bims-toxgon 2025-11-02 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–11–02
eighteen papers selected by
Lakesh Kumar, BITS Pilani

Toxoplasma effector TgWIP hijacks dendritic cell actin and motility via Nck1/Grb2 and the WAVE complex.
A guide to the apicomplexan cell cycle: endodyogeny and schizogony.
GNAT family Pat2 is required for long-term survival on glycerol and catalyzes lysine acetylation of glycerol kinase in hypersaline-adapted archaea.
Establishing TurboID Proximity Labeling and mAID Conditional Knockdown System in Cryptosporidium parvum.
[Cloning and bioinformatics analysis of surface antigen-related sequence protein SRS67 and SRS20A genes in Toxoplasma gondii].
Upregulated small GTPase immunity-associated proteins confer resistance to Neospora caninum in rat and bovine cells.
Histone Deacetylases in Neurodegenerative Diseases and Their Potential Role as Therapeutic Targets: Shedding Light on Astrocytes.
Lead Structure-Based Hybridization Strategy Reveals Major Potency Enhancement of SirReal-Type Sirt2 Inhibitors.
NAD+-Dependent Lysine Acetylation Regulates Glucose Uptake and Fatty Acid Oxidation in Cardiomyocytes.
PfATP2 is a flippase on the Plasmodium falciparum surface that is important for growth and influences parasite sensitivity to antiplasmodial compounds.
Corrigendum to "Identification of Tri- and Tetracyclic Pyrimidinediones as Sirtuin Inhibitors".
Chemical propulsion of hemozoin crystal motion in malaria parasites.
Pre-established ATF4 occupancy and chromatin organization instruct selective transcription activation during integrated stress response.
A Novel Method to Silence Genes in Cryptosporidium.
In Vitro Culture of Cryptosporidium spp. Using Stem Cell-Derived Intestinal Epithelial Monolayers.
Impact of histone post-translational modification inhibitors on lifespan, reproduction, and stress response in the rotifer Brachionus manjavacas.
Role of Histone H3 Lysine 4 Methylation in Chromatin Biology.
Metabolic reprogramming as a key regulator in Helicobacter pylori-infected gastric cancer.

mBio. 2025 Oct 31. e0187425

Toxoplasma effector TgWIP hijacks dendritic cell actin and motility via Nck1/Grb2 and the WAVE complex.

Pavel Morales, Daniel A Kramer, Caroline de Moraes de Siqueira, Abbigale J Brown, Lamba Omar Sangaré, Baoyu Chen, Jeroen P J Saeij.

  The intracellular parasite Toxoplasma gondii enhances its dissemination to distant organs by hijacking infected leukocytes via a Trojan Horse mechanism. Upon infecting dendritic cells (DCs), Toxoplasma induces a hypermigratory phenotype characterized by podosome dissolution and formation of F-actin stress fibers. We previously showed that these cytoskeletal changes depend on the effector protein Toxoplasma WAVE complex-interacting protein (TgWIP) secreted from parasites to infected leukocytes. Here, we identify the host adaptor proteins non-catalytic region of tyrosine kinase adaptor protein 1 and 2 (Nck1/2) and growth factor receptor-bound protein 2 (Grb2) as direct TgWIP interactors. TgWIP mainly uses two distinct proline-rich regions (PRRs) to interact with Nck1 and Grb2. Mutating these PRRs abrogates TgWIP binding to Nck1 and Grb2 and diminishes podosome dissolution and DC hypermotility. Furthermore, we show that TgWIP directly interacts with the actin nucleation-promoting factor WAVE regulatory complex (WRC) via a WRC-interacting receptor sequence (WIRS). Disrupting this interaction also influences actin cytoskeletal remodeling and DC hypermotility. Collectively, our data reveal that TgWIP directly interacts with multiple actin regulators, including Nck1, Grb2, and the WRC, to remodel the actin cytoskeleton of the host cells, elucidating a key mechanism that Toxoplasma exploits to enhance host cell migration and dissemination.IMPORTANCEThe parasite Toxoplasma gondii spreads throughout the body by hijacking immune cells and boosting their motility. This ability depends on secreted parasite proteins that manipulate the host cell's actin cytoskeleton. One such effector, Toxoplasma gondii WAVE-interacting protein (TgWIP), induces dramatic changes in host cell shape and movement, but how it does this has remained unclear. Here, we show that TgWIP directly interacts with multiple host actin-regulatory proteins using distinct sequence motifs. Disrupting these interactions prevents cytoskeletal remodeling and impairs parasite-induced immune cell migration. Our study reveals that Toxoplasma uses defined motifs to co-opt host signaling hubs that control cell motility. Understanding how pathogens exploit the cytoskeleton not only sheds light on host-pathogen interactions but may also reveal broader principles of cell migration relevant to immunity, cancer, and development.

