bims-toxgon Biomed News
on Toxoplasma gondii metabolism
Issue of 2025–11–09
fourteen papers selected by
Lakesh Kumar, BITS Pilani
  1. Toxoplasma gondii chromatin remodeler SWI/SNF controls parasite division and gene expression.
  2. Trem2 prevents adverse pregnancy outcomes induced by Toxoplasma gondii by promoting PPARγ-mediated P-STAT6 signaling.
  3. Kinetic Analysis of HDAC- and Sirtuin-Mediated Deacylation on Chemically Defined Histones and Nucleosomes.
  4. Function and therapeutic potential of transketolase enzymes in parasitic protists.
  5. Structural and functional characterization of TgGSK3, a druggable kinase in Toxoplasma gondii.
  6. A Single-Cell Methodology for Energy Metabolism Analysis in Parasitic Protozoa.
  7. Cysteine S-acetylation is a widespread post-translational modification on metabolic proteins.
  8. Hepatitis E Virus and Toxoplasma Gondii in Wild Boars from Southern Kyushu, Japan.
  9. Substrate-Guided Development of HDAC11-Selective Inhibitors Featuring α‑Amino Amide Zinc-Binding Groups.
  10. A Rapid Method for Purifying Intact Trypanosoma cruzi Amastigotes from Host Cells, In Vitro and In Vivo, for Downstream 'Omic Analysis.
  11. Machine learning-driven prediction of substrates for enzymes introducing or removing protein post-translational modifications.
  12. Mechanistic basis for protein conjugation in a diverged bacterial ubiquitination pathway.
  13. Regulation of RNA-binding proteins by small biomolecules.
  14. ptmK: A computationally efficient toolkit for high-throughput lysine PTM modeling in proteins.
  1. Nat Commun. 2025 Nov 05. 16(1): 9777
    Toxoplasma gondii chromatin remodeler SWI/SNF controls parasite division and gene expression.
    Dandan Hu, Xuan Li, Jiayi Huang, Xueqin Zou, Hongbin Si, Xun Suo, Xingju Song.
      Toxoplasma gondii is a zoonotic apicomplexan parasite that relies on highly orchestrated gene expression programs to coordinate its cell cycle progression. Although epigenetic mechanisms are recognized as pivotal drivers of developmental gene regulation in parasitic life cycles, the contributions of chromatin remodeling complexes to these processes remain largely unexplored. In this study, we focus on two core ATPase subunits of the SWI/SNF chromatin remodeling complex and investigate their roles in parasite biology and gene regulation. Our findings reveal that these SWI/SNF ATPases work coordinately, occupying the promoters of many tachyzoite-specific genes. Their deletion causes diminished chromatin accessibility and transcriptional reprogramming, downregulating tachyzoite-specific genes and unlocking certain transcripts normally confined to merozoite stage. Loss of these genes severely impairs parasite fitness and causes division defects, with incomplete endopolygeny accompanied by starch accumulation. TgSNF2b also interacts with the MORC remodeler to modulate chromatin architecture and gene expression. These findings provide new insights into the epigenetic regulation of gene expression and cell division in T. gondii and open new avenues for innovative strategies in toxoplasmosis control.
    DOI:  https://doi.org/10.1038/s41467-025-64751-x
  2. Int Immunopharmacol. 2025 Oct 31. pii: S1567-5769(25)01727-8. [Epub ahead of print]168(Pt 1): 115739
    Trem2 prevents adverse pregnancy outcomes induced by Toxoplasma gondii by promoting PPARγ-mediated P-STAT6 signaling.
    Yining Cao, Xinyue Wang, Zhiqing Zhang, Mingyan Shi, Tian Ming, Mei Yang, Jinling Chen.
