bims-toxgon 2025-07-27 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–07–27
23 papers selected by
Lakesh Kumar, BITS Pilani

Toxoplasma gondii virulence in mice is determined by the pseudokinase ROP5B and countered by an IRG-GBP protein interplay.
Sirtuin family in lung adenocarcinoma.
Sirtuins in mitophagy: key gatekeepers of mitochondrial quality.
HDACs and Their Inhibitors on Post-Translational Modifications: The Regulation of Cardiovascular Disease.
Sirtuins in Central Nervous System Tumors-Molecular Mechanisms and Therapeutic Targeting.
A chaperonin complex regulates organelle proteostasis in malaria parasites.
BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1.
The Fundamental Role of Nutrients for Metabolic Balance and Epigenome Integrity Maintenance.
The Class II histone deacetylase Hda1 is required for gene transcription, stress tolerance, and virulence in the insect pathogen, Beauveria bassiana.
Development of novel mitochondrial pyruvate carrier inhibitors for breast cancer treatment.
Design, Synthesis, and Cellular Characterization of a New Class of IPMK Kinase Inhibitors.
Structure of human mitochondrial pyruvate carrier MPC1 and MPC2 complex.
Modulation of histone tail electrostatic potentials in nucleosome core particles by acetylation and PARylation.
PFKM phosphorylates histone H3 and promotes mitotic progression by sensing the levels of citrate.
Precocious Eimeria magna transgenically expressing RHDV P2 subdomain induces immune responses in rabbits.
Modulation of Glutamine Synthetase adenylylation by nitrogen availability enables one-step purification in distinct post-translational states.
Host sphingolipids support Plasmodium berghei liver stage development.
Mechanistic Insights into Homoserine O-Acetyltransferase from Mycobacterium tuberculosis.
Histone Acetyltransferase MOF-Mediated AURKB K215 Acetylation Drives Breast Cancer Cell Proliferation via c-MYC Stabilization.
Investigating the binding mechanism of AML inhibitors based on panobinostat with HDAC3 proteins using Gaussian accelerated molecular dynamics.
SnRK1 as the Core Node Integrating Energy Homoeostasis, Stress Adaptation and Hormonal Crosstalk in Plants.
mTORC1 senses glutamine and other amino acids through GCN2.
Creation and validation of a proteome-wide yeast library for protein detection and analysis.

Front Immunol. 2025 ;16 1593785

Toxoplasma gondii virulence in mice is determined by the pseudokinase ROP5B and countered by an IRG-GBP protein interplay.

Shishir Singh, Mateo Murillo-León, Aura María Bastidas Quintero, Florence Melbert, Klaus Pfeffer, Daniel Degrandi, Tobias Steinfeldt.

  Toxoplasma gondii (T. gondii) virulence in mice depends on different multiprotein complexes that assemble at the parasitophorous vacuole membrane (PVM) of the parasite. Individual rhoptry proteins within these complexes inhibit different Immunity-Related GTPases (IRG proteins). The rhoptry pseudokinase ROP5 is a central element to achieve IRG-specific rhoptry kinase activity and/or efficient complex formation. The rop5 locus of each of the canonical T. gondii strains encodes three major isoforms, ROP5A, ROP5B and ROP5C, and was shown to have the largest impact on virulence. By reverse genetics, we have generated T. gondii strains expressing either ROP5A, ROP5B or ROP5C in a RHΔrop5 genetic background and demonstrate that ROP5B is mainly responsible for heightened virulence of type I T. gondii in laboratory strains of mice. In vivo virulence correlates with diminished vacuolar IRG protein loading and parasite control in vitro only in presence of ROP5B but not ROP5A or ROP5C. Our results suggest that ROP5A and ROP5C isoforms might have co-evolved with IRG proteins or other host cell resistance factors in evolutionarily important intermediate hosts beyond Mus musculus. The same parasite effectors that inhibit IRG protein accumulation and function reduce the vacuolar amount of Guanylate Binding Proteins (GBP proteins). However, a parasite effector targeting a GBP protein at the PVM has not been described yet. Using two different approaches, Yeast Two-Hybrid analysis and Protein-fragment complementation assay, we here identified three heterologous IRG:GBP pairs, GBP6:Irgb10, GBP5:Irgb10, GBP5:Irgb6, and demonstrate that the accumulation of these GTPases at the PVM is interdependent. Our results offer a novel perspective on the IRG and GBP protein-mediated control of T. gondii infections and may further advance the investigation of GBP-specific T. gondii effectors.