Keywords:  Grb2; Nck1; TgWIP effector; Toxoplasma gondii; WAVE regulatory complex; WIRS motif; actin cytoskeleton remodeling; cell motility; dendritic cell motility; podosome; proline-rich region

DOI:  https://doi.org/10.1128/mbio.01874-25
Trends Parasitol. 2025 Oct 31. pii: S1471-4922(25)00295-8. [Epub ahead of print]

A guide to the apicomplexan cell cycle: endodyogeny and schizogony.

Mrinalini Batra, Elena S Suvorova.

  This review focuses on recent advances in the field of cell division of eukaryotic pathogens of the phylum Apicomplexa, a group of pathogens known for their diverse modes of cell division. We cover two topics - an organization and a regulation of the apicomplexan cell cycles - using models of Toxoplasma gondii tachyzoites and Plasmodium falciparum merozoites of the red blood cell stage. The review emphasizes differences and similarities between the conventional cell cycle of the parasite's host cells and apicomplexan cell cycles, and between binary and multinuclear divisions of Apicomplexa. Although many factors play a role in cell cycle regulation, we concentrated on the central cell cycle regulators, cyclin-dependent kinase complexes.

Keywords:  Apicomplexa; Plasmodium; Toxoplasma gondii; cell cycle; endomitosis cyclin-dependent kinase

DOI:  https://doi.org/10.1016/j.pt.2025.10.005
mBio. 2025 Oct 27. e0251425

GNAT family Pat2 is required for long-term survival on glycerol and catalyzes lysine acetylation of glycerol kinase in hypersaline-adapted archaea.

Heather N Judd, Karol M Sanchez, Leah S Dublino, Gabriel J Zhang, David Yu, Daniel Gal, Ricardo L Couto-Rodríguez, Xin Wang, Julie A Maupin-Furlow.

  Lysine acetylation is a widespread post-translational modification that regulates key biological processes including metabolism and chromatin dynamics, yet its roles in archaea remain poorly understood. Here, we investigated two Gcn5-related N-acetyltransferase (GNAT) family homologs, pat1 and pat2, in the halophilic archaeon Haloferax volcanii (Hv). A ∆pat2 mutant exhibited premature cell death on glycerol, a phenotype not observed in the parent strain, ∆pat1 mutant, or on glucose. Complementation of the ∆pat2 mutant with plasmid-expressed pat2 restored survival on glycerol, confirming the essential role of pat2 in this process. In vitro assays revealed HvPat2 catalyzes lysine acetylation of glycerol kinase, HvGlpK, an enzyme required for growth on glycerol. Computational modeling predicted that HvPat2 residues E105, Y154, V110, and N147 may form hydrogen bonds with acetyl-CoA. To assess the importance of these residues, alanine substitutions were introduced. N147A and V110A complemented the ∆pat2 mutant for survival on glycerol but showed little or no activity in acetylating HvGlpK in vitro. E105A and Y154A had the most pronounced effects, failing to restore ∆pat2 survival on glycerol and showing no catalytic activity toward HvGlpK acetylation. Moreover, the Y154A variant co-purified with HVO_2384, a tandem CBS domain protein with a C-terminal ribosome hibernation factor domain, suggesting an additional regulatory interaction. These findings highlight the critical role of the GNAT HvPat2 in survival on glycerol, reveal its ability to acetylate a central glycerol metabolism enzyme in archaea, and offer mechanistic insight into GNAT family acetyltransferases.IMPORTANCEGNAT family homologs are widespread and diverse in their use of acyl-CoAs to acylate small molecules and proteins, functions difficult to predict based on in silico analysis alone. Here, we reveal a critical role for lysine acetylation in archaeal central carbon metabolism, identifying the GNAT family Pat2 of Haloferax volcanii as essential for long-term survival on glycerol (compared to glucose) and capable of mediating the lysine acetylation of glycerol kinase, a key enzyme in glycerol metabolism. Pat2 residues important for catalytic activity and a putative regulatory partner (HVO_2384) are also identified. The findings expand our understanding of GNAT family acyltransferases and highlight conserved mechanisms of metabolic control by post-translational modification across domains of life.

Keywords:  archaea; glycerol kinase; glycerol metabolism; halophiles; lysine acetylation; post-translational modification; regulation

DOI:  https://doi.org/10.1128/mbio.02514-25
Methods Mol Biol. 2026 ;2978 299-316

Establishing TurboID Proximity Labeling and mAID Conditional Knockdown System in Cryptosporidium parvum.

