bims-toxgon 2025-06-29 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–06–29
24 papers selected by
Lakesh Kumar, BITS Pilani

The critical role of Toxoplasma gondii GRA1 in nutrient salvage.
Piceatannol Induces Mitochondrial Dysfunction in Toxoplasma gondii.
A novel combined quadrivalent self-amplifying mRNA-LNP vaccine provokes protective immunity against acute and chronic toxoplasmosis in mice.
Detection of Toxoplasma Gondii Tachyzoites in Cerebrospinal Fluid: Once in a Blue Moon Finding.
Research Progress on the Interaction Between SIRT1 and Mitochondrial Biochemistry in the Aging of the Reproductive System.
Development of an Immunochromatographic Test with Recombinant MIC2-MIC3 Fusion Protein for Serological Detection of Toxoplasma gondii.
Benzamide-Containing Histone Deacetylase Inhibitors With Anticancer Therapeutic Potential.
Design and immunological evaluation of a multi-epitope vaccine candidate against Toxoplasma gondii incorporating MIC13, GRA1, and SAG1 antigens in BALB/c mice.
The Sirtuin Family FvSIRT5 and FvSIR2 Are Important for Fumonisin B Biosynthesis and Conidiation in Fusarium verticillioides.
Plasmodium falciparum acetyltransferase GCN5 acts as a dual regulator of essential glycolytic enzyme phosphoglycerate mutase.
Global analysis of Toxoplasma gondii prevalence in wild avian hosts: effects of phylogeny, ecology, and detection methods.
Aberrant histone modifications in pediatric brain tumors.
A nuclear branched-chain amino acid catabolism pathway controls histone propionylation in pancreatic cancer.
The effects of STAT3 acetylation on the transcriptional activity and tumorigenesis.
Landscape of Histone Posttranslational Modifications in Osteoarthritis.
Functional insights into Plasmodium actin depolymerizing factor interactions with phosphoinositides.
Toxoplasma gondii GRA16 Suppresses Aerobic Glycolysis by Downregulating c-Myc and TERT Expressions in Colorectal Cancer Cells.
Fluorescence Spectroscopy Reveals Resveratrol Binding to a Hydrophobic Pocket in Leishmania amazonensis Sir2-Related Protein 1 (LaSir2RP1).
RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum.
ULK1-dependent phosphorylation of OGT instructs the tumorigenicity of O-GlcNAcylation.
Sirtuin 5 inhibits mitochondrial metabolism in liver cancer cells and promotes apoptosis by mediating the desuccinylation of CS.
Phosphorylation-mediated Regulation of the NADPH-dependent Glutamate Dehydrogenase, SpGdh1, from Schizosaccharomyces pombe.
Artificial Intelligence (AI)-Based Protein Structure Prediction and Analysis.
GCN5 Is a Master Regulator of Gene Expression in the Malaria Parasite Plasmodium falciparum.

mBio. 2025 Jun 27. e0124225

The critical role of Toxoplasma gondii GRA1 in nutrient salvage.

Bolin Fan, Biyun Qin, Mingjun Li, Yuchao Zhu, Fuqiang Fan, Hao Xu, Lilan Xue, Yukun Chen, Ming Pan, Bang Shen.

  Toxoplasma gondii is an obligate intracellular pathogen that infects humans and many animals. It harbors unique secretory organelles to facilitate its parasitic lifestyle, including dense granules that secrete diverse proteins to different destinations. Yet the biological functions of these secretory proteins are mostly unknown. Here, we examined the roles of GRA1, the first dense granule protein discovered. GRA1 is secreted to the parasitophorous vacuole (PV), and its conditional depletion led to growth arrest of tachyzoites, suggesting a crucial role of GRA1 for parasite propagation during acute infection. Furthermore, GRA1 inactivation resulted in severe metabolic defects, including reduced glycolysis and tricarboxylic acid cycle activities and a drop in cellular ATP levels. GRA1 depletion also disrupted the integrity of the mitochondrion and apicoplasts. Mechanistically, disruption of GRA1 altered the structures of membranous tubules in the PV, called the intravacuolar network (IVN), which are thought to mediate the transport of molecules in and out of the parasites. Consistently, GRA1 inactivation impaired the secretion of various GRA proteins to the PV membrane (PVM) or host cells, including GRA17 that is involved in nutrient uptake from host cells. In agreement with the mislocalization of GRA proteins, mutants lacking GRA1 had a strong defect in absorbing nutrients like glucose and pantothenate from host cells. Consequently, the parasites displayed slower growth and a higher tendency to differentiate into bradyzoites. Together, these results suggest that GRA1 plays a vital role in maintaining the structural integrity of the IVN, thus contributing to the scavenging of host nutrients.
IMPORTANCE: Toxoplasma gondii critically relies on host nutrients for growth, but the underlying mechanisms are largely unknown. Here, we discovered that the secretory protein GRA1 in Toxoplasma played a crucial role in scavenging host nutrients to support parasite proliferation. GRA1 is the first reported GRA protein, but its function remains enigmatic since its discovery in 1989. GRA1 is secreted to the PV from the dense granules, which harbor many proteins that traffic to PV, PVM, and even host cells to perform diverse functions, including forming channels on the PVM to take up host nutrients to establish parasitism. GRA1 disruption impaired the structure of IVN and abolished the targeting of other GRA proteins to their destinations, which compromised the parasite's ability to import nutrients from the hosts. These findings reveal the functional mode of GRA1 in T. gondii and highlight its potential as a target for developing new interventions against toxoplasmosis.

Keywords:  GRA17; TCA cycle; dense granule protein; intravacuolar network; mitochondrion; pantothenate

DOI:  https://doi.org/10.1128/mbio.01242-25
Microorganisms. 2025 May 25. pii: 1203. [Epub ahead of print]13(6):

Piceatannol Induces Mitochondrial Dysfunction in Toxoplasma gondii.

Zhenhe Liu, Haolong Qiu, Yucong Jiang, Yuxi Mo, Linlin Lu, Yan Wang, Dandan Hu, Xingju Song.