      Decidual macrophages (DMs), required for the maintenance of a successful pregnancy, are vital target cells for Toxoplasma gondii (T. gondii) during adverse pregnancy induced by T. gondii. Triggering receptor expressed on myeloid cells 2 (Trem2) is a functional immune receptor on the surface of DMs, governing cell survival and phagocytosis. Our previous study demonstrated that Trem2 deficiency aggravates T. gondii-induced APOs. However, Trem2-related downstream signaling pathways in T. gondii-induced APOs remain unclear. Here, we demonstrated a significant decrease in PPARγ and phosphorylated-STAT6 (P-STAT6) in mouse placentas following T. gondii infection. Following knockout of the Trem2 gene, we found that T. gondii infection cannot regulate the expression of downstream signaling pathways on macrophages. Hence, Trem2 deficiency did not alter the expressions of P-STAT6 and PPARγ in infected mouse placentas, peritoneal macrophages, and bone marrow-derived macrophages (BMDMs). Consistently, overexpression of Trem2 in macrophages significantly activated the downstream signaling pathway and partially reversed the inhibitory effects of T. gondii antigens on P-STAT6 and PPARγ, similar to the effect of PPARγ agonists. Altogether, Trem2 is required for T. gondii to exert effects on P-STAT6/PPARγ in APOs. Our novel findings concerning Trem2 and its downstream PPARγ-mediated P-STAT6 signaling pathways might provide new preventive and therapeutic targets for toxoplasmosis.
    Keywords:  PPARγ; STAT6; Toxoplasma gondii; Trem2; adverse pregnancy outcome; decidual macrophage
    DOI:  https://doi.org/10.1016/j.intimp.2025.115739
  3. Curr Protoc. 2025 Nov;5(11): e70251
    Kinetic Analysis of HDAC- and Sirtuin-Mediated Deacylation on Chemically Defined Histones and Nucleosomes.
    Zhuoyi L Niu, Ling Zhang, Yuan-Fei Zhou, Zhipeng A Wang.
      Histone deacetylases (HDACs) and sirtuins (SIRTs) play essential roles in regulating chromatin structure and gene expression by catalyzing the removal of acyl groups from histone lysine residues. Accurate characterization of their deacetylation kinetics is critical for understanding their enzymatic mechanisms and for guiding inhibitor or activator development. Given the complexity of enzyme-nucleosome core particle (NCP) interactions, including the influence of histone composition, post-translational modifications, and DNA context, NCP-based assays provide a more physiologically relevant platform than those performed on peptide or free histone substrates. Here, we present optimized protocols for assessing HDAC and SIRT deacetylation kinetics using NCP substrates, including determination of Michaelis-Menten parameters, evaluation of inhibitor and activator potency (IC50 or EC50), and instructions for ensuring assay reproducibility. These methods enable robust comparison of small-molecule modulators under conditions that better mimic the native chromatin environment, supporting both mechanistic studies and drug discovery efforts. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assay of HDAC complex or SIRT deacylation on nucleosome substrates Basic Protocol 2: Assay of HDAC complex or SIRT deacylation on free histone proteins Basic Protocol 3: KM measurement for deacylation assay on nucleosome or cofactor Basic Protocol 4: Assessment of deacylation inhibitor or activator effects on NCP substrates.
    Keywords:  HDAC; deacylation; histone protein; inhibitor; nucleosome core particle; sirtuin
    DOI:  https://doi.org/10.1002/cpz1.70251
  4. Methods Enzymol. 2025 ;pii: S0076-6879(25)00290-3. [Epub ahead of print]722 97-115
    Function and therapeutic potential of transketolase enzymes in parasitic protists.
    Ningbo Xia, Nishith Gupta.
      Transketolase (TKT), the rate-limiting enzyme in the non-oxidative branch of the pentose phosphate pathway (PPP), catalyzes the reversible transfer of glycolaldehyde moieties between sugar phosphates. Here, we present wide-ranging methods to study TKT function in a clinically-relevant and globally-prevalent model intracellular pathogen, Toxoplasma gondii. The experimental framework utilizes heterologous expression of recombinant TgTKT proteins in a bacterial system, anti-TgTKT antibody production, CRISPR/Cas9-assisted genome editing to generate TgTKT-null mutants, and in-depth phenotyping, including 13C-based metabolomic analysis to determine the carbon flux in the acutely-infectious tachyzoite stage of T. gondii. The phenotypic studies comprise the parasite proliferation in vitro and virulence assessment in a murine model of acute toxoplasmosis. The data suggest TgTKT as a metabolic rheostat regulating nucleotide biosynthesis and enabling adaptation of this highly promiscuous parasite in different nutritional environments. Last but not least, the work presents the therapeutic potential of the TgTKT-null mutant as a metabolically-attenuated vaccine, highlights the evolutionary divergence of TgTKT proteins, and provides a robust foundation to investigate TgTKT orthologs in other pathogenic protozoan organisms.