Rui Xu, L David Sibley.

  Protein interaction networks and subcellular proteomes can provide key insights into the biological functions of protein complexes. Here, we describe a method for proximity-based labeling using TurboID to define protein interaction networks in Cryptosporidium parvum. In addition, we have developed an auxin-inducible degron (AID) labeling system for conditional protein degradation in C. parvum to facilitate functional studies. This chapter describes the procedures for generating miniTurbo or mAID-TIR1-tagged C. parvum strains and validating the TurboID and mAID systems for target genes.

Keywords:  CRISPR/Cas9; Conditional knockdown; Degron; Mass spectrometry; Proximity labeling

DOI:  https://doi.org/10.1007/978-1-0716-4824-7_19
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi. 2025 Jul 31. 37(4): 387-397

[Cloning and bioinformatics analysis of surface antigen-related sequence protein SRS67 and SRS20A genes in Toxoplasma gondii].

X Chen, D Yin, W Ma, T Yi, H Li, L Liu, Z Liu, M Du, S Zhou, Q Li.

   OBJECTIVE: To predict the structures and immunogenicity of surface antigen-related sequence protein SRS67 and SRS20A in Toxoplasma gondii using bioinformatics methods, and to generate prokaryotic expression vectors for protein expression, so as to identify the functions of recombinant SRS67 and SRS20A proteins and their potential as vaccine candidates against T. gondii.
METHODS: T. gondii SRS67 and SRS20A gene and amino acid sequences were downloaded from the ToxoDB database. The open reading frames (ORFs) of SRS67 and SRS20A genes were analyzed in the ORF Finder website. The relative molecular mass, isoelectric point, amino acid composition and lipophilicit index of SRS67 and SRS20A proteins were predicted using the ProtParam software. The protein hydrophilicity/hydrophobicity was predicted using the ProtScale tool, the transmembrane regions were predicted using the TMHMM software, the signal peptides were predicted in the SignalP-4.1 website, the secondary and tertiary structures of the proteins were predicted in the NPS@SPOMA and SWISS-MODEL websites. The phosphorylation sites of the proteins were predicted using the NetPhos-3.1 program, the antigenic epitopes of proteins were predicted using the Immuon medicine Group program. B-cell epitopes, helper T-cell (Th) epitopes, and cytotoxic T lymphocyte (CTL) epitopes were predicted using the IEDB and SYFPEITHI websites, and the antigenicity scores of epitopes were evaluated using the software VaxiJen 2.0 to select the dominant epitopes. Primer sequences were synthesized based on the SRS67 and SRS20A protein-coding gene sequences from the ToxoDB database, and SRS67 and SRS20A genes were amplified using PCR reactions with T. gondii cDNA as a template. The amplification products were subjected to double restriction-enzyme digestion, and the target fragments were recovered and ligated into DH5α competent cells with T4 ligase. Positive single colonies were selected and cultured, and the pET-32a-SRS67 and pET-32a-SRS20A recombinant plasmids were extracted, transformed into competent cells for induction of recombinant protein expression. The expression of recombinant proteins was determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting.
RESULTS: Bioinformatics analysis predicted that SRS67 and SRS20A genes were 633 bp and 987 bp in length, contained 7 and 15 ORFs, and encoded 210 and 328 amino acids, respectively. The SRS67 protein had a relative molecular mass of 23 135.65, a signal peptide (D = 0.590) and no transmembrane regions, contained 22 phosphorylation sites and 8 antigenic determinants, and was a hydrophilic protein. The SRS20A protein had a relative molecular mass of 34 944.91, a signal peptide (D = 0.697) and transmembrane regions, contained 39 phosphorylation sites and 15 antigenic determinants, and was a hydrophilic protein. The SRS67 and SRS20A proteins shared similar secondary structures, both containing α-helices, β-sheets, and random coils, and their tertiary structure models exhibited typical globular characteristics, with Global Model Quality Estimation scores of 0.74 and 0.77, respectively. The average antigenic propensity score was 1.046 4 for the SRS67 protein and 1.037 4 for the SRS20A protein, respectively. SRS67 and SRS20A proteins had 7 and 8 dominant B-cell epitopes, 10 and 20 dominant Th-cell epitopes, and 2 and 3 dominant CTL epitopes, respectively. As expected, the PCR amplification products of SRS67 and SRS20A genes were approximately 633 bp and 987 bp in size. The SRS67 recombinant protein exhibited the highest expression in the precipitate following induction with 0.1 mmol/L IPTG for 16 h, and the SRS20A recombinant protein showed the highest expression following induction with 0.5 mmol/L IPTG for 16 h. SDS-PAGE and Western blotting confirmed successful expression of the recombinant proteins.
CONCLUSIONS: The SRS67 and SRS20A proteins possess multiple cellular epitopes and exhibit favorable immunogenicity. The recombinant SRS67 and SRS20A proteins have been successfully expressed, which provides the theoretical evidence for deciphering protein functions and screening effective vaccine antigens against toxoplasmosis.