  Toxoplasma gondii, an obligate intracellular protozoan parasite infecting nucleated cells of warm-blooded vertebrates, causes severe complications in immunocompromised hosts. Current therapies remain limited by suboptimal efficacy and toxicity, necessitating novel anti-toxoplasmic agents. Piceatannol (PIC), a natural stilbenoid, demonstrates multifaceted bioactivity including antimicrobial and anti-parasitic effects, suggesting therapeutic potential against T. gondii. Our previous study revealed PIC's potent anti-parasitic activity, selectively inhibiting T. gondii proliferation and altering parasite morphology without host cytotoxicity. In this study, mechanistic analyses indicated that PIC disrupts mitochondrial integrity in tachyzoites, reducing mitochondrial membrane potential and ATP production while elevating ROS levels. Transcriptomic profiling identified significant suppression of oxidative phosphorylation-related genes, consistent with mitochondrial dysfunction. These findings establish PIC as a promising candidate targeting T. gondii through the mechanism of mitochondrial impairment.

Keywords:  RNA-seq; Toxoplasma gondii; autophagy; mitochondria; piceatannol

DOI:  https://doi.org/10.3390/microorganisms13061203
Infect Dis Poverty. 2025 Jun 23. 14(1): 55

A novel combined quadrivalent self-amplifying mRNA-LNP vaccine provokes protective immunity against acute and chronic toxoplasmosis in mice.

Qinli Wu, Zhongao Zhang, Hongkun Chu, Bing Xia, Weiqi Li, Jianzu Ding, Haojie Ding, Bin Zheng, Meng Gao, Youru Wang, Eman E El Shanawany, Feng Tan, Huayue Ye, Xunhui Zhuo, Shaohong Lu.

   BACKGROUND: Toxoplasma gondii, an intracellular parasitic protozoan, which infects almost all warm-blooded animals, including humans, causes toxoplasmosis. However, we lack effective drugs and vaccines to control toxoplasmosis, representing a clinical challenge. Therefore, safe and effective vaccines are urgently needed. In this study, a self-replicating mRNA vaccine comprising four T. gondii antigens: ROP18, TGME49_237490, TGME49_268230, and MIC13, named 4x-mRNA-LNP (lipid nanoparticle), was developed, and its protective efficacy was evaluated in mice.
METHODS: The expression of this vaccine in eukaryotic Human embryonic kidney 293 T (HEK-293 T) cells and mouse myoblast (C2C12) cells were analyzed, followed by enzyme-linked immunosorbent assay (ELISA) evaluation of the elicited humoral immune response. Subsequently, the vaccine-triggered immune responses in mice were detected, including antibody titers, T lymphocyte subsets, and cytokine levels. Finally, its immunoprotective effects were evaluated after challenging mice with T. gondii PRU oocysts or tachyzoites of different strains and analyzing the pathological changes, parasite loads, and mouse survival time. Western blotting and ELISA confirmed the successful eukaryotic expression and immunogenicity of 4x-mRNA, respectively. Statistical analyses, including the log-rank (Mantel-Cox) test, Student's t-test, and one-way ANOVA, were performed using GraphPad Prism software.
RESULTS: Mice vaccinated with 4x-mRNA-LNP generated higher levels of IgG1 and IgG2a antibodies (P < 0.05) and cytokines (IL-2, IL-4, IL-10, IL-12, IFN-γ) (P < 0.05) compared with the control group. The high specific IgG titer was maintained for at least 10 weeks after the last vaccination. The proportion of CD3+CD4+ T cells and CD3+CD8+ T cells also increased significantly (P < 0.05), along with increased spleen cell proliferation in 4x-mRNA-LNP-vaccinated mice. Notably, limited pathological changes and < 10 fg of parasites/mg were found in the immunized mice tissues post-pathogen challenge. During observation for 30 days, 4x-mRNA-LNP-immunized mice survived significantly longer under challenge with lethal doses of RH, ME49, or WH6 tachyzoites (survival rates = 60%, 80%, and 60%, respectively). Following PRU oocyst challenge, vaccinated mice had notably decreased cyst burdens (72.5%, P < 0.05) compared with control mice.
CONCLUSIONS: The 4x-mRNA-LNP vaccine triggered effective long-term antibody levels in mice, thus representing a promising candidate to further develop anti-toxoplasmosis vaccines.

Keywords:   Toxoplasma gondii ; Immune protection; Oocyst; Self-amplifying; mRNA vaccine

DOI:  https://doi.org/10.1186/s40249-025-01332-6
Cytopathology. 2025 Jun 23.

Detection of Toxoplasma Gondii Tachyzoites in Cerebrospinal Fluid: Once in a Blue Moon Finding.

Ananthanarayanan Udupi Suryanarayana, Vidhya Vikashini Balasubramaniam, Kalisetty Prashanthi, Debasis Gochhait, Hariswar Pari.

  Detection of tachyzoites of Toxoplasma gondii in cerebrospinal fluid led to the diagnosis of central nervous system (CNS) toxoplasmosis in a 20 years old male. The cerebrospinal fluid (CSF) was obtained by lumbar puncture and two cytology smears were prepared by cytocentrifugation, one of which was stained with the May-Grünwald Giemsa (MGG) stain and the other with Papanicolaou stain. Light microscopic examination revealed pleocytosis along with numerous intracellular phagocytosed as well as extracellular tachyzoites with cytomorphology characteristic of Toxoplasma gondii. The diagnosis was confirmed by the serological elevation of anti-Toxoplasma IgM levels.

Keywords:   Toxoplasma gondii ; cerebrospinal fluid; cytomorphology; tachyzoites; toxoplasmosis

DOI:  https://doi.org/10.1111/cyt.70005
Biology (Basel). 2025 Jun 02. pii: 643. [Epub ahead of print]14(6):

Research Progress on the Interaction Between SIRT1 and Mitochondrial Biochemistry in the Aging of the Reproductive System.

Yang Li, Kai Kang, Huimingda Bao, Siqi Liu, Bangyi Zhao, Guangdong Hu, Jiang Wu.

