bims-toxgon Biomed News
on Toxoplasma gondii metabolism
Issue of 2025–09–28
twenty-two papers selected by
Lakesh Kumar, BITS Pilani



  1. Microorganisms. 2025 Aug 31. pii: 2041. [Epub ahead of print]13(9):
      The conversion from fast-growing tachyzoites to slow-growing bradyzoites is the key factor in establishing the chronic infection and long-term persistence of Toxoplasma gondii. Environmental stressors, such as amino acid starvation and alkaline medium, can trigger the transformation of tachyzoites into bradyzoites. Under such stress conditions, ribosomes slow down, potentially leading to stalling, and ribosomal collisions typically activate ribosome-associated quality control (RQC) pathways. In this study, we investigated the role of T. gondii ribosome quality control complex subunit 2 (TgRqc2), which contains both NFACT and coiled-coil domains, in the parasite's survival and stage conversion. NFACT represents the "domain" found in the central players involved in RQC, human NEMF and its orthologs FbpA (known as RqcH), Caliban, and Tae2 (known as Rqc2). Phylogenetic analyses revealed that TgRqc2 formed a distinct clade with its orthologs in apicomplexan parasites. The deletion of TgRqc2 impaired T. gondii's invasion and replication. The Rqc2-knockout strain showed defects in plaque formation and bradyzoite development. Our findings demonstrate that TgRqc2 is essential for T. gondii's lytic cycle and the conversion of tachyzoites into bradyzoites. RNA-seq analysis further showed that the depletion of TgRqc2 significantly disrupted global transcriptional activity. However, the detailed molecular mechanisms involved remain to be elucidated. In conclusion, our results proved valuable insights that may aid in the development of therapeutic strategies to prevent chronic infection.
    Keywords:  NFACT; TgRqc2; Toxoplasma gondii; bradyzoite; tachyzoite
    DOI:  https://doi.org/10.3390/microorganisms13092041
  2. Microorganisms. 2025 Sep 04. pii: 2056. [Epub ahead of print]13(9):
      Toxoplasma gondii is a widely distributed intracellular parasite that disrupts host immune and metabolic homeostasis. Although accumulating evidence highlights the role of gut microbiota in parasitic infections, the effects of acute T. gondii infection on host gut microbial ecology remain poorly understood. In this study, metagenomic sequencing technology was used to systematically analyze the composition and functional alterations of the ileal microbiota in BALB/c mice on day 10 post-infection. Compared to uninfected controls, T. gondii infected mice exhibited a significant reduction in microbial diversity and a pronounced shift in community structure. Notably, there was an expansion of Proteobacteria, particularly the Enterobacteriaceae family, alongside a marked decline in beneficial taxa such as Actinobacteria and Bacillota. Functional annotation using the KEGG and CAZy databases revealed enrichment of metabolic pathways related to glycolysis/gluconeogenesis, O-antigen nucleotide sugar biosynthesis, bacterial secretion systems, and biofilm formation-Escherichia coli in the infected microbiota. These findings provide novel insights into the dysbiosis of gut microbiota and host-microbe interactions during acute T. gondii infection.
    Keywords:  KEEG and CAZy analyses; Toxoplasma gondii; dysbiosis; gut microbiome; metagenomic sequencing
    DOI:  https://doi.org/10.3390/microorganisms13092056
  3. Sci Rep. 2025 Sep 26. 15(1): 32979
      Toxoplasma gondii is a zoonotic parasite that infects almost all warm-blooded animals and humans and results in serious health problems. There is no drug treatment for chronic toxoplasmosis. Thus, a safe and protective vaccine is required by the community to combat against the chronic infection caused by T. gondii in humans and animals. Rhoptry (ROP) proteins of T. gondii have important roles in host cell invasion, penetration, and biogenesis of the parasitophorous vacuole. In this study, we aimed to develop a novel vaccine with recombinant ROP6 protein (rROP6), which was shown to be highly immunogenic in protein microarray screening with blood samples collected from animal models infected with T. gondii oocysts or tissue cysts. Initially, a comprehensive in silico analyses was performed to design ROP6 protein to be used as vaccine antigen. Then, rROP6 protein was expressed in Saccharomyces cerevisiae INVSc1 cells and purified by affinity chromatography. Next, rROP6 protein adjuvanted with Freund's (rROP6 + Freund) was administered to BALB/c mice two times at three-week intervals. Humoral and cellular immune responses were analyzed by Western blot, ELISA, flow cytometry, and cytokine ELISA. Protective efficacy was determined by orally infecting mice with T. gondii PRU strain tissue cysts. The level of protection was analyzed by investigating tissue cysts in brain homogenate of mice using microscopy and qPCR. According to the results, rROP6 + Freund induced a strong IgG response compared to only rROP6 (P < 0.01) and the rate of CD8+ T lymphocytes secreting IFN- γ significantly increased in mice administered with rROP6 + Freund compared to other mice groups (P < 0.05). According to challenge results, all the rROP6 + Freund vaccine administered mice survived and the number of tissue cysts and the amount of T. gondii DNA decreased significantly compared to controls (P < 0.01; P < 0.0001). In conclusion, compared to control groups, rROP6 + Freund vaccine induced a high level of protective immunity and provided a significant level of protection as demonstrated by significant reduction in tissue cysts. We conclude that the recombinant ROP6 protein produced in S. cerevisiae is an immunogenic, protective, and promising vaccine candidate antigen that can be used in vaccine formulations against chronic toxoplasmosis.