Keywords:  Bioinformatics analysis; Cloning; SRS20A; SRS67; Surface antigen 1-releated sequence protein; Toxoplasma gondii

DOI:  https://doi.org/10.16250/j.32.1915.2024275
Front Cell Infect Microbiol. 2025 ;15 1674380

Upregulated small GTPase immunity-associated proteins confer resistance to Neospora caninum in rat and bovine cells.

Abdur Rehman Azam, Md Mukthar Mia, Julie Bedwani, William H Witola.

   Background: Neosporosis is a leading cause of abortions and neonatal mortality resulting in significant global economic losses in cattle production, and is also a common cause of a fatal neuromuscular degenerative disease in dogs, for which there are no effective treatments nor prophylactics available. Elucidation of Neospora-specific mechanisms that resistant hosts employ to orchestrate defenses against the parasite could hold the key to unveiling novel strategies for developing effective control approaches against neosporosis. Previously, we reported that the Lewis rat resists intracellular Toxoplasma gondii growth by augmenting the expression of GTPase Immunity-Associated Proteins (GIMAPs), namely GIMAP 4, 5, and 6 that mediate the resistance phenotype.
Methods: Herein, we investigated the effect of upregulated expression of GIMAPs on the growth and proliferation of Neospora caninum (an evolutionarily close relative to T. gondii) in rat and bovine cells. First, we used two rat strains (Lewis and Brown Norway rats) to determine the effect of N. caninum infection on GIMAPs expression, and the ability of parasite proliferation in the respective rat cells and tissues. We analyzed the effect of GIMAP 4, 5 and 6-induced upregulation in permissible rat and bovine macrophages on N. caninum growth, and determined the molecular networks engaged by GIMAPs in orchestrating intracellular parasite killing.
Results: We found that, unlike the Brown Norway rat, the Lewis rat is refractory to N. caninum infection, with a concomitant augmentation of GIMAP 4, 5 and 6 expression in response to infection. Corroboratively, overexpression of GIMAP transgenes in a N. caninum-permissive rat macrophage cell line induced accumulation of LAMP 1 (lysosome marker protein) on the parasitophorous vacuole membrane (PVM), resulting in vacuole acidification and restriction of N. caninum proliferation. Further, we found that bovine GIMAP 4, 5 and 6 are orthologous to rat GIMAPs, with a conserved AIG1 domain. Intriguingly, overexpression of bovine GIMAP transgenes in a N. caninum-susceptible bovine macrophage cell line inhibited intracellular proliferation of the parasites.
Discussion: Collectively, our findings imply that upregulation of GIMAP 4, 5, and 6 mediate robust refractoriness to N. caninum through induction of lysosomal fusion to the otherwise non-fusogenic PVM, resulting in vacuole acidification and destruction of intracellular parasites.

Keywords:  GIMAPs; Neospora caninum; bovine; infection resistance; rat

DOI:  https://doi.org/10.3389/fcimb.2025.1674380
Pharmaceuticals (Basel). 2025 Sep 30. pii: 1471. [Epub ahead of print]18(10):

Histone Deacetylases in Neurodegenerative Diseases and Their Potential Role as Therapeutic Targets: Shedding Light on Astrocytes.

Pedro de Sena Murteira Pinheiro, Luan Pereira Diniz, Lucas S Franco, Michele Siqueira, Flávia Carvalho Alcantara Gomes.

  Histone deacetylases (HDACs) are crucial enzymes involved in the regulation of gene expression through chromatin remodeling, impacting numerous cellular processes, including cell proliferation, differentiation, and survival. In recent years, HDACs have emerged as therapeutic targets for neurodegenerative diseases (NDDs), such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, given their role in modulating neuronal plasticity, neuroinflammation, and neuronal survival. HDAC inhibitors (HDACi) are small molecules that prevent the deacetylation of histones, thereby promoting a more relaxed chromatin structure and enhancing gene expression associated with neuroprotective pathways. Preclinical and clinical studies have demonstrated that HDACi can mitigate neurodegeneration, reduce neuroinflammatory markers, and improve cognitive and motor functions, positioning them as promising therapeutic agents for NDDs. Given the complexity and multifactorial nature of NDDs, therapeutic success will likely depend on multi-target drugs as well as new cellular and molecular therapeutic targets. Emerging evidence suggests that HDACi can modulate the function of astrocytes, a glial cell type critically involved in neuroinflammation, synaptic regulation, and the progression of neurodegenerative diseases. Consequently, HDACi targeting astrocytic pathways represent a novel approach in NDDs therapy. By modulating HDAC activity specifically in astrocytes, these inhibitors may attenuate pathological inflammation and promote a neuroprotective environment, offering a complementary strategy to neuron-focused treatments. This review aims to provide an overview of HDACs and HDACi in the context of neurodegeneration, emphasizing their molecular mechanisms, therapeutic potential, and limitations. Additionally, it explores the emerging role of astrocytes as targets for HDACi, proposing that this glial cell type could enhance the efficacy of HDACs-targeted therapies in NDD management.