  The protein associated with the silencing information regulator 2-associated enzyme1 (SIRT1) is a highly conserved nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase and a key member of the sirtuin family. SIRT1 plays an essential role in various cellular physiological processes, primarily localized in the nucleus but also active in the cytoplasm and mitochondria. Recent studies have demonstrated its capacity to delay aging in multiple organs and tissues, although its underlying mechanisms remain incompletely understood. Additionally, SIRT1 exerts a significant influence on metabolic regulation and genetic processes. As the primary source of cellular energy, mitochondria are central to numerous biological functions. Mitochondrial dysfunction has been implicated in the onset and progression of various diseases and is increasingly recognized for its role in aging-related processes. This article investigates the interaction between SIRT1 and mitochondria in regulating reproductive system aging and elucidates their potential mechanisms of action, providing insights for clinical research into reproductive system aging.

Keywords:  aging; interaction; mitochondrial biochemistry; reproductive system; sirtuins

DOI:  https://doi.org/10.3390/biology14060643
Vet Sci. 2025 May 22. pii: 509. [Epub ahead of print]12(6):

Development of an Immunochromatographic Test with Recombinant MIC2-MIC3 Fusion Protein for Serological Detection of Toxoplasma gondii.

Jianzhong Wang, Yi Zhao, Jicheng Qiu, Jing Liu, Rui Zhou, Xialin Ma, Xiaojie Wu, Xiaoguang Li, Wei Mao, Yiduo Liu, Heng Zhang.

  Toxoplasma gondii is a globally significant zoonotic pathogen responsible for severe parasitic diseases in humans and animals. This study aimed to design, develop, and evaluate a novel immunochromatographic test (ICT) using a recombinant MIC2-MIC3 fusion protein (rMIC2-MIC3) for detecting specific antibodies against T. gondii. The ICT demonstrated exceptional sensitivity, capable of detecting T. gondii-specific antibodies in sera diluted up to 1:8. Specificity evaluation confirmed no cross-reactivity with antibodies against other parasites, such as Neospora caninum, Cryptosporidium suis, Eimeria tenella, and Sarcocystis tenella. Stability tests revealed the test strips maintained full functionality after 12 weeks of storage at 24 °C. The coincidence rate of the colloidal gold test strips prepared in this study with a commercial ELISA kit was 94.59%. Comparisons with advanced serodiagnostic tools, such as chimeric antigen-based ELISAs and recombinant protein diagnostics, further highlighted its robustness and applicability. These findings underscore the potential of the rMIC2-MIC3-based ICT as a reliable, economical, and accessible diagnostic tool for toxoplasmosis in veterinary and human medicine.

Keywords:  MIC2-MIC3 fusion protein; Toxoplasma gondii; antibodies against T. gondii; immunochromatographic test; serological detection

DOI:  https://doi.org/10.3390/vetsci12060509
Arch Pharm (Weinheim). 2025 Jun;358(6): e70028

Benzamide-Containing Histone Deacetylase Inhibitors With Anticancer Therapeutic Potential.

Juntao Song, Shujing Si, Jie Qin, Zhenguo Liu.

  Histone deacetylases (HDACs) could regulate gene expression, arrest the cell cycle, alter epigenetics, promote angiogenesis, and evade cancer cell survival and apoptosis. HDAC inhibitors could act on cancer cells through multiple mechanisms, primarily by regulating gene expression, inducing cell-cycle arrest, promoting apoptosis, inhibiting angiogenesis, enhancing the immune response, and modifying the epigenome, representing valuable chemical entities for cancer therapy. The benzamide derivatives can chelate with the zinc ion at the active site of HDACs, interact with the surrounding amino acid residues in the active site cavity of HDACs, and cause conformational changes in HDACs. Accordingly, benzamide derivatives are useful HDAC inhibitors, and the benzamide-containing HDAC inhibitors have the potential to demonstrate robust anticancer activity. The purpose of this review is to summarize the current scenario of benzamide-containing HDAC inhibitors with anticancer therapeutic potential developed since 2020 to facilitate further rational exploitation of more effective candidates.

Keywords:  anticancer potential; benzamide; histone deacetylases; mechanisms of action; structure–activity relationship

DOI:  https://doi.org/10.1002/ardp.70028
Food Waterborne Parasitol. 2025 Sep;40 e00269

Design and immunological evaluation of a multi-epitope vaccine candidate against Toxoplasma gondii incorporating MIC13, GRA1, and SAG1 antigens in BALB/c mice.

Zahra Hosseininejad, Ahmad Daryani, Mahdi Fasihi-Ramandi, Hossein Asgarian-Omran, Tooran Nayeri, Samira Dodangeh, Afsaneh Amouei, Javad Javidnia, Sabah Mayahi, Shahabeddin Sarvi, Sargis A Aghayan.

  Toxoplasmosis, caused by the apicomplexan parasite Toxoplasma gondii, is a globally significant yet neglected disease that can cause serious clinical consequences in humans and extensive losses in the livestock industry. However, no effective vaccine has been provided for this parasite, so this study was designed to evaluate the immunogenicity of a chimeric multi-epitope antigen as a potential toxoplasmosis vaccine candidate in a murine model. The multi-epitope vaccine candidate, designed with bioinformatics tools, MGS: a chimera of T. gondii MIC13, GRA1, and SAG1 antigens, was expressed in Escherichia coli BL21 and purified by immobilized metal affinity chromatography using a His Ni-NTA column. Mice were immunized with MGS protein alone or adjuvanted with Freund's adjuvant, calcium phosphate (CaPNs), or chitosan (CNs) nano-adjuvants on days 0, 21, and 35. Humoral and cellular immune responses to MGS (alone or adjuvanted with Freund's, CNs, or CaPNs) were compared to control groups (PBS, Freund's alone, CNs alone, CaPNs alone) through ELISA assays. The MGS protein, either alone or formulated with adjuvants, significantly increased specific antibody titers, particularly the IgG2a subtype and the cytokine IFN-γ. The highest levels of total antibodies, IFN-γ, and IL-4 were observed in the MGS-Freund group. It also enhanced the proliferation rate of splenic lymphocytes and improved the survival rate of BALB/c mice following challenge with the RH strain of Toxoplasma. The findings demonstrate that the MGS protein significantly enhances both Th1 and Th2 immune responses in experimental groups. These results support the efficacy of multi-epitope vaccines as a promising strategy for the development of effective vaccines against toxoplasmosis.

