038/s41467-022-35267-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Phenotypic switching between tachyzoite and bradyzoite is the fundamental mechanism underpinning the pathogenicity and adaptability of the protozoan parasite Toxoplasma gondii. Although accumulation of cytoplasmic starch granules is a hallmark of the quiescent bradyzoite stage, the regulatory factors and mechanisms contributing to amylopectin storage in bradyzoites are incompletely known. Here, we show that T. gondii protein phosphatase 2A (PP2A) holoenzyme is composed of a catalytic subunit PP2A-C, a scaffold subunit PP2A-A and a regulatory subunit PP2A-B. Disruption of any of these subunits increased starch accumulation and blocked the tachyzoite-to-bradyzoite differentiation. PP2A contributes to the regulation of amylopectin metabolism via dephosphorylation of calcium-dependent protein kinase 2 at S679. Phosphoproteomics identified several putative PP2A holoenzyme substrates that are involved in bradyzoite differentiation. Our findings provide novel insight into the role of PP2A as a key regulator of starch metabolism and bradyzoite differentiation in T. gondii.
Collapse
Affiliation(s)
- Jin-Lei Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China.
| | - Ting-Ting Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Qin-Li Liang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Zhi-Wei Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Meng Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Xing-Quan Zhu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, 030801, People's Republic of China.
| |
Collapse
|
87
|
Leger MM, Stairs C. Eukaryotic evolution: Spatial proteomics sheds light on mitochondrial reduction. Curr Biol 2022; 32:R1308-R1311. [PMID: 36473440 DOI: 10.1016/j.cub.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-organelle spatial proteomics has revolutionized animal cell biology, but its use in protists has so far been limited. A new study delivers the first such proteome of a free-living protist, uncovering a previously overlooked function of highly reduced mitochondria.
Collapse
Affiliation(s)
- Michelle M Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Courtney Stairs
- Microbiology Research Group, Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden.
| |
Collapse
|
88
|
Reduced mitochondria provide an essential function for the cytosolic methionine cycle. Curr Biol 2022; 32:5057-5068.e5. [PMID: 36347252 PMCID: PMC9746703 DOI: 10.1016/j.cub.2022.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/15/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The loss of mitochondria in oxymonad protists has been associated with the redirection of the essential Fe-S cluster assembly to the cytosol. Yet as our knowledge of diverse free-living protists broadens, the list of functions of their mitochondrial-related organelles (MROs) expands. We revealed another such function in the closest oxymonad relative, Paratrimastix pyriformis, after we solved the proteome of its MRO with high accuracy, using localization of organelle proteins by isotope tagging (LOPIT). The newly assigned enzymes connect to the glycine cleavage system (GCS) and produce folate derivatives with one-carbon units and formate. These are likely to be used by the cytosolic methionine cycle involved in S-adenosyl methionine recycling. The data provide consistency with the presence of the GCS in MROs of free-living species and its absence in most endobionts, which typically lose the methionine cycle and, in the case of oxymonads, the mitochondria.
Collapse
|
89
|
Butterworth S, Torelli F, Lockyer EJ, Wagener J, Song OR, Broncel M, Russell MRG, Moreira-Souza ACA, Young JC, Treeck M. Toxoplasma gondii virulence factor ROP1 reduces parasite susceptibility to murine and human innate immune restriction. PLoS Pathog 2022; 18:e1011021. [PMID: 36476844 PMCID: PMC9762571 DOI: 10.1371/journal.ppat.1011021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/19/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Toxoplasma gondii is an intracellular parasite that can infect many host species and is a cause of significant human morbidity worldwide. T. gondii secretes a diverse array of effector proteins into the host cell which are critical for infection. The vast majority of these secreted proteins have no predicted functional domains and remain uncharacterised. Here, we carried out a pooled CRISPR knockout screen in the T. gondii Prugniaud strain in vivo to identify secreted proteins that contribute to parasite immune evasion in the host. We demonstrate that ROP1, the first-identified rhoptry protein of T. gondii, is essential for virulence and has a previously unrecognised role in parasite resistance to interferon gamma-mediated innate immune restriction. This function is conserved in the highly virulent RH strain of T. gondii and contributes to parasite growth in both murine and human macrophages. While ROP1 affects the morphology of rhoptries, from where the protein is secreted, it does not affect rhoptry secretion. Finally, we show that ROP1 co-immunoprecipitates with the host cell protein C1QBP, an emerging regulator of innate immune signaling. In summary, we identify putative in vivo virulence factors in the T. gondii Prugniaud strain and show that ROP1 is an important and previously overlooked effector protein that counteracts both murine and human innate immunity.