Keywords:  HDACi; HDACs; aging; astrocyte; neurodegenerative diseases

DOI:  https://doi.org/10.3390/ph18101471
Int J Mol Sci. 2025 Oct 10. pii: 9855. [Epub ahead of print]26(20):

Lead Structure-Based Hybridization Strategy Reveals Major Potency Enhancement of SirReal-Type Sirt2 Inhibitors.

Matthias Frei, Ricky Wirawan, Thomas Wein, Franz Bracher.

  Selective and potent inhibitors of the NAD+-dependent deacetylase Sirt2 represent a valuable epigenetic strategy for the treatment of currently incurable diseases such as Parkinson's disease, Huntington's disease, Alzheimer's disease, and multiple sclerosis. Guided by molecular docking and MM/GBSA validation studies, a lead structure-based hybridization strategy was developed, resulting in a series of very effective Sirt2 inhibitors. With RW-93, we present a highly potent and subtype selective Sirt2 inhibitor (IC50 = 16 nM), which as a next generation SirReal-type inhibitor significantly surpasses established Sirt2 inhibitors and contributes to the extension of the current SAR profile. The structural modification strategy employed in this study proved to be highly promising, resulting in the identification of the most potent low-molecular-weight Sirt2 inhibitor reported to date, providing a promising target for further medicinal chemistry-driven SAR studies.

Keywords:  SirReal2; Sirt2 inhibitor; highly potent and selective Sirt2 inhibitor; hybridization strategy; sirtuin 2 inhibitor; structural optimization; structure–activity relationship

DOI:  https://doi.org/10.3390/ijms26209855
Metabolites. 2025 Sep 23. pii: 636. [Epub ahead of print]15(10):

NAD+-Dependent Lysine Acetylation Regulates Glucose Uptake and Fatty Acid Oxidation in Cardiomyocytes.

Ettore Vanni, Christophe Montessuit.

   BACKGROUND/OBJECTIVES: Stimulation of glucose uptake in response to ischemic stress is important for cardiomyocyte post-ischemic function and survival. In the diabetic myocardium chronically exposed to an excess of circulating lipids, this mechanism is impaired, making the myocardium more sensitive to ischemia-reperfusion injury (IRI). In vitro studies have shown that exposure to fatty acids (FAs) reduces basal and stimulated glucose uptake in cardiomyocytes. Preliminary results indicate reduced NAD+ levels and increased protein lysine acetylation in FA-exposed cardiomyocytes. This study aims to investigate whether intracellular NAD+ reduction is responsible for FA-induced increase in protein acetylation and impaired glucose uptake.
METHODS: Primary rat cardiomyocytes were chronically treated with the sirtuin deacetylase inhibitor nicotinamide (NAM) in absence of FAs to induce protein acetylation. Conversely, we replenished NAD+ concentration using nicotinamide riboside (NR) to induce protein deacetylation in FA-exposed cardiomyocytes.
RESULTS: Similar to FA exposure, NAM treatment increased protein acetylation and impaired metabolic-stress-stimulated glucose uptake in cardiomyocytes. In contrast, NR supplementation reduced protein acetylation and improved metabolic-stress-stimulated glucose uptake in FA-exposed cardiomyocytes. Neither NAM nor NR influenced insulin-stimulated glucose uptake. Both NAM and FAs induced hydroxyacyl-CoA dehydrogenase trifunctional enzyme subunit α (HADHA) acetylation on lysine residues K166 and K214 and enhanced palmitate oxidation. Conversely, NR treatment induced HADHA deacetylation and reduced palmitate uptake and oxidation in FA-exposed cardiomyocytes.
CONCLUSIONS: In cardiomyocytes, protein hyperacetylation, resulting from either FA exposure or sirtuin inhibition, impairs metabolic-stress-stimulated glucose uptake and is associated with increased FA oxidation.