    Keywords:   Saccharomyces cerevisiae ; Toxoplasma gondii ; ROP6; Recombinant protein vaccine; Rhoptry
    DOI:  https://doi.org/10.1038/s41598-025-14988-9
  4. J Phys Chem B. 2025 Sep 24.
      Sirtuins are a class of NAD-dependent histone deacetylases that regulate important biological pathways in prokaryotes and eukaryotes. This enzyme family comprises seven members, named SIRT1 to SIRT7. Among them, Sirtuin 6 (SIRT6) is a human sirtuin that deacetylates histones and plays a key role in DNA repair, telomere maintenance, carbohydrate and lipid metabolism, and lifespan. SIRT6's structure consists of a zinc finger domain, a Rossmann fold domain containing the NAD+ binding site, and disordered N-terminal and C-terminal (CTD) extensions. The specific role of the CTD in SIRT6's interaction with nucleosomes for histone deacetylation remains unclear. Here, we resort to extended molecular dynamics simulations to uncover the dynamical behavior of the full-length SIRT6 bound to a nucleosome core particle. Our simulations reveal that the CTD preferentially interacts with DNA at the entry/exit near the enzyme's docking site, exhibiting a variety of different binding modes. In specific cases, the CTD contributes to the promotion of DNA unwrapping and enhances H3K27 accessibility to SIRT6's active site, suggesting a pivotal role of this domain for H3K27 deacetylation. This work provides new structural insights into the binding process of the full-length SIRT6 to a nucleosome core particle, shedding light on the conformational behavior and functional role of its CTD. It constitutes an important step toward understanding of SIRT6 deacetylation mechanisms and specificity.
    DOI:  https://doi.org/10.1021/acs.jpcb.5c02221
  5. Plant J. 2025 Sep;123(6): e70495
      Lysine acetylation is a crucial post-translational modification that regulates protein function, stability, and subcellular localization. While extensively studied in mammalian systems, its role in plants remains largely unexplored. In this study, we identify the histone acetyltransferase HAG1 and the histone deacetylase HDA6 as key antagonistic regulators of the transcription factor WRKY63 acetylation. Using bimolecular fluorescence complementation assays, split-luciferase assays, and co-immunoprecipitation assays, we demonstrate that WRKY63 interacts with HAG1 and HDA6. Furthermore, the N-terminal region of WRKY63 is essential for these interactions. HAG1-mediated acetylation enhances WRKY63 nuclear localization, whereas HDA6-mediated deacetylation reduces its nuclear retention. Moreover, transient transcriptional assays indicate that HDA6 represses WRKY63-mediated transcriptional activation. Our findings highlight the broader significance of lysine acetylation beyond histone modification, uncovering an antagonistic regulatory network that fine-tunes transcription factor activity in plants.