Collapse
Affiliation(s)
- Simon Butterworth
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Francesca Torelli
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Eloise J. Lockyer
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jeanette Wagener
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ok-Ryul Song
- High-Throughput Screening Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Malgorzata Broncel
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Matt R. G. Russell
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | | | - Joanna C. Young
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Moritz Treeck
- Signalling In Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
90
|
Haase R, Dos Santos Pacheco N, Soldati-Favre D. Nanoscale imaging of the conoid and functional dissection of its dynamics in Apicomplexa. Curr Opin Microbiol 2022; 70:102226. [PMID: 36332501 DOI: 10.1016/j.mib.2022.102226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/08/2022]
Abstract
Members of the Apicomplexa phylum are unified by an apical complex tailored for motility and host cell invasion. It includes regulated secretory organelles and a conoid attached to the apical polar ring (APR) from which subpellicular microtubules emerge. In coccidia, the conoid is composed of a cone of spiraling tubulin fibers, two preconoidal rings, and two intraconoidal microtubules. The conoid extrudes through the APR in motile parasites. Recent advances in proteomics, cryo-electron tomography, super-resolution, and expansion microscopy provide a more comprehensive view of the spatial and temporal resolution of proteins belonging to the conoid subcomponents. In combination with the phenotyping of targeted mutants, the biogenesis, turnover, dynamics, and function of the conoid begin to be elucidated.
Collapse
Affiliation(s)
- Romuald Haase
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | - Nicolas Dos Santos Pacheco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.
| |
Collapse
|
91
|
Maclean AE, Hayward JA, Huet D, van Dooren GG, Sheiner L. The mystery of massive mitochondrial complexes: the apicomplexan respiratory chain. Trends Parasitol 2022; 38:1041-1052. [PMID: 36302692 PMCID: PMC10434753 DOI: 10.1016/j.pt.2022.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
The mitochondrial respiratory chain is an essential pathway in most studied eukaryotes due to its roles in respiration and other pathways that depend on mitochondrial membrane potential. Apicomplexans are unicellular eukaryotes whose members have an impact on global health. The respiratory chain is a drug target for some members of this group, notably the malaria-causing Plasmodium spp. This has motivated studies of the respiratory chain in apicomplexan parasites, primarily Toxoplasma gondii and Plasmodium spp. for which experimental tools are most advanced. Studies of the respiratory complexes in these organisms revealed numerous novel features, including expansion of complex size. The divergence of apicomplexan mitochondria from commonly studied models highlights the diversity of mitochondrial form and function across eukaryotic life.
Collapse
Affiliation(s)
- Andrew E Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Jenni A Hayward
- Research School of Biology, Australian National University, Canberra, Australia
| | - Diego Huet
- Center for Tropical & Emerging Diseases, University of Georgia, Athens, GA, USA; Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK.
| |
Collapse
|
92
|
Crook OM, Lilley KS, Gatto L, Kirk PD. Semi-Supervised Non-Parametric Bayesian Modelling of Spatial Proteomics. Ann Appl Stat 2022; 16:22-aoas1603. [PMID: 36507469 PMCID: PMC7613899 DOI: 10.1214/22-aoas1603] [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] [Indexed: 02/02/2023]
Abstract
Understanding sub-cellular protein localisation is an essential component in the analysis of context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to sub-cellular locations within the cell. Novel modelling considerations to capture the complex nature of these data are thus necessary. We approach analysis of spatial proteomics data in a non-parametric Bayesian framework, using K-component mixtures of Gaussian process regression models. The Gaussian process regression model accounts for correlation structure within a sub-cellular niche, with each mixture component capturing the distinct correlation structure observed within each niche. The availability of marker proteins (i.e. proteins with a priori known labelled locations) motivates a semi-supervised learning approach to inform the Gaussian process hyperparameters. We moreover provide an efficient Hamiltonian-within-Gibbs sampler for our model. Furthermore, we reduce the computational burden associated with inversion of covariance matrices by exploiting the structure in the covariance matrix. A tensor decomposition of our covariance matrices allows extended Trench and Durbin algorithms to be applied to reduce the computational complexity of inversion and hence accelerate computation. We provide detailed case-studies on Drosophila embryos and mouse pluripotent embryonic stem cells to illustrate the benefit of semi-supervised functional Bayesian modelling of the data.