Keywords:  GRA1; MIC13; Multi-epitope; SAG1; Toxoplasma gondii; Vaccine

DOI:  https://doi.org/10.1016/j.fawpar.2025.e00269
Phytopathology. 2025 Jun 22.

The Sirtuin Family FvSIRT5 and FvSIR2 Are Important for Fumonisin B Biosynthesis and Conidiation in Fusarium verticillioides.

Cui Yang, Maozhu Jiang, Zhaoqun Wu, Dayong Li, Xiaochi Dong, Xinjie Wang, Chunxiang Zhou, Cheng Liu, Zijun Yang, Xuchen Liu, Jing Sun, Jie Gao, Wenxian Sun.

  In ﬁlamentous fungi, the modification of histone acetylation and deacetylation are crucial for the regulation of secondary metabolism and pathogenicity. So far there has been no functional study on histone deacetylases (HDACs) in Fusarium verticillioides, a causal agent of destructive diseases of maize. Herein, we identified and characterized the HDACs FvSIRT5 and FvSIR2 in F. verticillioides. Results showed that the disruption of FvSIRT5 and FvSIR2 lead to increased and morphologically abnormal conidia, and consequently high expression levels of conidiation-specific genes. Deletion of FvSIRT5 and FvSIR2 also affected autophagy, which may resulted in the defects of conidial and hyphal viability. Fumonisin B production was significantly reduced in the Δsirt5 and Δsir2 mutants, the expression of genes (FUMs and PKSs) involved in secondary metabolism was also significantly down regulated. Notably, FvSIRT5 and FvSIR2 may be involved in histone acetylation at H3K9, H3K14, H3K27, and H4K16 residues, which has never been reported in fungi. Interestingly, FvSIRT5 and FvSIR2 interact with ORC1 (origin recognition complex subunit 1) and some alternative splice forms (ASFs) of FUM21 (fumonisin biosynthetic transcription factor). Moreover, mutations of FvSIRT5 and FvSIR2 are dispensible for virulence in F. verticillioides. Taken together, these results suggest that FvSIRT5 and FvSIR2 are important for histone H3 and H4 acetylation and further for transcriptional regulation of genes related to conidiation and secondary metabolism in F. verticillioides.

Keywords:  Fungal Pathogens; Genomics; Molecular

DOI:  https://doi.org/10.1094/PHYTO-10-24-0308-R
FEBS J. 2025 Jun 26.

Plasmodium falciparum acetyltransferase GCN5 acts as a dual regulator of essential glycolytic enzyme phosphoglycerate mutase.

Ankita Tehlan, Poonam Nagar, Reena Prajapati, Krishanu Bhowmick, Amarjeet Kumar, Inderjeet Kaur, Naidu Subbarao, Suman Kumar Dhar.

  Lysine acetylation is emerging as a key player in cellular regulation across species by controlling the fate of metabolic proteins as well as modulating gene expression via histone modification. Phosphoglycerate mutase, a conserved enzyme of the sole energy-yielding pathway of glycolysis in the human malaria parasite Plasmodium falciparum, is indispensable for its growth. Here, we demonstrate that P. falciparum phosphoglycerate mutase PfPGM1 (phosphoglycerate mutase) is regulated via lysine acetylation. In mammalian cells, acetylation of phosphoglycerate mutase modulates its catalytic activity, although the acetyl transferase enzyme remains elusive. However, the parasites exhibit a unique way of regulating the fate of PfPGM1 via acetylation that modulates its stability, thus providing an increased protein pool for the rapid growth and proliferation of the parasites. We show that K100, a critical residue for PfPGM1 catalytic activity, is acetylated by the essential histone acetyltransferase PfGCN5. Downregulation of PfGCN5 through a knockdown approach in the parasites along with cycloheximide treatment indeed leads to a reduction of PfPGM1 protein. Additionally, PfGCN5 occupies the promoter of PfPGM1 in a stage-specific manner, and downregulation of PfGCN5 protein leads to a reduced transcript level of PfPGM1. Collectively, our data highlight a dual regulation of PfPGM1 by PfGCN5 through acetylation of the protein as well as regulation of the transcription of the gene. Such dual control is not only rare but showcases the importance of the above two proteins and their potential as excellent targets against malaria.

Keywords:  GCN5; Plasmodium falciparum; acetylation; phosphoglycerate mutase (PGM); stability

DOI:  https://doi.org/10.1111/febs.70164
Int J Parasitol. 2025 Jun 20. pii: S0020-7519(25)00117-1. [Epub ahead of print]

Global analysis of Toxoplasma gondii prevalence in wild avian hosts: effects of phylogeny, ecology, and detection methods.

Katherine E Buschang, Jerusha Bennett, Clément Lagrue, Robert Poulin.

  Toxoplasma gondii is an Apicomplexan protozoan parasite that infects warm-blooded animals, including birds. Birds may play a significant role in the parasite's transmission due to their diverse habitats, diets, dispersal abilities, and potential as prey for predators. However, information on T. gondii infection dynamics in avian hosts is limited globally. To address this, we conducted a systematic review of 82 studies reporting T. gondii prevalence in wild birds. Using generalized linear mixed models, we analyzed global prevalence patterns across avian taxa and explored predictors of prevalence, including bird order, habitat type, trophic level, and lifestyle, in serological and direct (e.g., genetic and histological) detection studies. We also assessed the strength of the phylogenetic signal in T. gondii prevalence among avian lineages. The global distribution of studies was geographically clustered, with direct detection methods more frequently used in Europe and North America. Certain bird orders, particularly Anseriformes, Accipitriformes, and Strigiformes, exhibited higher prevalence rates, suggesting their important roles in T. gondii transmission. Ecological factors, such as habitat characteristics and trophic levels (e.g., omnivores), were significant predictors of infection. Although phylogenetic analysis revealed a weak phylogenetic signal, high prevalence values were observed in hawks, owls, and falcons. These findings consolidate existing knowledge and emphasize the importance of targeted surveillance efforts. They highlight critical gaps in research on T. gondii transmission in avian hosts and provide direction for future studies. Such insights can inform wildlife management strategies and efforts to mitigate zoonotic disease risks associated with T. gondii.