    Keywords:  D-Erythrose-4-phosphate; D-Fructose-6-phosphate; D-Glyceraldehyde-3-phosphate; D-Ribose-5-phosphate; D-Xylulose-5-phosphate; D-sedoheptulose-7-phosphate; Glycolysis; Nucleotide biosynthesis; Pentose phosphate pathway; Plasmodium; TCA cycle; Toxoplasma
    DOI:  https://doi.org/10.1016/bs.mie.2025.07.010
  5. Nat Commun. 2025 Nov 05. 16(1): 9765
    Structural and functional characterization of TgGSK3, a druggable kinase in Toxoplasma gondii.
    Silvia Diaz-Martin, Christopher Swale, Valeria Bellini, Irina Dobrescu, Janine Wenker, Marie-Pierre Brenier-Pinchart, Laurence Braun, Alwéna Tollec, Charlotte Corrao, Yohann Couté, Caroline Mas, Fabrice Laurent, Matthew Bowler, Mohamed-Ali Hakimi, Alexandre Bougdour.
      Toxoplasma gondii and Cryptosporidium species are apicomplexan parasites of significant medical and veterinary importance. Although current therapeutic options for toxoplasmosis and cryptosporidiosis demonstrate notable efficacy, their clinical efficacy is often limited by suboptimal efficacy and frequent adverse effects. Moreover, therapeutic alternatives remain limited or nonexistent, particularly for cryptosporidiosis, for which nitazoxanide is currently the only approved medication to treat diarrhea in adults and children older than 1 year of age. To identify alternative therapeutic options for addressing these health challenges, we performed a phenotypic screening of an FDA-approved drug repurposing library against Toxoplasma. This screening identifies LY2090314 as a potent inhibitor of T. gondii and Cryptosporidium growth in mammalian cells. Through a target deconvolution strategy combining forward genetics, transcriptome sequencing, and computational mutation analysis, we elucidate the parasiticidal mechanism of LY2090314 and demonstrate that TgGSK3 kinase is its primary molecular target. We also report the first X-ray crystal structure of LY2090314 bound to TgGSK3, resolved at 2.1 Å, which reveals an interaction mode characteristic of type I ATP-competitive inhibitors. Furthermore, interactome analysis uncovers functional connections between TgGSK3 and key cytoskeletal and signaling regulators, providing insights into compound's effects. Collectively, these findings validate TgGSK3 as a promising therapeutic target for toxoplasmosis and offer mechanistic insights into apicomplexan GSK3 biology.
    DOI:  https://doi.org/10.1038/s41467-025-64701-7
  6. Methods Mol Biol. 2026 ;2982 339-351
    A Single-Cell Methodology for Energy Metabolism Analysis in Parasitic Protozoa.
    Salomé C Vilchez-Larrea, Rafael J Argüello, Guillermo D Alonso.
      The metabolic adaptability of Trypanosoma cruzi, the causative agent of Chagas disease, and other trypanosomatids across their life cycle stages is a defining feature of their biology and pathogenicity. Studying parasite and host cell metabolic profiles during infections is crucial to understanding disease progression and developing targeted therapeutic interventions. Traditionally, researchers have faced limitations in effectively capturing the dynamic nature of metabolic shifts in real time, hindering our ability to unravel the complex interplay between the host and the pathogen. Approaching these questions requires a high-throughput technique capable of assessing the metabolic changes and preferences of both the parasite and the host cell under physiological conditions in infected cells and tissues. A novel analytical technique that promises to push forward our understanding of metabolic profiles during Trypanosoma cruzi infections has now been developed. Here, we describe the potential to exploit the Single-Cell Energetic Metabolism by Profiling Translation Inhibition (SCENITH™) to examine the energetic metabolism of T. cruzi during its distinct developmental stages-epimastigote, trypomastigote, and amastigote-allowing to unveil the metabolic shifts that underpin their survival and proliferation in diverse host environments. Additionally, SCENITH allows to study how infected host cells' metabolism changes in the presence of parasites. The variability in metabolic pathways offers a unique perspective for identifying and developing stage-specific drug targets, presenting opportunities for more effective therapeutic interventions.