Collapse
|
93
|
Sparvoli D, Delabre J, Penarete‐Vargas DM, Kumar Mageswaran S, Tsypin LM, Heckendorn J, Theveny L, Maynadier M, Mendonça Cova M, Berry‐Sterkers L, Guérin A, Dubremetz J, Urbach S, Striepen B, Turkewitz AP, Chang Y, Lebrun M. An apical membrane complex for triggering rhoptry exocytosis and invasion in Toxoplasma. EMBO J 2022; 41:e111158. [PMID: 36245278 PMCID: PMC9670195 DOI: 10.15252/embj.2022111158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/13/2023] Open
Abstract
Apicomplexan parasites possess secretory organelles called rhoptries that undergo regulated exocytosis upon contact with the host. This process is essential for the parasitic lifestyle of these pathogens and relies on an exocytic machinery sharing structural features and molecular components with free-living ciliates. However, how the parasites coordinate exocytosis with host interaction is unknown. Here, we performed a Tetrahymena-based transcriptomic screen to uncover novel exocytic factors in Ciliata and conserved in Apicomplexa. We identified membrane-bound proteins, named CRMPs, forming part of a large complex essential for rhoptry secretion and invasion in Toxoplasma. Using cutting-edge imaging tools, including expansion microscopy and cryo-electron tomography, we show that, unlike previously described rhoptry exocytic factors, TgCRMPs are not required for the assembly of the rhoptry secretion machinery and only transiently associate with the exocytic site-prior to the invasion. CRMPs and their partners contain putative host cell-binding domains, and CRMPa shares similarities with GPCR proteins. Collectively our data imply that the CRMP complex acts as a host-molecular sensor to ensure that rhoptry exocytosis occurs when the parasite contacts the host cell.
Collapse
Affiliation(s)
- Daniela Sparvoli
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | - Jason Delabre
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | | | - Shrawan Kumar Mageswaran
- Department of Biochemistry and Biophysics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lev M Tsypin
- Department of Molecular Genetics and Cell BiologyUniversity of ChicagoChicagoILUSA
- Present address:
Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Justine Heckendorn
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | - Liam Theveny
- Department of Biochemistry and Biophysics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Marjorie Maynadier
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | - Marta Mendonça Cova
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | - Laurence Berry‐Sterkers
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | - Amandine Guérin
- Department of Pathobiology, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Jean‐François Dubremetz
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| | - Serge Urbach
- IGFUniversité de Montpellier, CNRS, INSERMMontpellierFrance
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell BiologyUniversity of ChicagoChicagoILUSA
| | - Yi‐Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Maryse Lebrun
- Laboratory of Pathogen Host InteractionsUMR 5235 CNRS, Université de MontpellierMontpellierFrance
| |
Collapse
|
94
|
Oliveira Souza RO, Jacobs KN, Back PS, Bradley PJ, Arrizabalaga G. IMC10 and LMF1 mediate mitochondrial morphology through mitochondrion-pellicle contact sites in Toxoplasma gondii. J Cell Sci 2022; 135:279336. [PMID: 36314270 PMCID: PMC9845740 DOI: 10.1242/jcs.260083] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022] Open
Abstract