Keywords:  Toxoplasma gondii; birds; phylogenetic distribution; prevalence; toxoplasmosis

DOI:  https://doi.org/10.1016/j.ijpara.2025.06.007
Front Oncol. 2025 ;15 1587157

Aberrant histone modifications in pediatric brain tumors.

Erin T Hamanishi, Derek Dang, Sriram Venneti.

  Epigenetic modifications, particularly histone post-translational modifications (PTMs), are central to pediatric brain tumor pathogenesis, impacting chromatin structure, gene expression, and genomic stability. Disruptions in histone PTMs, especially lysine methylation and acetylation, arising due to histone mutations or aberrant enzyme modulation are critical drivers of oncogenesis. Lysine methylation, catalyzed by histone methyltransferases (KMTs), modulates chromatin interactions and gene expression through activation or repression, depending on the methylation state and the specific histone residue. Key enzymes, including histone methyltransferases and demethylases, and associated proteins exemplify the functions of writers, readers, and erasers in maintaining histone modification balance. Similarly, histone acetylation, a dynamic process regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), plays a crucial role in pediatric brain tumors. Alterations in these components lead to aberrant gene expression and tumorigenesis. Understanding these disrupted processes offers potential for targeted therapies to rewire oncogenic chromatin states and potentially improve patient outcomes.

Keywords:  epigenetics; histone acetylation; histone methylation; histone modifications; pediatric

DOI:  https://doi.org/10.3389/fonc.2025.1587157
bioRxiv. 2025 Apr 26. pii: 2025.04.23.650241. [Epub ahead of print]

A nuclear branched-chain amino acid catabolism pathway controls histone propionylation in pancreatic cancer.

Christina Demetriadou, Michael Noji, Austin L Good, Erick Mitchell-Velasquez, Sharan Venkatesh, Daniel S Kantner, Jennifer Pennise, Pedro Costa-Pinheiro, Laura V Pinheiro, Taku Harada, Phuong T T Nguyen, Adam Chatoff, Emily Megill, Claudia V Da Silva Crispim, Mariola M Marcinkiewicz, Jordan L Meier, Zoltan Arany, Irfan Asangani, Emma E Furth, Ben Z Stanger, Nathaniel W Snyder, Kathryn E Wellen.

Branched-chain amino acid (BCAA) catabolism contributes prominently to the TCA cycle in the healthy pancreas but is suppressed in pancreatic ductal adenocarcinoma (PDA). The impact of this metabolic remodeling on cancer phenotypes remains poorly understood. Here, we find that the BCAA isoleucine is a primary source of propionyl-CoA in PDA cells. Reduction of propionyl-CoA availability by either genetic perturbation or isoleucine and valine starvation decreases histone propionylation (Kpr) without impacting histone acetylation on specific lysine sites, correlating with reduced transcription of certain lipid- and immune-related genes. Mechanistically, we find that multiple enzymes of isoleucine catabolism unexpectedly localize to and carry out multi-step isoleucine oxidation within the nuclei of PDA cells. Importantly, nuclear localization of the rate-limiting branched-chain alpha ketoacid dehydrogenase (BCKDH) complex is essential for isoleucine-dependent Kpr and gene regulation. Moreover, we demonstrate that isoleucine-sensitive Kpr and its associated gene expression are driven by the MYST family of lysine acyltransferases (KATs), and that the BCKDHA subunit of the BCKDH complex interacts with KAT7 within the nuclear compartment. BCAA catabolism enzymes are apparent in the nuclei of PanIN lesions in mice and PDA tumors in patients, contrasting that in healthy pancreatic acinar and ductal cells. Collectively, these findings unveil a nuclear isoleucine catabolism pathway and highlight its role in controlling histone Kpr and tumorigenic transcriptional programs in PDA.

DOI: https://doi.org/10.1101/2025.04.23.650241
Biochem Pharmacol. 2025 Jun 24. pii: S0006-2952(25)00341-7. [Epub ahead of print] 117076

The effects of STAT3 acetylation on the transcriptional activity and tumorigenesis.

Huaying Yan, Linmei Tang, Zhu Yuan, Yaodan Zhang.

  Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that regulate various cellular behaviors, including proliferation, survival, differentiation, metastasis, immune response and metabolism. STAT3 is tightly regulated to maintain a transiently active state in normal cells while persistent STAT3 activation often occurs in cancers. The activated STAT3 undergo several post-translational modifications including phosphorylation, acetylation, methylation, ubiquitination, and SUMOylation, which in turn affect the STAT3 signaling. Due to the important role of STAT3 acetylation in its transcription activity and oncogenesis, targeting STAT3 acetylation may be a potentially therapeutic strategy for human cancers. Although regulation of STAT3 signaling by acetylation has been summarized more than ten years ago, a comprehensive review on STAT3 acetylation and its roles in tumorigenesis as well as its therapeutic implication is missing. In this review, we systematically summarize the recent advances of the role ofSTAT3 acetylation in tumorigenesis. We begin by discussing the process of protein acetylation, then focus on the effect of STAT3 acetylation on the transcriptional activity and its role in carcinogenesis. Lastly, we summarize the recent progress in current development of STAT3 acetylation-related inhibitors. We hope this review will shed light on the critical role of STAT3 acetylation in tumorigenesis, and also provide theoretical basis for future drug design and discovery of STAT3 acetylation-targeting inhibitors.

Keywords:  Post-translational modifications; STAT3 acetylation; STAT3 acetylation-targeting inhibitors; Tumorigenesis

DOI:  https://doi.org/10.1016/j.bcp.2025.117076
J Inflamm Res. 2025 ;18 7893-7906

Landscape of Histone Posttranslational Modifications in Osteoarthritis.

Siyu Zhao, Jia Zheng, Songkai Yue, Xiaoyang Chen, Yonghui Dong.