    Keywords:  Flow Cytometry; Host–Parasite interaction; Metabolic profile; SCENITH; Trypanosoma cruzi
    DOI:  https://doi.org/10.1007/978-1-0716-4848-3_22
  7. NPJ Metab Health Dis. 2025 Nov 07. 3(1): 43
    Cysteine S-acetylation is a widespread post-translational modification on metabolic proteins.
    E Keith Keenan, Akshay Bareja, Yannie Lam, Paul A Grimsrud, Matthew D Hirschey.
      Protein acetylation is a fundamental regulatory mechanism occurring primarily on lysine amino acids. Here we report systematic in vivo characterization of cysteine S-acetylation as a widespread post-translational modification in mammalian tissues. By developing specialized sample preparation methods that preserve the labile thioester bond, we identified over 400 sites of cysteine acetylation in mouse liver, mirroring the abundance of lysine acetylation. Proteomic surveys across nine murine tissues revealed tissue-specific acetylation patterns that are enriched on metabolic enzymes in the cytoplasm. Cold exposure in mice triggers coordinated remodeling of the brown adipose tissue cysteine acetylome. Functional studies demonstrate that the acetylation of GAPDH Cys150 abolishes catalytic activity and correlates with nuclear enrichment, paralleling the known effects of S-nitrosylation on this enzyme. These findings establish cysteine acetylation as a widespread modification of metabolic proteins that responds to changes in cellular acetyl-CoA availability, fundamentally expanding the landscape of protein acetylation beyond lysine.
    DOI:  https://doi.org/10.1038/s44324-025-00081-2
  8. Ecohealth. 2025 Nov 02.
    Hepatitis E Virus and Toxoplasma Gondii in Wild Boars from Southern Kyushu, Japan.
    Hirano Shinji, Ijiri Moe, Fujimoto Yoshikazu, Matsuu Aya.
      This study investigated the seroprevalence of zoonotic hepatitis E virus and Toxoplasma gondii (T. gondii) in wild boars from southern Kyushu, Japan, from 2014 to 2021, including increased hunting until 2015. The seroprevalence was 16.38% for hepatitis E virus (n = 116; 95% CI 10.74-24.17) and 12.40% for T. gondii (n = 130; 95% CI 7.78-19.20). A decreasing trend for hepatitis E virus was observed (P = 0.05777). As the first study on wild boars in southern Kyushu, it provides insights into hepatitis E virus and T. gondii epidemiology, suggesting that managing boar density could help control diseases.
    Keywords:   Toxoplasma gondii ; Epidemiology; Hepatitis E virus; Japan; Seroprevalence; Wild boar
    DOI:  https://doi.org/10.1007/s10393-025-01765-3
  9. ACS Omega. 2025 Oct 28. 10(42): 50577-50587
    Substrate-Guided Development of HDAC11-Selective Inhibitors Featuring α‑Amino Amide Zinc-Binding Groups.
    Sebastian Hilscher, Marat Meleshin, Fady Baselious, Cyril Barinka, Wolfgang Sippl, Mike Schutkowski, Cordelia Schiene-Fischer.