    Keywords:  Arabidopsis; HAG1; HDA6; WRKY63; acetylation; histone acetyltransferase; histone deacetylase; post‐translational modifications
    DOI:  https://doi.org/10.1111/tpj.70495
  6. Bioact Mater. 2025 Dec;54 602-613
      Cell membrane-derived nanovesicles (CMNVs) are nanoscale lipid bilayer structures obtained from cellular membranes that serve as biomimetic drug delivery platforms, offering immune evasion, targeting, and surface functionalization capabilities. While most CMNVs originate from mammalian cells, Toxoplasma gondii (T. gondii), a genetically tractable protozoan with a structurally distinct membrane, offers a high-yield and underexplored source for producing T. gondii-derived CMNVs (TgCMNVs). These vesicles are obtained from the parasite's plasma membrane and inner membrane complex and retain unique features including abundant GPI-anchored SRS proteins, phosphatidylthreonine-rich lipids, and an editable genome, enabling versatile engineering via genetic and chemical strategies. We review methods for TgCMNV fabrication, purification, and functionalization, and evaluate their potential in immunomodulation, attenuation of tissue injury, cancer immunotherapy, and self-adjuvanting vaccine design. By combining intrinsic immune engagement with programmable surface architecture, TgCMNVs could serve as a complementary and adaptable platform alongside established CMNV systems. Finally, we discuss key translational considerations, including scalable production, immunogenicity control, regulatory compliance, and stability testing, which will be essential for assessing the feasibility of TgCMNVs in clinical applications.
    Keywords:  Cell membrane-derived nanovesicles; Genetic engineering of nanovesicles; Immune modulation; Targeted drug delivery; Toxoplasma gondii; Vaccines
    DOI:  https://doi.org/10.1016/j.bioactmat.2025.08.037
  7. mBio. 2025 Sep 25. e0194125
      Apicomplexan parasites possess unique secretory organelles called rhoptries, which are reservoirs for rhoptry neck proteins (RONs) and rhoptry bulb proteins (ROPs) that aid in host cell attachment, invasion, and intracellular proliferation. In Plasmodium falciparum, the RON6 (PfRON6) locus is indispensable, limiting its functional investigation. Using a rodent malaria model, we show the role of P. berghei RON6 (PbRON6), a putative ortholog of PfRON6, in the invasion of RBC, hepatocytes, and during liver stage development. PbRON6 localizes to the sporozoite membrane and has an extracellular C-terminal domain. RON6-depleted parasites fail to maintain infectivity and virulence, leading to prolonged survival of mice. The mutants induce chronic malaria and hyper-reactive malarial splenomegaly, characterized by decreased B and T lymphocytes concurring with loss of lymphoid follicles. Our findings provide a rationale for targeting PbRON6 in pre-erythrocytic stages to prevent clinical malaria and also for understanding the basis of hyper-reactive splenomegaly in mice using the PbΔron6 mutant model.IMPORTANCEPlasmodium sporozoites are infective to mammalian hepatocytes. Prior to entry into the cell, sporozoites release proteins from their apical cell organelles called micronemes and rhoptries. The secreted proteins contact the hepatocyte membrane to create a structure called a moving junction (MJ) that progressively invaginates inside the cell, utilizing the parasite's actomyosin molecular motor. This activity finally culminates in establishing an intracellular vacuole that harbors the parasite. As MJ is crucial for intracellular infection, targeting the components of this complex has implications in reducing malaria infection. We show that a rhoptry resident protein, RON6, is required for the invasion of merozoites and sporozoites, together with a role in the development of parasites in the hepatocytes. Consistent with its probable role in hepatocyte invasion, the RON6 is localized to the sporozoite membrane, with its C-terminal domain being extracellular. Our observations reveal that RON6 maintains the virulence of the parasite, and mutants lacking RON6 enhance host survival and induce hyper-reactive malarial splenomegaly.
    Keywords:  EEFs; Plasmodium; hepatocytes; rhoptries; splenomegaly; sporozoites
    DOI:  https://doi.org/10.1128/mbio.01941-25
  8. J Transl Med. 2025 Sep 24. 23(1): 1001
       BACKGROUND: Metabolic reprogramming is a hallmark of cancer cells, enabling them to meet the heightened energetic and biosynthetic demands required for rapid growth and proliferation. Recently, non-canonical functions of metabolic enzymes have garnered significant attention in cancer research. Pyruvate kinase 2 (PKM2) has been identified as a key player in transcriptional regulation within the nucleus, presenting new opportunities for therapeutic interventions in cancer.
    METHODS: In this study, the cells (A549 and H1299) were treated with indicator concentration of triclabendazole. The effects of triclabendazole on proliferation was detected by CCK8 assay, colony formation assay, EdU staining, and cell count assay. A tumorigenesis study in nude mice was performed to demonstrate the inhibitory effect of triclabendazole on tumor growth. PKM2 nuclear translocation, HDAC6-mediated deacetylation, glycolytic flux downregulation, and activation of AMPK/mTOR signaling pathway were used to elucidate the mechanistic role of triclabendazole in lung cancer progression.