Keywords:  IRG/GBP proteins; T. gondii virulence; co-evolution; host cell resistance; pseudokinases

DOI:  https://doi.org/10.3389/fimmu.2025.1593785
Discov Oncol. 2025 Jul 23. 16(1): 1398

Sirtuin family in lung adenocarcinoma.

Cui Chen, Xiumin Liu, Zhe Xu, Juan Xu, Lei Gong, Xiaobo Wang.

  Lung cancer is a highly aggressive malignancy that accounts for one of the greatest mortality rate in humans globally. Among various types of lung malignancies, lung adenocarcinoma (LUAD) stands out as the most common form. Sirtuins (SIRTs) are class III nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases that comprise seven members (SIRT1-7). Sirtuins play a essentail role in various biological processes such as cellular differentiation, inflammation, apoptosis, metabolism, immune response, oxidative stress, mitochondrial homeostasis, and autophagy. Therefore, it is considered a potential therapeutic target for different kinds of pathologies including cancer, kidney diseases, and other conditions. While several reviews have been published on sirtuins and lung cancer, there remains a gap in the review regarding sirtuins specifically in LUAD. Herein, we not only elaborate on the roles of different sirtuins and their mechanisms in LUAD, but also discuss the potential application of sirtuins inhibitors and activators for LUAD therapy.

Keywords:  LUAD; Progression; Regulation; Sirtuins; Therapy

DOI:  https://doi.org/10.1007/s12672-025-03217-4
Mol Cell Biochem. 2025 Jul 24.

Sirtuins in mitophagy: key gatekeepers of mitochondrial quality.

Francisco Alejandro Lagunas-Rangel.

  Mitochondria are highly dynamic organelles essential for cellular energy production. However, they are also a primary source of reactive oxygen species, making them particularly vulnerable to oxidative damage. To preserve mitochondrial integrity, cells employ quality control mechanisms such as mitophagy, a selective form of autophagy that targets damaged or dysfunctional mitochondria for degradation. Among the key regulators of mitophagy are the sirtuins, a family of NAD+-dependent deacetylases. SIRT1, SIRT3, and SIRT6 generally promote mitophagy, whereas SIRT2, SIRT4, SIRT5, and SIRT7 often act as negative regulators. Sirtuin-mediated regulation of mitophagy is critical for maintaining cellular homeostasis and is implicated in a variety of physiological and pathological conditions. The aim of this review is to provide an overview focused on describing how sirtuins influence the mitophagy process. It highlights the different molecular mechanisms by which individual members of the sirtuin family modulate mitophagy, either by promoting or suppressing it, depending on the context. In addition, the review explores the relevance of sirtuin-regulated mitophagy in health and disease, emphasizing some conditions under which altered sirtuin activity could be harnessed for therapeutic benefit.

Keywords:  FOXO transcription factors; Mitochondria; PINK1-PARKIN pathway; Receptor-mediated mitophagy; Ubiquitin-mediated mitophagy

DOI:  https://doi.org/10.1007/s11010-025-05358-0
Cells. 2025 Jul 20. pii: 1116. [Epub ahead of print]14(14):

HDACs and Their Inhibitors on Post-Translational Modifications: The Regulation of Cardiovascular Disease.

Siyi Yang, Yidong Sun, Wei Yu.

  Cardiovascular diseases (CVD), such as myocardial hypertrophy, heart failure, atherosclerosis, and myocardial ischemia/reperfusion (I/R) injury, are among the major threats to human health worldwide. Post-translational modifications alter the function of proteins through dynamic chemical modification after synthesis. This mechanism not only plays an important role in maintaining homeostasis and plays a crucial role in maintaining normal cardiovascular function, but is also closely related to the pathological state of various diseases. Histone deacetylases (HDACs) play an important role in the epigenetic regulation of gene expression, and play important roles in post-translational modification by catalyzing the deacetylation of key lysine residues in nucleosomal histones, which are closely associated with the occurrence and development of cardiovascular diseases. Recent studies indicate that HDAC inhibitors (HDACis) may represent a new class of drugs for the treatment of cardiovascular diseases by influencing post-translational modifications. In this review, we systematically summarize the mechanism of action of HDACs and HDACis in post-translational modifications related to common cardiovascular diseases, providing new ideas for the treatment of CVD, and explore possible future research directions on the relationship between HDAC and HDACi in post-translational modifications and cardiovascular diseases.

Keywords:  HDAC; HDACi; cardiovascular disease (CVD); post-translational modification (PTM)

DOI:  https://doi.org/10.3390/cells14141116
Cells. 2025 Jul 19. pii: 1113. [Epub ahead of print]14(14):

Sirtuins in Central Nervous System Tumors-Molecular Mechanisms and Therapeutic Targeting.