  Osteoarthritis (OA) is a complex, progressive, and age-associated disease characterized by aberrant epigenetic expression. Epigenetic analysis has helped clarify the role of histone post-translational modifications (PTMs) in OA. PTMs affect histone structure and function and, therefore, regulate the expression of genes implicated in various biological processes. The roles of histone methylation and acetylation in OA progression-including extracellular collagen degradation and matrix destruction-have been thoroughly analyzed. Though several studies have shown that histone PTMs are related to OA, summative investigations in this area are lacking. The present literature review examines the relationships between histone PTMs and OA. It focuses mainly on methylation, acetylation, phosphorylation, lactylation, ubiquitination, and the roles of the histone methyltransferase (HMT)/histone demethylase (HDMT) and histone acetyltransferase (HAT)/histone deacetylase (HDAC) families in OA development. We used epigenetic tools for discovering new OA treatments. This review offers new perspectives for future studies on OA pathogenesis and treatment.

Keywords:  cartilage; drug targets; epigenetic; histone modifications; osteoarthritis

DOI:  https://doi.org/10.2147/JIR.S514599
J Biol Chem. 2025 Jun 19. pii: S0021-9258(25)02249-5. [Epub ahead of print] 110399

Functional insights into Plasmodium actin depolymerizing factor interactions with phosphoinositides.

Devaki Lasiwa, Inari Kursula.

  Malaria is caused by protozoan parasites, Plasmodium spp., that belong to the phylum Apicomplexa. The life cycle of these parasites depends on two different hosts; the definitive host, or vector, is a mosquito, and the intermediate host is a vertebrate, such as human. Malaria parasites use a unique form of substrate-dependent motility for host cell invasion and egress, which is dependent on an actomyosin motor complex called the glideosome. Apicomplexa have a small set of actin regulators, which are poorly conserved compared to their equivalents in higher eukaryotes. Actin depolymerizing factors (ADFs) are key regulators responsible for accelerating actin turnover in eukaryotic cells. The activity of ADFs is regulated by membrane phosphoinositides. Malaria parasites express two ADF isoforms at different life stages. ADF1 differs substantially from canonical ADF/cofilins and from Plasmodium ADF2 in terms of both structure and function. Here, we studied the interaction of both Plasmodium ADFs with phosphoinositides using biochemical and biophysical methods and mapped their binding sites on ADF1. Both Plasmodium ADFs bind to different phosphoinositides, and binding in vitro requires the formation of vesicles or micelles. Interaction with phosphoinositides increases the α-helical content of the parasite ADFs, and the affinities are in the micromolar range. The binding site for PI(4,5)P2 in PfADF1 involves a small, positively charged surface patch.

Keywords:  Plasmodium; actin binding protein; actin regulation; anionic vesicles; electrostatic interaction; intrinsic tryptophan fluorescence spectroscopy; protein-lipid interaction

DOI:  https://doi.org/10.1016/j.jbc.2025.110399
Biomol Ther (Seoul). 2025 Jun 25.

Toxoplasma gondii GRA16 Suppresses Aerobic Glycolysis by Downregulating c-Myc and TERT Expressions in Colorectal Cancer Cells.

Ji-Eun Lee, Seung-Hwan Seo, Do-Won Ham, Eun-Hee Shin.

  Despite its relatively low adenosine triphosphate (ATP) production efficiency, cancer cells reprogram their metabolism to utilize aerobic glycolysis for rapid proliferation. This "Warburg effect" not only provides biosynthetic precursors but also creates a tumor-favorable microenvironment. Key oncogenic regulators such as protein kinase B (AKT), nuclear factor kappa B (NF-κB), and cellular myelocytomatosis oncogene (c-Myc) enhance glycolytic activity by inducing the expression of enzymes including glucose transporters (GLUTs), hexokinase 2 (HK2), lactate dehydrogenase A (LDHA), and monocarboxylate transporters (MCTs). Moreover, telomerase reverse transcriptase (TERT), beyond its canonical role in telomere maintenance, also promotes glycolysis via the NF-κB and c-Myc pathways. From a therapeutic perspective, aerobic glycolysis contributes to glucose-mediated chemoresistance, limiting the efficacy of irinotecan in colorectal cancer (CRC). In this study, we investigated the role of Toxoplasma gondii-derived dense granule protein 16 (GRA16) in modulating glycolysis and irinotecan sensitivity. In HCT116 CRC cells stably expressing GRA16, AKT and NF-κB signaling were suppressed, leading to the downregulation of c-Myc and TERT. This resulted in decreased expression of GLUTs, HK2, LDHA, and MCTs, ultimately reducing glucose uptake and lactate production. Functional assays revealed that GRA16 induced G2/M cell cycle arrest, increased apoptosis, and suppressed proliferation. Notably, GRA16-expressing cells treated with irinotecan exhibited increased Sub-G1 accumulation and late-apoptotic and necrotic populations. Furthermore, siRNA-mediated silencing of c-Myc confirmed its key role in regulating TERT and glycolytic enzymes. These findings indicate that GRA16 suppresses aerobic glycolysis via the c-Myc/TERT axis and enhances irinotecan sensitivity, offering a promising strategy to overcome chemoresistance in CRC.

Keywords:  Aerobic glycolysis; Colorectal cancer cell; GRA16; Irinotecan; TERT; c-Myc

DOI:  https://doi.org/10.4062/biomolther.2025.040
Protein J. 2025 Jun 22.

Fluorescence Spectroscopy Reveals Resveratrol Binding to a Hydrophobic Pocket in Leishmania amazonensis Sir2-Related Protein 1 (LaSir2RP1).

Melissa R Fessel, Ana P R Povinelli, Veronica S Fontes, Maria Isabel N Cano, Carlos H I Ramos.

  Resveratrol, a natural phytoalexin synthesized by certain plants in response to injury, exhibits antimicrobial properties and various medically significant effects, including anticancer and antiaging activities. Although its exact mechanism of action is still under investigation, it is believed to involve its interaction with a group of protein deacetylases known as sirtuins. Sirtuins are crucial in regulating metabolism, stress responses, and processes such as lifespan extension through caloric restriction. In this study, we report the inhibitory effect of resveratrol on the growth of Leishmania amazonensis promastigotes, highlighting its potential as a microbicide. Through fluorescence spectroscopy assays and in silico analysis, we identified and characterized the interaction between resveratrol and Sir2-related protein 1 from L. amazonensis (rLaSir2RP1). Our results demonstrate a direct interaction between resveratrol and rLaSir2RP1, characterized by a binding constant of 105 M-1. This interaction involves a single binding site located near a hydrophobic pocket, which includes its solely tryptophan residue.