Keywords:  NAD metabolites; cardiomyocytes; heart; metabolism; post-translational modification; protein acetylation

DOI:  https://doi.org/10.3390/metabo15100636
PLoS Pathog. 2025 Oct 27. 21(10): e1013645

PfATP2 is a flippase on the Plasmodium falciparum surface that is important for growth and influences parasite sensitivity to antiplasmodial compounds.

Deyun Qiu, Eleanor England, Adele M Lehane.

Antimalarials play a crucial role in the fight against malaria. However, resistance of the most virulent malaria parasite, Plasmodium falciparum, to front-line antimalarials is spreading. To identify new antimalarials, millions of compounds have been screened for their ability to inhibit the growth of blood-stage P. falciparum parasites. To gain insight into the mode of action of novel compounds and the ease by which parasites can acquire resistance to them, many have been tested in 'in vitro evolution' experiments, in which parasites are exposed to the compound for a prolonged period of time. In a recent study, parasite resistance to two compounds, MMV007224 and MMV665852, was associated with amplification of the pfatp2 gene, implicating PfATP2, a putative phospholipid flippase, as a parasite drug target or resistance determinant. These two compounds, along with MMV665794 (which is structurally related to MMV007224), had previously been reported to dysregulate pH in parasites. Here, we show that PfATP2 localises to the parasite surface and is important for parasite growth. We demonstrate that parasites genetically engineered to overexpress PfATP2 display reduced sensitivity to MMV665794, MMV007224 and MMV665852 compared to parasites with a normal expression level of the protein, and that parasites in which PfATP2 is knocked down become hypersensitive to the three compounds. We show that PfATP2 expression level does not affect the cytosolic pH of parasites, or the potency by which MMV665794 or MMV007224 dysregulate parasite pH. We show that PfATP2-overexpressing parasites internalise a fluorescent phosphatidylserine analogue (NBD-PS) at a greater rate than parasites with a normal expression level of PfATP2, and that parasites in which PfATP2 is knocked down have a reduced rate of NBD-PS uptake. Further, we provide evidence that MMV665794 and MMV007224 give rise to a reduction in NBD-PS internalisation. Together, our data are consistent with PfATP2 serving as a major ATP-dependent phosphatidylserine internalisation mechanism on the parasite plasma membrane, and being a potential target of MMV665794 and MMV007224.

DOI: https://doi.org/10.1371/journal.ppat.1013645
ChemMedChem. 2025 Oct 27. e202500819

Corrigendum to "Identification of Tri- and Tetracyclic Pyrimidinediones as Sirtuin Inhibitors".

DOI: https://doi.org/10.1002/cmdc.202500819
Proc Natl Acad Sci U S A. 2025 Nov 04. 122(44): e2513845122

Chemical propulsion of hemozoin crystal motion in malaria parasites.

Erica M Hastings, Tomasz Skóra, Keith R Carney, Henry C Fu, Tamara C Bidone, Paul A Sigala.

  Malaria parasites infect red blood cells where they digest host hemoglobin and release free heme inside a lysosome-like organelle called the food vacuole. To detoxify excess heme, parasites form hemozoin crystals that rapidly tumble inside this compartment. Hemozoin formation is critical for parasite survival and central to antimalarial drug activity. Although the static structural properties of hemozoin have been extensively investigated, crystal motion and its underlying mechanism have remained puzzling. We used quantitative image analysis to determine the timescale of motion, which requires the intact vacuole but does not require the parasite itself. Using single particle tracking and Brownian dynamics simulations with experimentally derived interaction potentials, we found that hemozoin motion exhibits unexpectedly tight confinement but is much faster than thermal diffusion. Hydrogen peroxide, which is generated at high levels in the food vacuole, has been shown to stimulate the motion of synthetic metallic nanoparticles via surface-catalyzed peroxide decomposition that generates propulsive kinetic energy. We observed that peroxide stimulated the motion of isolated crystals in solution and that conditions that suppress peroxide formation slowed hemozoin motion inside parasites. These data suggest that surface-exposed metals on hemozoin catalyze peroxide decomposition to drive crystal motion. This work reveals hemozoin motion in malaria parasites as a biological example of an endogenous self-propelled nanoparticle. This mechanism of propulsion likely serves a physiological role to reduce oxidative stress to parasites from hydrogen peroxide produced by large-scale hemoglobin digestion during blood-stage infection.

Keywords:  Plasmodium; brownian diffusion; digestive vacuole; hydrogen peroxide catalysis; nanoparticle dynamics

DOI:  https://doi.org/10.1073/pnas.2513845122
Nat Commun. 2025 Oct 28. 16(1): 9502

Pre-established ATF4 occupancy and chromatin organization instruct selective transcription activation during integrated stress response.