      Histone deacetylases (HDACs) play a pivotal role in various biological pathways and represent interesting drug targets. Therefore, HDAC inhibitors (HDACi) with high isoform selectivity and a zinc-binding group different from hydroxamic acid, because of its low metabolic stability, are required. HDAC11, as a highly potent defatty-acylase, differs from other HDACs in its substrate preference. Starting from this finding, we developed specific inhibitors for HDAC11 based on a peptide containing a fatty-acylated lysine side chain as the selectivity tail. The introduction of different heteroatoms at the fatty acyl residue was used to generate potent zinc-binding groups in combination with the scissile amide bond, as well as to suppress substrate properties of the resulting compounds. Further optimization resulted in a highly potent and selective HDAC11 inhibitor 31, which exhibits low nanomolar inhibition against HDAC11 without targeting other HDACs and is active in cells. The data presented here may help expand the range of zinc-binding groups utilized in HDAC inhibitors. Furthermore, the concept of the selectivity tail was demonstrated to facilitate straightforward access to selective defatty-acylase inhibitors.
    DOI:  https://doi.org/10.1021/acsomega.5c08195
  10. Methods Mol Biol. 2026 ;2982 395-408
    A Rapid Method for Purifying Intact Trypanosoma cruzi Amastigotes from Host Cells, In Vitro and In Vivo, for Downstream 'Omic Analysis.
    Francisco Olmo, Shiromani Jayawardhana, Richard L Atherton, John M Kelly.
      Amastigotes are the replicative intracellular life cycle stage of the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease. They have the ability to proliferate in any nucleated mammalian cell. A greater understanding of amastigote biology would greatly aid drug development since this life cycle stage is the principal target of chemotherapy. Reports have linked recrudescence following drug treatment with the possible existence of a quiescent amastigote phenotype. However, the lack of a rapid and straightforward method for isolating amastigotes from infected host cells has limited research progress in this area. This is particularly the case with omics technology, where the current complex fractionation and purification procedures can act to perturb RNA and protein expression. Here, we outline a methodology that largely overcomes these problems. Our protocol exploits MP Bio-Lysing Matrix M tubes to promote the differential lysis of host cells and the release of intact amastigotes in a 1-min time frame. Immediate treatment of the lysate with CellCover reagent then maintains RNA and protein in their native states. Amastigotes stabilized in this way can undergo further manipulations, such as cell sorting, without modification of their proteome or transcriptome profiles. This methodology, which is flexible and widely applicable, should greatly benefit research into the intracellular life cycle of T. cruzi.
    Keywords:  Amastigotes; Chagas disease; Life cycle; Rapid purification; Trypanosoma cruzi
    DOI:  https://doi.org/10.1007/978-1-0716-4848-3_26
  11. Commun Chem. 2025 Nov 07. 8(1): 340
    Machine learning-driven prediction of substrates for enzymes introducing or removing protein post-translational modifications.
    Nashira H Ridgeway, Anand Chopra, Valentina Lukinović, Michal Feldman, François Charih, Dan Levy, James R Green, Kyle K Biggar.
      The exploration of post-translational modifications (PTMs) within the proteome is pivotal for advancing our understanding of disease and the function of cancer therapeutics. However, identifying genuine sites of PTMs introduced or removed by an enzyme of interest amid numerous candidates is challenging. We present a machine learning (ML)-driven search method, which combines ML with enzyme-mediated modification of complex peptide arrays to predict unexplored PTM sites for an enzyme of interest. Experimental validation confirmed that this approach correctly predicted 37-43% of proposed PTM sites, unveiling candidate sites of the methyltransferase SET8 and the deacetylases SIRT1-7. Our approach marks an important performance increase over traditional in vitro methods across separate enzyme classes. Mass spectrometry analysis confirmed the dynamic methylation status of several predicted SET8 substrates, and the deacetylation of 64 unique sites identified for SIRT2. This method has also revealed changes in SET8-regulated substrate network among breast cancer missense mutations, collectively revealing insight into differential enzyme function in disease. By disentangling the substrate features that dictate PTM-inducing enzyme specificity, this approach demonstrates potential in uncovering enzyme-substrate networks within PTM pathways.
    DOI:  https://doi.org/10.1038/s42004-025-01717-6
  12. Nat Struct Mol Biol. 2025 Nov 03.
    Mechanistic basis for protein conjugation in a diverged bacterial ubiquitination pathway.
    Qiaozhen Ye, Minheng Gong, Jiaxi Cai, Lydia R Chambers, Huilin Zhou, Raymond T Suhandynata, Kevin D Corbett.