    RESULTS: This study discovered that triclabendazole, a novel benzimidazole derivative, commonly used against Fasciola hepatolithiasis, effectively inhibited the nuclear translocation of PKM2. This inhibition resulted in the downregulation of glycolytic flux, ultimately suppressing lung cancer cell proliferation. Notably, triclabendazole reduced PKM2 acetylation by promoting the interaction between PKM2 and histone deacetylase 6 (HDAC6), thus blocking PKM2 nuclear localization. Moreover, we also demonstrated that triclabendazole-mediated inhibition of cell proliferation is driven by the downregulation of glycolysis, which enhanced AMP-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) signaling. Consistently, triclabendazole administration significantly inhibited tumor growth in vivo, correlating with the blockade of PKM2 nuclear translocation and lactate production decreased.
    CONCLUSION: Our findings revealed that triclabendazole inhibits PKM2 nuclear localization and glycolysis through an HDAC6-dependent mechanism, leading to the activation of AMPK/mTOR signaling and suppression of lung cancer cell proliferation. These results suggested that triclabendazole holds promise as a potential therapeutic agent, with the HDAC6-PKM2 axis representing a novel target for lung cancer treatment.
    Keywords:  Deacetylation; Glycolysis; HDAC6; Lung cancer; PKM2; Proliferation; Triclabendazole
    DOI:  https://doi.org/10.1186/s12967-025-06905-5
  9. Mol Biol Rep. 2025 Sep 26. 52(1): 954
      Metabolic reprogramming is a hallmark of tumors, whereby cancer cells remodel their own metabolism to meet the biosynthetic, energetic, and signaling demands required for rapid proliferation and malignant transformation. Posttranslational modifications (PTMs) serve as dynamic molecular switches that fine-tune cellular metabolic networks by precisely modulating the activity, stability, and subcellular localization of metabolic enzymes. This regulatory plasticity drives context-dependent metabolic reprogramming in tumor cells, enabling them to adapt to fluctuating physiological demands or pathological stressors while establishing tumor-specific metabolic signatures critical for survival and progression. Among PTMs, lysine succinylation-a recently identified modification catalyzed by succinyl-CoA-has emerged as a critical regulator of cancer metabolism. This unique modification involves the transfer of a negatively charged four-carbon succinyl group to lysine residues, inducing conformational and functional changes in target proteins. Notably, succinylation is evolutionarily conserved across eukaryotes and prokaryotes and has a broad influence on central metabolic pathways, including the tricarboxylic acid (TCA) cycle, amino acid metabolism, and lipid homeostasis. Mounting evidence highlights its dual roles in both sustaining tumorigenic metabolism and directly activating oncogenic signaling cascades. This review summarizes current insights into how succinylation rewires tumor metabolism and delineates its mechanistic contributions to cancer progression.
    Keywords:  Cancer; Lysine succinylation; Metabolic reprogramming; Posttranslational modification; Succinyl-CoA
    DOI:  https://doi.org/10.1007/s11033-025-11061-6
  10. Int J Mol Sci. 2025 Sep 09. pii: 8791. [Epub ahead of print]26(18):
      This article provides a comprehensive review and explores the gaps in current knowledge of lysine metabolism in humans and its potential nutritional and therapeutic indications. The first part of this study examines lysine sources, requirements, transport through the plasma membrane, lysine catabolism, and its disorders. The central part is focused on post-translational modifications of lysine in proteins, primarily desmosine formation in elastin, hydroxylation in collagen, covalent bonds with glutamine, methylation, ubiquitination, sumoylation, neddylation, acylation, lactylation, carbamylation, and glycation. Special sections are devoted to using lysine as a substrate for homoarginine and carnitine synthesis and in nutrition and medicine. It is concluded that the identification and detailed knowledge of writers, readers, and erasers of specific post-translational modifications of lysine residues in proteins is needed for a better understanding of the role of lysine in epigenetic regulation. Further research is required to explore the influence of lysine availability on homoarginine formation and how the phenomenon of lysine-arginine antagonism can be used to influence immune and cardiovascular functions and cancer development. Of unique importance is the investigation of the use of lysine in osteoporosis therapy and in reducing the resorption of harmful substances in the kidneys, as well as the therapeutic potential of polylysine and lysine analogs.