Agnieszka Nowacka, Martyna Śniegocka, Maciej Śniegocki, Ewa Aleksandra Ziółkowska.

  Sirtuins (SIRTs), a family of NAD+-dependent enzymes, play crucial roles in epigenetic regulation, metabolism, DNA repair, and stress response, making them relevant to glioma biology. This review systematically summarizes the molecular mechanisms and context-specific functions of SIRT1-SIRT7 in central nervous system tumors, with particular focus on gliomas. SIRT1, SIRT3, SIRT5, and SIRT7 are often overexpressed and promote glioma cell proliferation, stemness, therapy resistance, and metabolic adaptation. Conversely, SIRT2, SIRT4, and SIRT6 generally exhibit tumor-suppressive functions by inducing apoptosis, inhibiting invasion, and counteracting oncogenic signaling. Preclinical studies have identified several sirtuin modulators-both inhibitors and activators-that alter tumor growth, sensitize cells to temozolomide, and regulate pathways such as JAK2/STAT3, NF-κB, and mitochondrial metabolism. Emerging evidence positions sirtuins as promising targets for glioma therapy. Future studies should evaluate sirtuin modulators in clinical trials and explore their potential for patient stratification and combined treatment strategies.

Keywords:  ATRT; CNS tumors; GBM; GSCs; NAD+-dependent deacetylases; SIRT; cell metabolism; central nervous system tumors; glioblastoma; glioblastoma stem cells; glioma; histones; medulloblastoma; oncogene; sirtuins; tumor suppressor

DOI:  https://doi.org/10.3390/cells14141113
PLoS Pathog. 2025 Jul;21(7): e1013275

A chaperonin complex regulates organelle proteostasis in malaria parasites.

Amanda Tissawak, Yarden Rosin, Shirly Katz Galay, Alia Qasem, Michal Shahar, Nirit Trabelsi, Ora Furman-Schueler, Steven M Johnson, Anat Florentin.

The apicoplast of Plasmodium parasites serves as a metabolic hub that synthesize essential biomolecules. Like other endosymbiotic organelles, 90% of the apicoplast proteome is encoded by the cell nucleus and transported to the organelle. Evidence suggests that the apicoplast has minimal control over the synthesis of its proteome and therefore it is unclear how organelle proteostasis is regulated. Here, we identified and investigated a large and conserved chaperonin (CPN) complex with a previously unknown function. Using genetic tools, we demonstrated that ablation of the apicoplast CPN60 subunit leads to parasite death due to organellar damage, immediately within its first replication cycle, deviating from the delayed death phenotype commonly observed for apicoplast translation inhibitors. Unlike its close orthologues in other prokaryotic and eukaryotic cells, CPN60 is not upregulated during heat shock (HS) and does not affect HS response in the parasite. Instead, we found that it is directly involved in proteostasis through interaction with the Clp (caseinolytic protease) proteolytic complex. We showed that CPN60 physically binds both the active and inactive forms of the Clp complex, and manipulates its stability. A computational structural model of a possible interaction between these two large complexes suggests a stable interface. Finally, we screened a panel of inhibitors for the bacterial CPN60 orthologue GroEL, to test the potential of chaperonin inhibition as antimalarial. These inhibitors demonstrated an anti-Plasmodium activity that was not restricted to apicoplast function, with additional targets outside of this organelle. Taken together, this work reveals how balanced activities of proteolysis and refolding safeguard the apicoplast proteome, and are essential for organelle biogenesis.

DOI: https://doi.org/10.1371/journal.ppat.1013275
Nucleic Acids Res. 2025 Jul 19. pii: gkaf650. [Epub ahead of print]53(14):

BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1.

Alan Monziani, Rotem Ben-Tov Perry, Hadas Hezroni, Igor Ulitsky.

Chromatin modifications play a key role in regulating gene expression during development and adult physiology. Histone acetylation, particularly H3K27ac, is associated with increased activity of gene regulatory elements such as enhancers and promoters. However, the regulation of the machinery that writes, reads, and erases this modification remains poorly understood. In particular, the SIN3A-HDAC1 complex possesses histone deacetylase activity, yet it commonly resides at active regulatory regions. Here, we study BAHCC1, a large chromatin-associated protein essential for viability and recently reported to play a largely repressive role. We show that in neuronal lineage cells, BAHCC1 is mainly associated with regulatory elements marked with H3K27ac. BAHCC1 interacts and co-occupies shared genomic regions with the SIN3A scaffold protein, but not with its paralog SIN3B, and its perturbations lead to altered acetylation and expression of proximal genes in a neuronal cell line and primary cortical neurons. The regulated genes are enriched for those functioning in neurogenesis and cell migration, and primary cortical neurons with reduced Bahcc1 expression display impaired neurite outgrowth. We thus propose a model in which BAHCC1 antagonizes SIN3A histone deacetylation and positively regulates the expression of genes that are important for growth and migration-related processes in the neuronal lineage.