The single mitochondrion of Toxoplasma gondii is highly dynamic, being predominantly in a peripherally distributed lasso-shape in intracellular parasites and collapsed in extracellular parasites. The peripheral positioning of the mitochondrion is associated with apparent contacts between the mitochondrion membrane and the parasite pellicle. The outer mitochondrial membrane-associated protein LMF1 is critical for the correct positioning of the mitochondrion. Intracellular parasites lacking LMF1 fail to form the lasso-shaped mitochondrion. To identify other proteins that tether the mitochondrion of the parasite to the pellicle, we performed a yeast two-hybrid screen for LMF1 interactors. We identified 70 putative interactors localized in different cellular compartments, such as the apical end of the parasite, mitochondrial membrane and the inner membrane complex (IMC), including with the pellicle protein IMC10. Using protein-protein interaction assays, we confirmed the interaction of LMF1 with IMC10. Conditional knockdown of IMC10 does not affect parasite viability but severely affects mitochondrial morphology in intracellular parasites and mitochondrial distribution to the daughter cells during division. In effect, IMC10 knockdown phenocopies disruption of LMF1, suggesting that these two proteins define a novel membrane tether between the mitochondrion and the IMC in Toxoplasma. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
| | - Kylie N. Jacobs
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Peter S. Back
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Peter J. Bradley
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Gustavo Arrizabalaga
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA,Author for correspondence ()
| |
Collapse
|
95
|
Essential Functions of Calmodulin and Identification of Its Proximal Interacting Proteins in Tachyzoite-Stage Toxoplasma gondii via BioID Technology. Microbiol Spectr 2022; 10:e0136322. [PMID: 36214684 PMCID: PMC9602672 DOI: 10.1128/spectrum.01363-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Toxoplasma gondii (T. gondii) is a pathogen belonging to the apicomplexan phylum, and it threatens human and animal health. Calcium ions, a critical second messenger in cells, can regulate important biological processes, including parasite invasion and egress. Calmodulin (CaM) is a small, highly conserved, Ca2+-binding protein found in all eukaryotic cells. After binding to Ca2+, CaM can be activated to interact with various proteins. However, little is known about CaM's function and its interacting proteins in T. gondii. In this study, we successfully knocked down CaM in the T. gondii parent strain TATI using a tetracycline-off system with the Toxoplasma CaM promoter. The results indicated that CaM was required for tachyzoite proliferation, invasion, and egress and that CaM depletion resulted in apicoplast loss, thus threatening parasite survival in the next lytic cycle. In the tachyzoite stage, CaM loss caused significant anomalies in the parasite's basal constriction, motility, and parasite rosette-like arrangement in the parasitophorous vacuole (PV). These phenotypic defects caused by CaM depletion indicate the importance of CaM in T. gondii. Therefore, it is important to identify the CaM-interacting proteins in T. gondii. Applying BioID technology, more than 300 CaM's proximal interacting proteins were identified from T. gondii. These CaM partners were broadly distributed throughout the parasite. Furthermore, the protein interactome and transcriptome analyses indicated the potential role of CaM in ion binding, cation binding, metal ion binding, calcium ion binding, and oxidation-reduction. Our findings shed light on the CaM function and CaM-interactome in T. gondii and other eukaryotes. IMPORTANCE Toxoplasma gondii is an intracellular pathogen that threatens human and animal health. This unicellular parasite is active in many biological processes, such as egress and invasion. The implementation efficiency of T. gondii biological processes is dependent on signal transmission. Ca2+, as a second messenger, is essential for the parasite's life cycle. Calmodulin, a ubiquitous Ca2+ receptor protein, is highly conserved and mediates numerous Ca2+-dependent events in eukaryotes. Few CaM functions or regulated partners have been characterized in T. gondii tachyzoites. Here, we reported the essential functions of calmodulin in T. gondii tachyzoite and the identification of its interacting partners using BioID technology, shedding light on the CaM function and CaM-interactome in Toxoplasma gondii and other eukaryotes.