    Keywords:  cadaverine; carnitine; desmosine; homoarginine; homocitrulline; lysine–arginine antagonism; saccharopine
    DOI:  https://doi.org/10.3390/ijms26188791
  11. Biochem Pharmacol. 2025 Sep 21. pii: S0006-2952(25)00626-4. [Epub ahead of print]242(Pt 3): 117361
      Phosphoinositide 3-kinases (PI3Ks) and histone deacetylase 6 (HDAC6) have been widely studied as promising therapeutic targets in cancer. Both play key roles in maintaining cellular homeostasis, and their dysregulation is closely linked to oncogenesis. Consequently, several dual PI3K/HDAC6 inhibitors have been developed as potential anticancer agents. This review explores the cellular and molecular functions of PI3K and HDAC6, their involvement in cancer progression, and the structural and pharmacological properties of dual-targeting inhibitors. Additionally, we discuss future perspectives for designing clinically effective dual PI3K/HDAC6 inhibitors.
    Keywords:  Cancer; Dual targeting; Histone deacetylase 6; Inhibitors; Phosphoinositide 3-Kinase
    DOI:  https://doi.org/10.1016/j.bcp.2025.117361
  12. Vaccines (Basel). 2025 Aug 27. pii: 910. [Epub ahead of print]13(9):
      Background/Objectives: Toxoplasma gondii is a major cause of zoonotic infections in both humans and animals, resulting in significant mortality in susceptible species, such as New World primates and marsupials. Toxoplasmosis is particularly concerning in zoos and wildlife reserves, where outbreaks threaten conservation efforts for endangered species. In the absence of a commercially available vaccine against toxoplasmosis for humans and captive wild animals, current prevention strategies are limited to restricting the access of cats to enclosures, controlling rodent populations, and maintaining strict food hygiene. Recent research has shown promising results with an intranasal vaccine (VXN-Toxo) composed of maltodextrin nanoparticles conjugated with a purified, inactivated T. gondii parasite. This experimental vaccine does not pose a risk of causing disease and offers advantages such as better stability compared with live pathogen-based vaccines. Methods: This study presents a large-scale evaluation of the effect of VXN-Toxo administered to captive wildlife across 20 zoos in Europe and the Americas between 2017 and 2025. Seven hundred and eighty-four animals, representing over 58 species (including primates, marsupials, rodents, and felids), were vaccinated without any adverse events reported. Results: Retrospective mortality data from 20 participating zoological institutions revealed an overall 96.7% reduction-and, in many cases, a complete elimination-of toxoplasmosis-associated deaths post vaccination. Conclusions: These results demonstrate, for the first time, consistent and broad-spectrum protection against T. gondii of different strains in a wide array of captive wildlife species. This universal vaccine represents a promising tool for toxoplasmosis prevention in zoological collections, with significant implications for animal health and conservation strategies.
    Keywords:  T. gondii; inactivated vaccine; toxoplasmosis
    DOI:  https://doi.org/10.3390/vaccines13090910
  13. J Inflamm (Lond). 2025 Sep 26. 22(1): 39
      Immune cells can rewire their metabolism in response to various stimuli. Crosstalk between the nucleus and mitochondria allows for tight regulation of this metabolic reprogramming. Research has emerged showing several TCA cycle-derived metabolites exhibiting moonlighting functions in the nucleus, modulating chromatin modifications in order to control inflammation. These TCA cycle-derived metabolites include acetyl-CoA, α-ketoglutarate, succinate, fumarate, itaconate, and succinyl-CoA which can modify DNA or histone to drive or inhibit gene expression. In this review, we look at the mechanisms of TCA cycle metabolites' non-canonical functions in the nucleus in the context of inflammation. In addition, we discuss the known and possible links between these metabolites' nuclear moonlighting functions and the pathogenesis of diseases, including inflammatory diseases and cancers.