Keywords:   Leishmania ; Fluorescence; Resveratrol; Sirtuin

DOI:  https://doi.org/10.1007/s10930-025-10275-8
Cell Rep. 2025 Jun 25. pii: S2211-1247(25)00699-0. [Epub ahead of print]44(7): 115928

RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum.

Thomas Hollin, Zeinab Chahine, Steven Abel, Charles Banks, Charisse Flerida A Pasaje, Todd Lenz, Jacques Prudhomme, Caitlyn Marie Ybanez, Anahita S Abbaszadeh, Jacquin C Niles, Laurence Florens, Karine G Le Roch.

  The human malaria parasite, Plasmodium falciparum, contains a non-photosynthetic and essential plastid called the apicoplast. This organelle is of major interest for its unique biology and potential as an attractive drug target. In this study, we characterize PfRAP03 and PfRAP08, two members of the RAP (RNA-binding domain abundant in apicomplexans) protein family. We generate inducible knockdown lines in P. falciparum to validate that both RAP proteins are essential for parasite survival and localize to the apicoplast. Transcriptomic analysis demonstrates that PfRAP03 and PfRAP08 depletion significantly affect apicoplast gene expression. Using enhanced crosslinking immunoprecipitation sequencing (eCLIP-seq) method, we show that apicoplast ribosomal RNAs and transfer RNAs are the targets of PfRAP03 and PfRAP08, respectively. Collectively, our results establish the role of these RAP proteins in controlling apicoplast gene expression in P. falciparum, revealing parasite-specific organellar pathways with biomedical significance.

Keywords:  CP: Microbiology; Plasmodium; RAP protein; RNA binding; apicoplast; malaria; post-transcriptional regulation

DOI:  https://doi.org/10.1016/j.celrep.2025.115928
Sci China Life Sci. 2025 Jun 25.

ULK1-dependent phosphorylation of OGT instructs the tumorigenicity of O-GlcNAcylation.

Zhuan Lv, Qingen Da, Yumiao Li, Aiyun Yuan, Guangcan Shao, Xiaoxuan Lu, Yue Wang, Xuefang Zhang, Jingjing Liu, Meng-Qiu Dong, Yuanyuan Ruan, Chen Wu, Kunfu Ouyang, Jing Li.

  Investigations from the last four decades have correlated high O-linked N-acetylglucosamine (O-GlcNAc) levels with various cancer types, but it is not known how OGT responds to diverse nutrients to finetune cellular O-GlcNAcylation levels. Herein we identified a critical OGT phosphorylation site by unc-51 like autophagy activating kinase 1 (ULK1) under glucose depletion. First, we demonstrated that glucose levels modulate the interaction between OGT and ULK1 and cellular O-GlcNAcylation levels. Low glucose induces high O-GlcNAcylation, which could be reversed by ULK1 inhibition. Then, using mass spectrometry, we showed that ULK1 phosphorylates OGT at Ser576 and stabilizes OGT. Further biochemical experiments revealed that Ser576 phosphorylation inhibits Lys604 ubiquitination by stimulating OGT binding with BAP1, a de-ubiquitinase for OGT. Strikingly, using the OGTS576A knock-in cells, we found that in mouse xenograft models OGT-S576A completely abolishes the tumorigenicity of OGT, probably due to low O-GlcNAcylation. In sum, we found that ULK1 phosphorylates OGT at Ser-576 under glucose deprivation, which stabilizes OGT by promoting OGT-BAP1 association and is pivotal for O-GlcNAcylation levels and tumorigenesis. As low glucose is often associated with tumor progression, our work not only unearths a key mechanism of how OGT is regulated by glucose levels, but also offers new therapeutic opportunities targeting OGT.

Keywords:  BAP1; O-GlcNAcylation; O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT); ULK1; glucose

DOI:  https://doi.org/10.1007/s11427-024-2924-6
Front Immunol. 2025 ;16 1560989

Sirtuin 5 inhibits mitochondrial metabolism in liver cancer cells and promotes apoptosis by mediating the desuccinylation of CS.

Huimin Cao, Dongsheng Wei, Han Li, Mei Zhao, Yixin Ma, Liang Kong, Guoyuan Sui, Lianqun Jia.

   Background: Citrate synthase (CS) is a key rate-limiting enzyme in the tricarboxylic acid (TCA) cycle and plays a crucial role in cancer progression. However, the mechanism by which CS promotes liver cancer growth remains unclear. The aim of this study is to elucidate the role of CS and its post-translational modifications (PTMs) in the initiation and progression of hepatocellular carcinoma (HCC).
Methods: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to detect protein lysine succinylation in human liver cancer and adjacent non-cancerous tissues. A HCC model was established in male C57BL/6 mice through intraperitoneal injection of DEN. The expression of SIRT5 and CS in HCC mice was assessed by RT-qPCR, immunohistochemistry, and Western blotting. HepG2 cells were cultured, and co-immunoprecipitation (Co-IP) was performed to evaluate the interaction between SIRT5 and CS. Western blotting was used to measure the succinylation levels of CS. In addition, Mito-Tracker Red CMXRos staining, reactive oxygen species (ROS) measurement, ATP level assay, EdU cell proliferation assay, colony formation assay, TUNEL staining, and flow cytometry were used to investigate the effects of CS succinylation and desuccinylation on mitochondrial function and cell proliferation in hepatocellular carcinoma cells.
Results: A total of 358 differentially modified proteins were identified in human liver cancer tissues. These differentially modified proteins were primarily enriched in the mitochondria, and CS exhibited high levels of succinylation in HCC tissues. In mouse liver cancer tissues, SIRT5 expression was reduced while CS expression was increased. Furthermore, SIRT5 was found to interact with CS, mediating the de-succinylation of CS at the lysine 375 site. Additionally, succinylation at the K375 site of CS was shown to enhance mitochondrial activity and ATP content in HepG2 cells, while reducing intracellular ROS levels and promoting cell proliferation. In contrast, de-succinylation of CS at the K375 site significantly impaired mitochondrial function and ATP levels, increased ROS levels, and induced apoptosis in HepG2 cells.
Conclusion: Succinylation of CS is crucial for maintaining mitochondrial function and promoting cell proliferation in liver cancer cells. Targeting SIRT5-mediated de-succinylation of CS may represent a promising therapeutic strategy for the treatment of hepatocellular carcinoma.