Collapse
|
96
|
Zhai B, Xie S, Peng J, Qiu Y, Liu Y, Zhu X, He J, Zhang J. Glycosylation Analysis of Feline Small Intestine Following Toxoplasma gondii Infection. Animals (Basel) 2022; 12:ani12202858. [PMID: 36290246 PMCID: PMC9597833 DOI: 10.3390/ani12202858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Toxoplasma gondii has a serious impact on public health and the economic development of animal husbandry. Glycosylation, especially N-glycosylation, the pattern modification of proteins, is closely related to the biological functions of proteins, and our study used it to analyze glycosylation alterations in the small intestine of cats infected with T. gondii. The results of the present study showed that 56 glycosylated peptides were upregulated and 37 glycosylated peptides were downregulated. Additionally, we also identified eight N-glycosylated proteins of T. gondii including eight N-glycopeptides and eight N-glycosylation sites. Moreover, the protein eEF2 and its corresponding peptide sequence were identified, with GO terms (i.e., cellular process and metabolic process, cell and cell part, and catalytic activity) that were significantly enriched in the T. gondii MAPK pathway. In addition, the Clusters of Orthologous Groups of proteins (COG) function prediction results showed that posttranslational modification, protein turnover, and chaperones (11%) had the highest enrichment for T. gondii. The host proteins ICAM-1 and PPT1 and the endoplasmic reticulum stress pathway may play an important role in the glycosylation of T. gondii-infected hosts. Our study may provide a new target for T. gondii detection to prevent the spread of T. gondii oocysts in the future. Abstract Toxoplasma gondii (T. gondii) is responsible for severe human and livestock diseases, huge economic losses, and adversely affects the health of the public and the development of animal husbandry. Glycosylation is a common posttranslational modification of proteins in eukaryotes, and N-glycosylation is closely related to the biological functions of proteins. However, glycosylation alterations in the feline small intestine following T. gondii infection have not been reported. In this study, the experimental group was intragastrically challenged with 600 brain cysts of the Prugniuad (Pru) strain that were collected from infected mice. The cats’ intestinal epithelial tissues were harvested at 10 days post-infection and then sent for protein glycosylation analysis. High-performance liquid chromatography coupled to tandem mass spectrometry was used to analyze the glycosylation alterations in the small intestine of cats infected with T. gondii. The results of the present study showed that 56 glycosylated peptides were upregulated and 37 glycosylated peptides were downregulated in the feline small intestine infected by T. gondii. Additionally, we also identified eight N-glycosylated proteins of T. gondii including eight N-glycopeptides and eight N-glycosylation sites. The protein A0A086JND6_TOXGO (eEF2) and its corresponding peptide sequence were identified in T. gondii infection. Some special GO terms (i.e., cellular process and metabolic process, cell and cell part, and catalytic activity) were significantly enriched, and the Clusters of Orthologous Groups of proteins (COG) function prediction results showed that posttranslational modification, protein turnover, and chaperones (11%) had the highest enrichment for T. gondii. Interestingly, eEF2, a protein of T. gondii, is also involved in the significantly enriched T. gondii MAPK pathway. The host proteins ICAM-1 and PPT1 and the endoplasmic reticulum stress pathway may play an important role in the glycosylation of Toxoplasma-infected hosts. This is the first report showing that T. gondii oocysts can undergo N-glycosylation in the definitive host and that eEF2 is involved, which may provide a new target for T. gondii detection to prevent the spread of T. gondii oocysts in the future.
Collapse
Affiliation(s)
- Bintao Zhai
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou 730050, China
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Shichen Xie
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Junjie Peng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yanhua Qiu
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou 730050, China
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Yang Liu
- College of Life Science, Ningxia University, Yinchuan 750021, China
| | - Xingquan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Junjun He
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (J.H.); (J.Z.)
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou 730050, China
- Correspondence: (J.H.); (J.Z.)
| |
Collapse
|
97
|
Roumégous C, Abou Hammoud A, Fuster D, Dupuy JW, Blancard C, Salin B, Robinson DR, Renesto P, Tardieux I, Frénal K. Identification of new components of the basal pole of Toxoplasma gondii provides novel insights into its molecular organization and functions. Front Cell Infect Microbiol 2022; 12:1010038. [PMID: 36310866 PMCID: PMC9613666 DOI: 10.3389/fcimb.2022.1010038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The Toxoplasma gondii tachyzoite is a singled-cell obligate intracellular parasite responsible for the acute phase of toxoplasmosis. This polarized cell exhibits an apical complex, a hallmark of the phylum Apicomplexa, essential for motility, invasion, and egress from the host cell. Located on the opposite end of the cell is the basal complex, an elaborated cytoskeletal structure that also plays critical roles in the lytic cycle of the parasite, being involved in motility, cell division, constriction and cytokinesis, as well as intravacuolar cell-cell communication. Nevertheless, only a few proteins of this structure have been described and functionally assessed. In this study, we used spatial proteomics to identify new basal complex components (BCC), and in situ imaging, including ultrastructure expansion microscopy, to position them. We thus confirmed the localization of nine BCCs out of the 12 selected candidates and assigned them to different sub-compartments of the basal complex, including two new domains located above the basal ring and below the posterior cup. Their functional investigation revealed that none of these BCCs are essential for parasite growth in vitro. However, one BCC is critical for constricting of the basal complex, likely through direct interaction with the class VI myosin heavy chain J (MyoJ), and for gliding motility. Four other BCCs, including a phosphatase and a guanylate-binding protein, are involved in the formation and/or maintenance of the intravacuolar parasite connection, which is required for the rosette organization and synchronicity of cell division.