Peipei Jiang, Qian Bian.

Cells rapidly and extensively remodel their transcriptome in response to stress to restore homeostasis, but the underlying mechanisms are not fully understood. Here, we characterize the dynamic changes in transcriptome, epigenetics, and 3D genome organization during the integrated stress response (ISR). ISR induction triggers widespread transcriptional changes within 6 h, coinciding with increased binding of ATF4, a key transcriptional effector. Notably, ATF4 binds to hundreds of genes even under non-stress conditions, priming them for stronger activation upon stress. The transcriptional changes at ATF4-bound sites during ISR do not rely on increased H3K27 acetylation, chromatin accessibility, or rewired enhancer-promoter looping. Instead, ATF4-mediated gene activation is linked to the redistribution of CEBPγ from non-ATF4 sites to a subset of ATF4-bound regions, likely by forming an ATF4/CEBPγ heterodimer. CEBPγ preferentially targets the sites pre-occupied by ATF4, as well as genomic regions exhibiting a unique higher-order chromatin structure signature. Thus, the transcriptional responses during ISR are largely pre-wired by intrinsic chromatin properties. These findings provide critical insights into transcriptional remodeling during ISR with broader implications for other stress responses.

DOI: https://doi.org/10.1038/s41467-025-64577-7
Methods Mol Biol. 2026 ;2978 139-155

A Novel Method to Silence Genes in Cryptosporidium.

Alejandro Castellanos-Gonzalez.

  A major bottleneck for developing new drugs and vaccines against cryptosporidiosis has been the lack of methods to study gene function in this parasite. Silencing of genes using small interference RNA (siRNA) is a powerful methodology to investigate gene function in multiple organisms and has been widely used to identify drug targets for multiple pathogens. Cryptosporidium does not possess the enzymes of the classical siRNA pathway. Therefore, its genes cannot be silenced by standard siRNA technology. To circumvent that problem, we developed a strategy to knock down Cryptosporidium mRNA by reconstituting the effector arm of the siRNA pathway using recombinant enzymes and synthetic single-strand RNA (ssRNA). We have induced silencing of several genes in Cryptosporidium by transfecting parasites with hybrid complexes formed between recombinant human Argonaute (hAgo2) and Cryptosporidium ssRNA. We have used this methodology to study the role of selected genes in host-parasite interactions. It also can be used to identify potential targets for chemotherapy. Standardized protocols to silence genes in Cryptosporidium parasites are described in this chapter. In addition, we described the use of ssRNA/Ago complexes as a novel strategy to reduce Cryptosporidium infection.

Keywords:  Ago 2; Argonaute; Cryptosporidium; Gene silencing; RNAi; siRNA

DOI:  https://doi.org/10.1007/978-1-0716-4824-7_11
Methods Mol Biol. 2026 ;2978 317-345

In Vitro Culture of Cryptosporidium spp. Using Stem Cell-Derived Intestinal Epithelial Monolayers.

Valentin Greigert, Georgia Wilke, Yi Wang, Soumya Ravindran, Matthew Freese, Thaddeus Stappenbeck, William Witola, L David Sibley.

  Cryptosporidium parvum has a complex life cycle consisting of asexual and sexual phases that culminate in oocyst formation in vivo. The most widely used cell culture platforms to study C. parvum only support a few days of growth and do not allow the parasite to proceed past the sexual stages to complete oocyst formation. Additionally, these cell culture platforms are mostly adenocarcinoma cell lines, which do not adequately model the parasite's natural environment in the small intestine. We present a method for generating mouse primary intestinal epithelial cell monolayers that support long-term Cryptosporidium parvum growth, as well as human primary intestinal epithelial cell monolayers that facilitate long-term growth of C. parvum and C. hominis. Stem cells are grown as spheroids and plated onto transwells, allowing for separate apical and basolateral compartments. In the apical chamber, the cell growth medium was removed to create an "air-liquid interface" that enhanced host cell differentiation and supported Cryptosporidium growth including all stages of the life cycle. The use of primary intestinal cells to grow Cryptosporidium in vitro will be a valuable tool for studying host-parasite interactions using a convenient in vitro model that more closely resembles the natural niche in the intestine.

Keywords:  Air; Cryptosporidium; Long-term growth; Primary cell; Transwell; liquid interface

DOI:  https://doi.org/10.1007/978-1-0716-4824-7_20
PLoS One. 2025 ;20(10): e0324769

Impact of histone post-translational modification inhibitors on lifespan, reproduction, and stress response in the rotifer Brachionus manjavacas.

Nelia Luviano Aparicio, Meghan Dryburgh, Colleen M McMaken, Alyssa Liguori, Kristin E Gribble.