Keywords:  PTMs (post-translational modifications); apoptosis; citrate synthase; hepatocellular carcinoma; mitochondrial metabolism; succinylation

DOI:  https://doi.org/10.3389/fimmu.2025.1560989
J Biol Chem. 2025 Jun 25. pii: S0021-9258(25)02272-0. [Epub ahead of print] 110422

Phosphorylation-mediated Regulation of the NADPH-dependent Glutamate Dehydrogenase, SpGdh1, from Schizosaccharomyces pombe.

Yi-Fan Wang, Takeo Tomita, Ayako Yoshida, Saori Kosono, Makoto Nishiyama.

  Glutamate dehydrogenase from the yeast Schizosaccharomyces pombe (SpGdh1) is a pivotal enzyme that catalyzes the conversion of 2-oxoglutarate and ammonium to glutamate using NADPH as a coenzyme. Although SpGdh1 is phosphorylated at several residues, the impact of phosphorylation on enzyme activity and the underlying molecular mechanisms remain unclear. To elucidate the phosphorylation-mediated regulation of SpGdh1, we determined the crystal structure of SpGdh1 binding 2-iminoglutarate (2-IG) and NADP+. The results of the structural analysis revealed that four serine residues for phosphorylation were located near the active site. Ser252 directly interacted with the 2'-phosphate group of the adenine ribose moiety of NADP+, suggesting that the phosphorylation of Ser252 interfered with NADP+ binding. To confirm this hypothesis, we prepared SpGdh1 phosphorylation-mimic (Ser to Glu) variants of SpGdh1 at these four Ser residues. The results of a kinetic analysis revealed that the replacement of these four residues increased the apparent KmNADP(H) value and decreased catalytic efficiency, kcat/KmNADP(H).In contrast, substitutions decreased the apparent KmNAD(H) value and increased catalytic efficiency, kcat/KmNAD(H). Therefore, the Ser to Glu replacement caused net shifts in the coenzyme specificities (NADPH to NADH and NADP+ to NAD+) of 55- and 2900-fold, respectively. This is the first study to reveal the effects of the phosphorylation of SpGdh1 on its activity.

Keywords:  Schizosaccharomyces pombe; coenzyme specificity; crystal structure; enzyme kinetics; glutamate dehydrogenase; protein phosphorylation

DOI:  https://doi.org/10.1016/j.jbc.2025.110422
Methods Mol Biol. 2025 ;2952 39-57

Artificial Intelligence (AI)-Based Protein Structure Prediction and Analysis.

Ashwani Kumar, Aanchal Gupta, Shubham Kumar, Apoorva Haldkar, Hansa Wali.

  One of the significant challenges in fields of drug discovery and bioinformatics is the prediction of protein's 3-D structure due to its computational complexity. The vast conformational space and intricate energy functions make it hard to accurately predict protein structures. Two main approaches exist: template-based protein structure prediction uses known protein structures, while template-free protein structure prediction tackles proteins without known structures. Despite recent advancements, precise structures for complex proteins remain elusive for effective drug design. Predicting structures solely from amino acid sequences, known as ab initio prediction, is still unresolved. With an increasing number of proteins lacking known structures, sophisticated artificial intelligence (AI) methods are crucial for further progress. However, AI researchers face hurdles owing to the complex nature of protein structure prediction and limited comprehensive resources. This book chapter provides a comprehensive description of template-free protein structure prediction research, including essential concepts and computational methods. It discusses challenges, offers insights, and suggests directions for future studies to advance computational prediction of protein structure effectively.

Keywords:  Artificial intelligence; Bioinformatics; Deep learning; Protein structural prediction; Search optimization

DOI:  https://doi.org/10.1007/978-1-0716-4690-8_3
Cells. 2025 Jun 10. pii: 876. [Epub ahead of print]14(12):

GCN5 Is a Master Regulator of Gene Expression in the Malaria Parasite Plasmodium falciparum.

Amuza Byaruhanga Lucky, Ahmad Rushdi Shakri, Xiaoying Liang, Hui Min, Xiao-Lian Li, Swamy Rakesh Adapa, Rays H Y Jiang, Liwang Cui, Chengqi Wang, Jun Miao.

  GCN5-containing SAGA complex is evolutionarily conserved across yeast, plants, and humans and acts as a general transcription coactivator in the genome-wide regulation of genes. In Plasmodium falciparum, PfGCN5 forms a divergent complex, and the mis-localization of this complex by deleting the PfGCN5 bromodomain (ΔBrd) causes a plethora of growth defects. To directly test the PfGCN5 function, we performed conditional knockdown (KD) of PfGCN5. Whereas PfGCN5 KD phenotypically recapitulated the ΔBrd growth defects, it caused fewer transcriptional alterations compared to ΔBrd. To decipher the mechanism by which PfGCN5 regulates gene expression, we applied a new chromatin landscape analysis tool, CUT&Tag-seq, to map the chromatin localization of PfGCN5 and its deposited histone mark H3K9ac. Compared to ChIP-seq, CUT&Tag-seq identified substantially more H3K9ac peaks in the promoters of its target genes, with the peak intensity positively correlated with the levels of gene expression. CUT&Tag-seq analysis was remarkably more sensitive in mapping chromatin positions of PfGCN5, which colocalized with H3K9ac. The genes enriched with PfGCN5/H3K9ac signals at their promoters are involved in broad biological processes. Notably, PfGCN5's positions overlapped with sequence motifs recognized by multiple apetela2 (AP2)-domain-containing transcription factors (AP2 TFs), suggesting that they recruited PfGCN5 to these promoters. Additionally, PfGCN5 was also colocalized with AP2-LT, further validating that AP2-LT is an integral component of the PfGCN5 complex. Collectively, these findings establish PfGCN5 as a master gene regulator in controlling general and parasite-specific cellular processes in this low-branching parasitic protist.

Keywords:  GCN5; Plasmodium falciparum; gene regulation; histone acetyltransferase; malaria; transcription factor

DOI:  https://doi.org/10.3390/cells14120876