    Keywords:  Epigenetics; Immunometabolism; Inflammation; Metabolites; TCA cycle
    DOI:  https://doi.org/10.1186/s12950-025-00461-x
  14. Protein Sci. 2025 Oct;34(10): e70318
      Identifying amino acid residues that are critical for the catalytic function of enzymes is essential for elucidating reaction mechanisms, facilitating drug discovery, and advancing protein engineering. However, experimentally and computationally distinguishing residues that maintain structural integrity from those directly involved in enzymatic function remains a major challenge. In this study, we developed a methodology to identify amino acid residues that influence substrate specificity in enzymes with homologous structures. We framed the sequence comparison as a classification problem, treating each residue as a feature, thereby enabling the rapid and objective identification of key residues responsible for functional differences. To validate the proposed method, we applied it to three enzyme pairs-trypsin/chymotrypsin, adenylyl cyclase/guanylyl cyclase, and lactate dehydrogenase (LDH)/malate dehydrogenase (MDH). The results confirmed the accurate prediction of previously identified specificity-determining residues. Furthermore, we conducted experiments on the LDH/MDH pair and successfully introduced mutations into key residues to alter substrate specificity, enabling LDH to utilize oxaloacetate while maintaining its expression levels. These findings demonstrate the potential of this method for efficiently identifying residues that govern substrate specificity. We have further developed this approach into a practical tool, the EZSCAN: Enzyme Substrate-specificity and Conservation Analysis Navigator (https://ezscan.pe-tools.com/), which enables rapid identification of amino acid residues critical for enzyme function.
    Keywords:  enzyme; software; substrate specificity
    DOI:  https://doi.org/10.1002/pro.70318
  15. Pathogens. 2025 Sep 19. pii: 948. [Epub ahead of print]14(9):
      The actin cytoskeleton plays a crucial role in fundamental eukaryotic processes such as morphogenesis, motility, endocytosis, intracellular trafficking, and cell division. However, our understanding of actin and its associated proteins in trypanosomatid parasites like Leishmania remains limited. Over the past two decades, considerable progress has been made in elucidating the structure and functions of Leishmania actin and its core regulators. Notably, these findings are primarily derived from studies of the insect-stage promastigote form, while the roles of the actin machinery during the disease-causing amastigote stage within mammalian hosts remain largely unexplored. This review consolidates the current knowledge of actin and its interactors in Leishmania promastigotes, highlighting their potential roles in parasite development and stage-specific differentiation. Additionally, it explores the potential of targeting the cytoskeletal system as a strategy for novel therapeutic interventions against Leishmaniasis. The review concludes by identifying critical knowledge gaps and proposing future research directions to better understand actin-driven pathogenesis in this important human parasite.
    Keywords:  Leishmania; actin; actin-binding proteins; functions; structure
    DOI:  https://doi.org/10.3390/pathogens14090948
  16. Subcell Biochem. 2025 ;115 253-279
      Nuclear lamins, a crucial type of intermediate filament protein, primarily form the inner nuclear membrane and are essential for maintaining nuclear integrity throughout various cell cycle stages. However, recent research has uncovered their broader functions as key scaffolds in nuclear sub-compartmentalization, 3D genome organization, and gene regulation. These functions are dynamically regulated by several post-translational modifications (PTMs), including phosphorylation, acetylation, SUMOylation, methylation, ubiquitination, farnesylation, and O-GlcNAcylation. Lamin PTMs influence chromatin stability, nuclear organization, stress responses, cellular differentiation, metabolism, and ageing. The pathological implications of lamin dysfunction are profound. Altered PTM patterns have been associated with multiple disorders, including laminopathies, metabolic syndromes, premature ageing diseases like Hutchinson-Gilford progeria, and even cancer.This chapter discusses how dysregulated lamin PTMs lead to nuclear instability and chromatin disorganization and contribute to disease progression. Understanding how PTMs affect lamin function opens avenues for therapeutic strategies targeting lamin-related disorders. This research is critical for developing innovative treatments aimed at restoring nuclear integrity and normal cellular function, ultimately improving disease outcomes.
    Keywords:  Ageing; Cancer; Cell cycle; Chromatin organization; Laminopathies; Nuclear lamins; PTMs; Stress
    DOI:  https://doi.org/10.1007/978-3-032-00537-3_11
  17. Nucleic Acids Res. 2025 Sep 23. pii: gkaf916. [Epub ahead of print]53(18):
      Histone acetylation is widely assumed to directly instruct gene activation. Among acetylated residues, H4K16ac is one of the most abundant modifications, conserved across all eukaryotes. Despite its established role in X-chromosome hyperactivation in Drosophila, its function in mammalian cells has remained elusive. Here, we show that in human somatic cells, H4K16ac does not substantially affect gene expression, but instead controls the spatiotemporal program of genome replication. By combining a meta-analysis of public datasets and perturbation experiments designed to minimize confounding effects, we found that H4K16ac is neither associated with nor required for transcriptional activity. Rather, H4K16ac depletion resulted in premature replication of heterochromatic regions and widespread alterations in replication timing across the genome. These defects were driven by the aberrant activation of cryptic replication origins at long terminal repeats-repetitive elements typically marked by H4K16ac and whose sequence context resembles that of canonical origins in euchromatic regions. Our findings reveal an unexpected role for one of the most prevalent chromatin modifications and uncover a new regulatory mechanism that safeguards genome replication fidelity.