Epigenetic modifications, including histone post-translational modifications, are central drivers of age-associated structural and functional changes in the genome, influencing gene expression and leading to changes in cellular resilience. Epigenetic modifications are thus a target for therapies to prevent or treat age-related decline in health and lifespan. In this study, we measured the effects of inhibiting histone deacetylases (HDACs) and the histone methyltransferase, SETDB1, on lifespan, reproduction, and stress response in the rotifer Brachionus manjavacas, a model organism for aging studies. Rotifers were exposed to three pharmaceutical compounds, the HDAC inhibitors β-hydroxybutyrate and sodium butyrate and the SETDB1 inhibitor mithramycin A. Changes in global histone modification levels, lifespan, reproduction, and heat stress resistance were quantified. Global histone acetylation levels increased with β-hydroxybutyrate and sodium butyrate treatments. Histone 3 lysine 9 trimethylation (H3K9me3) levels were reduced by treatment with mithramycin A. β-hydroxybutyrate significantly extended lifespan without modifying heat stress resistance. In contrast, mithramycin A increased both lifespan and heat stress tolerance. Sodium butyrate specifically improved heat stress resistance without affecting lifespan. Importantly, none of the three treatments had a significant impact on lifetime reproduction. These findings provide insights into the role of histone modifications in aging and suggest potential interventions targeting epigenetic marks to promote longevity and resilience.

DOI: https://doi.org/10.1371/journal.pone.0324769
Molecules. 2025 Oct 14. pii: 4075. [Epub ahead of print]30(20):

Role of Histone H3 Lysine 4 Methylation in Chromatin Biology.

Bernhard Lüscher, Philip Bussmann, Janina Müller.

  Specific expression of genes is fundamental for defining the identity and the functional state of cells. Sequence-specific transcription factors interpret the information contained in DNA sequence motifs and recruit cofactors to modify chromatin and control RNA polymerases. This multi-step process typically involves several transcription factors and cofactors with different enzymatic activities. Post-translational modifications (PTMs) of histones are one key mechanism to control chromatin structure and polymerase activity and thus gene transcription. The methylation of histone H3 at lysine 4 (H3K4) is a modification of accessible chromatin, including enhancers and promoters, and also sites of recombination and some forms of DNA damage. H3K4 methylation is catalyzed by six lysine methyltransferase complexes, referred to as KMT2 or COMPASS-like complexes. These are important in processes related to transcription and contribute to recombination in T and B cells. PRDM9 and ASH1L are H3K4 methyltransferases involved in meiotic recombination and DNA repair, respectively. In transcription, H3K4 mono- and tri-methylation are located at enhancers and promoters, respectively. These modifications, either alone or in combination with other histone PTMs, provide binding sites for transcriptional cofactors. Through these sites, H3K4 methylation affects chromatin accessibility and histone PTMs, typically resulting in a favorable environment for transcription. H3K4 tri-methylation also recruits and regulates RNA polymerase II (RNAPII) complexes, which interact with KMT2 complexes, generating positive feedforward loops to promote transcription. Thus, H3K4 methylation has broad activities that are key to different chromatin-associated processes.

Keywords:  COMPASS; PROTAC; RNAPII; acetylation; chromatin; gene expression; histone modification; methylation; transcription; transcription factor

DOI:  https://doi.org/10.3390/molecules30204075
Gastric Cancer. 2025 Oct 31.

Metabolic reprogramming as a key regulator in Helicobacter pylori-infected gastric cancer.

Ruofan Cao, Feifei Zhou, Cuiyu Zhu, Hongwei Xu.

  Helicobacter pylori (H. pylori) infection is a recognized risk factor for gastric cancer (GC), which is the leading cause of cancer-related deaths worldwide. As a Class I carcinogen, H. pylori plays a central role in the occurrence and development of GC. Recent studies have highlighted the critical role of metabolic reprogramming inthe gastric cancer, and H. pylori infection has been shown to significantly alter metabolic pathways in gastric cancer. This review explores the mechanisms by which H. pylori infection drives metabolic changes in GC, particularly in glycolysis, lipid metabolism, and amino acid metabolism. By altering these metabolisms, H. pylori enhances the survival, proliferation, and metastasis of tumor cells, and also promotes immune evasion. Therefore, understanding the ways in which H. pylori-induced metabolic reprogramming of GC cells is essential for identifying new therapeutic targets. By summarizing the latest research progress of these metabolic pathways, new strategies and directions can be provided for gastric cancer treatment.

Keywords:   Helicobacter pylori ; Gastric cancer; Metabolic reprogramming; Therapy

DOI:  https://doi.org/10.1007/s10120-025-01675-x