Collapse
Affiliation(s)
- Chloé Roumégous
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Aya Abou Hammoud
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Damien Fuster
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | | | - Corinne Blancard
- Univ. Bordeaux, CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, Bordeaux, France
| | - Bénédicte Salin
- Univ. Bordeaux, CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, Bordeaux, France
| | - Derrick R. Robinson
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Patricia Renesto
- IAB, Team Biomechanics of Host-Apicomplexa Parasite, INSERM U1209, CNRS UMR5309, Grenoble Alpes University, Grenoble, France
| | - Isabelle Tardieux
- IAB, Team Biomechanics of Host-Apicomplexa Parasite, INSERM U1209, CNRS UMR5309, Grenoble Alpes University, Grenoble, France
| | - Karine Frénal
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- *Correspondence: Karine Frénal,
| |
Collapse
|
98
|
Crook OM, Davies CTR, Breckels LM, Christopher JA, Gatto L, Kirk PDW, Lilley KS. Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Nat Commun 2022; 13:5948. [PMID: 36216816 PMCID: PMC9550814 DOI: 10.1038/s41467-022-33570-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
The steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different subcellular niches upon perturbation of the subcellular environment. Differential localisation, that is a change in the steady-state subcellular location of a protein, provides a step towards mechanistic insight of subcellular protein dynamics. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we describe a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to several datasets recovers well-studied translocations. In an application to cytomegalovirus infection, we obtain insights into the rewiring of the host proteome. Integration of other high-throughput datasets allows us to provide the functional context of these data.
Collapse
Affiliation(s)
- Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK.
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
| | - Colin T R Davies
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Laurent Gatto
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium
| | - Paul D W Kirk
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
| |
Collapse
|
99
|
Dass S, Mather MW, Morrisey JM, Ling L, Vaidya AB, Ke H. Transcriptional changes in Plasmodium falciparum upon conditional knock down of mitochondrial ribosomal proteins RSM22 and L23. PLoS One 2022; 17:e0274993. [PMID: 36201550 PMCID: PMC9536634 DOI: 10.1371/journal.pone.0274993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022] Open
Abstract
The mitochondrion of malaria parasites is an attractive antimalarial drug target, which require mitoribosomes to translate genes encoded in the mitochondrial (mt) DNA. Plasmodium mitoribosomes are composed of highly fragmented ribosomal RNA (rRNA) encoded in the mtDNA. All mitoribosomal proteins (MRPs) and other assembly factors are encoded in the nuclear genome. Here, we have studied one putative assembly factor, RSM22 (Pf3D7_1027200) and one large subunit (LSU) MRP, L23 (Pf3D7_1239100) in Plasmodium falciparum. We show that both proteins localize to the mitochondrion. Conditional knock down (KD) of PfRSM22 or PfMRPL23 leads to reduced cytochrome bc1 complex activity and increased sensitivity to bc1 inhibitors such as atovaquone and ELQ-300. Using RNA sequencing as a tool, we reveal the transcriptomic changes of nuclear and mitochondrial genomes upon KD of these two proteins. In the early phase of KD, while most mt rRNAs and transcripts of putative MRPs were downregulated in the absence of PfRSM22, many mt rRNAs and several MRPs were upregulated after KD of PfMRPL23. The contrast effects in the early phase of KD likely suggests non-redundant roles of PfRSM22 and PfMRPL23 in the assembly of P. falciparum mitoribosomes. At the late time points of KD, loss of PfRSM22 and PfMRPL23 caused defects in many essential metabolic pathways and transcripts related to essential mitochondrial functions, leading to parasite death. In addition, we enlist mitochondrial proteins of unknown function that are likely novel Plasmodium MRPs based on their structural similarity to known MRPs as well as their expression profiles in KD parasites.
Collapse
Affiliation(s)
- Swati Dass
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Mather
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joanne M. Morrisey
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Liqin Ling
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Akhil B. Vaidya
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hangjun Ke
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
100
|
Liu S, Storti M, Finazzi G, Bowler C, Dorrell RG. A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum. FRONTIERS IN PLANT SCIENCE 2022; 13:950467. [PMID: 36212359 PMCID: PMC9546453 DOI: 10.3389/fpls.2022.950467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.
Collapse
Affiliation(s)
- Shun Liu
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Mattia Storti
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| |
Collapse
|