    DOI:  https://doi.org/10.1093/nar/gkaf916
  18. Prog Mol Biol Transl Sci. 2025 ;pii: S1877-1173(25)00096-1. [Epub ahead of print]217 109-134
      Autophagy is a catabolic process that preserves cellular homeostasis by degrading and recycling damaged organelles and proteins, particularly during metabolic stress, nutrient deprivation, oxidative stress, and inflammation. It is tightly regulated by key molecular pathways, including AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR). Core autophagy-related proteins such as Unc-51-like kinase 1 (ULK1), autophagy-related genes (ATG4, ATG5, ATG7), and microtubule-associated protein 1 light chain 3 (LC3), orchestrate autophagosome formation and cargo degradation. Autophagy influences cellular fate, promoting survival or programmed cell death, and plays a critical role in stem cell differentiation. Impaired autophagy contributes to neurodegenerative diseases by enabling toxic protein accumulation, while its dysregulation affects lipid metabolism and insulin sensitivity in metabolic syndromes and cancers. This chapter explores the molecular mechanisms of autophagy, its regulatory networks, and its implications in disease, emphasizing potential therapeutic interventions. Understanding these pathways provides insights into novel strategies for targeting autophagy in various pathological conditions.
    Keywords:  Autophagy; Cancer; Cell death; P53
    DOI:  https://doi.org/10.1016/bs.pmbts.2025.06.015
  19. mSphere. 2025 Sep 24. e0032925
      Hsp90 is considered to be the master regulator of chaperone activity within the cellular context. In addition to aiding client maturation and maintaining protein homeostasis, Hsp90 serves various non-canonical functions in model eukaryotes: ranging from protein-trafficking into the nucleus to transcriptional regulation, from chromatin remodeling to assembly and disassembly of protein complexes during DNA repair and telomere maintenance. In performing all these trades, Hsp90 collaborates with its co-chaperones in a client-specific or function-specific manner. Hsp90 undergoes various conformational changes during its chaperone cycle, which is regulated via several post-translational modifications (PTM). Different combinations of such PTMs, known as the chaperone code, also play key regulatory roles for Hsp90 functions. Here, we examine various cellular functions of Hsp90 in protozoan parasites, particularly those that shuttle between insect host and human host, adapting to a temperature difference of at least 10°C. Our analyses reveal that most of the prominent co-chaperones are present in all these parasites, except for one that is essential in model eukaryotes. We reviewed the biochemical correlates of Hsp90 and its co-chaperone interactions and realized that the physiological significance of such interplay is largely unknown in the protozoan parasites. One striking observation is the lack of sequence conservation of the parasitic co-chaperones with their human counterparts, making them attractive drug targets. Our analyses revealed that in spite of the identification of few PTMs of parasitic Hsp90 proteins, the chaperone codes remain largely elusive.IMPORTANCEHsp90 is a pivotal molecular chaperone involved in maintaining proteostasis and facilitating the maturation of diverse client proteins. Beyond its canonical folding functions, Hsp90 plays non-canonical roles in nuclear trafficking, transcriptional regulation, chromatin remodeling, and DNA repair. These activities are tightly regulated through interactions with specific co-chaperones and through post-translational modifications, collectively forming the "chaperone code." This study examines Hsp90's role in thermal adaptation of protozoan parasites when shuttling between the insect and human hosts. Here, we summarize the canonical and diverse non-canonical functions of Hsp90 in three protozoan parasites: Plasmodium, Leishmania, and Trypanosoma. We highlight all the Hsp90 isoforms found in these three parasites and also illustrate all the co-chaperones and post-translational modifications of Hsp90 found to be present in these protozoan parasites. Importantly, the divergence in co-chaperone sequences from human homologs in these parasites presents a promising avenue for targeted antiparasitic drug discovery and development.