      Ubiquitination is a fundamental eukaryotic protein post-translational modification pathway, in which ubiquitin or a ubiquitin-like protein (Ubl) is typically conjugated to a lysine of a target protein. Ubiquitination is initiated by adenylation of the Ubl C terminus, followed by sequential formation of Ubl-cysteine thioester intermediates with E1, E2 and (optionally) E3 proteins before formation of the final Ubl-lysine isopeptide linkage. Recent work has revealed two ubiquitination-related bacterial pathways in the context of antiphage immunity. Bioinformatics analyses have hinted at the existence of additional uncharacterized bacterial pathways that include ubiquitination-like machinery. Here, we describe the architecture and biochemical mechanisms of an alternative Bub (bacterial ubiquitination-like) pathway, revealing structural parallels and mechanistic differences when compared to other ubiquitination pathways. We show that Bub operons encode functional E1, E2 and Ubl proteins that are related to their eukaryotic counterparts but likely function through oxyester rather than thioester intermediates. We also identify an enzyme family in Bub operons with a conserved catalytic site and a role in Ubl-target conjugation. The genomic context of Bub operons suggests that they also function in antiphage immunity and we present evidence that one Bub pathway may regulate translation in response to stress. Overall, our results reveal an uncharacterized family of bacterial ubiquitination-related pathways with a distinctive biochemical mechanism.
    DOI:  https://doi.org/10.1038/s41594-025-01696-1
  13. Nat Rev Mol Cell Biol. 2025 Nov 06.
    Regulation of RNA-binding proteins by small biomolecules.
    Weili Miao, Douglas F Porter, Vanessa Lopez-Pajares, Paul A Khavari.
      RNA-binding proteins (RBPs) are essential for post-transcriptional gene regulation, including for RNA modification such as N6-methyladenosine (m6A), splicing, polyadenylation, localization, translation and decay. Dysregulation of RBPs has been causally linked to a wide array of human diseases, including cancer, neurodegenerative diseases, metabolic disorders and tissue differentiation abnormalities. Although RBPs have traditionally been studied through their RNA, protein and post-translational interactions, growing evidence shows that small biomolecules (SBMs) such as sugars, nucleotides, metabolites such as S-adenosylmethionine (SAM) and NAD(P)H, and drugs can directly bind RBPs and modulate their structure, localization and RNA-binding activity. These context-dependent and concentration-dependent interactions link RBP regulation to cellular metabolism and are a key focus of current research. In this Review, we discuss the expanding landscape of SBM-binding RBPs and the functions of these RBPs in condensate formation, RNA localization, processing and translation. We highlight the molecular principles that underlie these interactions and their functional relevance to human diseases. We also examine recent advances in the identification of SBM-RBP interactions and the innovative methodologies that are driving discoveries in this rapidly advancing field. Together, these insights underscore the potential of SBMs to modulate RBPs and inform novel therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41580-025-00914-4
  14. Biophys J. 2025 Nov 01. pii: S0006-3495(25)00730-1. [Epub ahead of print]
    ptmK: A computationally efficient toolkit for high-throughput lysine PTM modeling in proteins.
    Chenjie Feng, Peng Zhang, Lei Bao, Yideng Jiang, Renmin Han.
      Lysine residues in proteins are frequently modified post-translationally, adding functional complexity to the proteome and playing critical roles in cellular regulation and disease. However, modeling these modifications in 3D protein structures remains challenging due to the limited availability of accessible and high-throughput computational tools. We present ptmK, a lightweight, standalone toolkit that enables rapid generation of lysine-modified protein structures with atomic precision. Without relying on complex infrastructure or external dependencies, ptmK supports more than 30 common lysine modifications and outputs all-atom structural models in PDB format (computationally generated). In addition to structure generation, ptmK also evaluates the modification likelihood of each lysine site based on solvent accessibility and proximity to functional regions. By integrating site evaluation with customizable modeling, ptmK enables scalable structural analysis and functional prioritization of lysine post-translational modifications.
    Keywords:  PTMs; lysine residues; modification probabilities; protein structures
    DOI:  https://doi.org/10.1016/j.bpj.2025.10.039
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