    Keywords:  Hsp90; Leishmania; Plasmodium; Trypanosoma; chaperone code; co-chaperone
    DOI:  https://doi.org/10.1128/msphere.00329-25
  20. Int J Mol Sci. 2025 Sep 20. pii: 9204. [Epub ahead of print]26(18):
      Methylation reactions catalyzed by S-adenosylmethionine (SAM)-dependent methyltransferases are essential to numerous biological functions, including gene expression regulation, epigenetic modifications, and biosynthesis of natural products. Dysregulation of these enzymes is associated with diseases, including cancer and neurodevelopmental disorders, making them attractive drug targets. This review explores the contribution of computational methods, particularly quantum chemical calculations and molecular dynamics (MD) simulations, in elucidating the mechanisms of SAM-dependent methyltransferases. These techniques enable detailed characterization of transition states and reaction pathways, often inaccessible by experimental methods. The review discusses molecular modeling approaches such as the quantum chemical cluster approach (QM-cluster) and hybrid QM/MM methods, emphasizing their applications in studying methyl group transfer, substrate specificity, and the roles of water molecules and metal ions in catalysis. Additionally, dynamic aspects of enzyme function are addressed using classical MD and QM/MM MD simulations. Case studies demonstrate how computational predictions align with experimental data and enable rational design of selective inhibitors and engineered enzymes with altered specificity. Overall, computational chemistry offers a powerful, atomistic view of SAM-dependent methyltransferases, not only complementing experimental studies but also providing a foundation for the design of future experiments in this field.
    Keywords:  MD; QM-cluster; QM/MM; methyltransferases; reaction mechanisms
    DOI:  https://doi.org/10.3390/ijms26189204
  21. Microorganisms. 2025 Sep 16. pii: 2154. [Epub ahead of print]13(9):
      Minute virus of canines (MVC), which is a member of the Bocaparvovirus genus, is a non-enveloped, single-stranded DNA virus that causes respiratory and gastrointestinal disease in canines, as well as causing infertility and fetal death in pregnant dogs. The non-structural small protein NP1 of bocaparvoviruses is a unique feature that distinguishes the bocaparvovirus subfamily from other parvovirus subfamilies. In the life cycle of the MVC, NP1 plays an indispensable role in viral DNA replication and pre-mRNA processing. Currently, there is a paucity of studies reporting the characterization of host cell proteins interacting with NP1 during MVC replication. In this study, we screened and identified host cell proteins interacting with MVC-NP1 through immunoprecipitation (IP) combined with liquid chromatography and tandem mass spectrometry (LC-MS/MS) analysis; MCM7 (Mini-chromosome Maintenance Protein 7) has been identified and confirmed to interact directly with NP1 through its N-terminal domain. Furthermore, functional studies reveal that MCM7 is essential in MVC replication. The knockdown of MCM7 decreased the expression of this MVC protein significantly, as well as suppressing MVC replication by arresting the cell cycle in the G0/G1 phase during infection. Conversely, up-regulating MCM7 can rehabilitate the expression of MVC proteins, as well as supporting MVC replication. In conclusion, this study elucidates the interaction between the NP1 protein of MVC and the host factor MCM7, demonstrating that MCM7 is a key factor in the replication process of MVC. These findings provide a potential target for future antiviral therapy.
    Keywords:  MCM7; NP1; minute virus of canines; protein interaction; viral replication
    DOI:  https://doi.org/10.3390/microorganisms13092154
  22. Microbiol Res. 2025 Sep 19. pii: S0944-5013(25)00304-0. [Epub ahead of print]302 128345
      Cytokinesis, the final step of cell division, must be precisely coordinated with the cellular metabolic status, yet the underlying regulatory mechanisms remain poorly understood. Here we show that in Schizosaccharomyces pombe, glucose signaling promotes cytokinesis via the evolutionarily conserved cAMP-PKA signaling pathway. Loss of the Pka1 catalytic subunit delays assembly and constriction of the contractile actomyosin ring (CAR), whereas constitutive PKA activation enhances CAR integrity and accelerates cytokinesis. Mechanistically, Pka1 downregulates the basal activity of the stress-activated MAPK Sty1 under glucose-rich conditions, thereby stabilizing the formin For3 and its nucleated actin cables, which collaborate to regulate CAR dynamics. Remarkably, cAMP-PKA signaling also facilitates cytokinesis through a parallel, actin cable-independent mechanism. Additionally, mitochondrial respiration contributes to cytokinesis in the presence of glucose through a PKA-independent pathway. These findings reveal a multilayered network that links carbon source metabolism to cytoskeletal organization and underscore the importance of tight PKA activity control for robust cell division.
    Keywords:  Actin; CAR; Cytokinesis; Formin; Glucose; MAPK; Schizosacharomyces pombe; cAMP-PKA
    DOI:  https://doi.org/10.1016/j.micres.2025.128345