DOI: https://doi.org/10.1093/nar/gkaf650
Epigenomes. 2025 Jul 09. pii: 23. [Epub ahead of print]9(3):

The Fundamental Role of Nutrients for Metabolic Balance and Epigenome Integrity Maintenance.

Ana Paula de Souza, Vitor Marinho, Marcelo Rocha Marques.

  Epigenetic modifications act as crucial regulators of gene activity and are influenced by both internal and external environmental factors, with diet being the most impactful external factor. On the other hand, cellular metabolism encompasses a complex network of biochemical reactions essential for maintaining cellular function, and it impacts every cellular process. Many metabolic cofactors are critical for the activity of chromatin-modifying enzymes, influencing methylation and the global acetylation status of the epigenome. For instance, dietary nutrients, particularly those involved in one-carbon metabolism (e.g., folate, vitamins B12 and B6, riboflavin, methionine, choline, and betaine), take part in the generation of S-adenosylmethionine (SAM), which represents the main methyl donor for DNA and histone methylation; α-ketoglutarate and ascorbic acid (vitamin C) act, respectively, as a co-substrate and cofactor for Ten-eleven Translocation (TET), which is responsible for DNA demethylation; and metabolites such as Acetyl-CoA directly impact histone acetylation, linking metabolism of the TCA cycle to epigenetic regulation. Further, bioactive compounds, such as polyphenols, modulate epigenetic patterns by affecting methylation processes or targeting epigenetic enzymes. Since diet and nutrition play a critical role in shaping epigenome functions and supporting human health, this review offers a comprehensive update on recent advancements in metabolism, epigenetics, and nutrition, providing insights into how nutrients contribute to metabolic balance, epigenome integrity maintenance and, consequently, disease prevention.

Keywords:  DNA methylation; TCA cycle; diet; epigenetic; histone modification; metabolism; one-carbon cycle

DOI:  https://doi.org/10.3390/epigenomes9030023
Pest Manag Sci. 2025 Jul 21.

The Class II histone deacetylase Hda1 is required for gene transcription, stress tolerance, and virulence in the insect pathogen, Beauveria bassiana.

Qing Cai, Jia-Tao Xie, Dao-Hong Jiang.

   BACKGROUND: The Hda1 protein, a conserved Class II histone deacetylase, plays a key role in deacetylating histone proteins and regulating gene transcription. Although its importance has been established in various organisms, the functional role of Hda1 in insect pathogenic fungi has not been thoroughly investigated.
RESULTS: In this study, we explore the function of BbHda1 in the entomopathogenic fungus Beauveria bassiana. The absence of BbHda1 dramatically enhanced bulk acetylation of histone H4, but had no observable effect on histone H3 acetylation. Consequently, the deletion of BbHda1 led to several notable phenotypic changes, including decreased conidial yield, slowed conidial germination and impaired conidial properties. Additionally, the ΔBbHda1 mutant exhibited reduced resistance to multiple stresses, such as oxidative stress, cell wall perturbation and DNA damage. Notably, the ΔBbHda1 mutant displayed significantly slower growth in insect hemocoel and reduced virulence. Comparative transcriptomic analysis revealed a wide array of downregulated genes involved in various biological processes, including secondary metabolism, chemoperception and response, detoxification involving cytochrome P450, and multiple drug transporters and virulence factors. Our findings revealed that BbHda1 is essential for modulating sporulation, multistress resistance and fungal virulence, primarily through its control of histone acetylation and transcriptional regulation.
CONCLUSION: These results elucidated the critical role of BbHda1 in development, stress response, and virulence in B. bassiana, and provide valuable insights into the post-translational mechanisms underlying fungal pathogenesis. © 2025 Society of Chemical Industry.

Keywords:  conidial properties; entomopathogenic fungi; gene transcription; histone deacetylase; stress resistance; virulence

DOI:  https://doi.org/10.1002/ps.70046
J Biol Chem. 2025 Jul 16. pii: S0021-9258(25)02336-1. [Epub ahead of print] 110486

Development of novel mitochondrial pyruvate carrier inhibitors for breast cancer treatment.

Tanner J Schumacher, Zachary S Gardner, Jon Rumbley, Conor T Ronayne, Venkatram R Mereddy.

  Reprogrammed metabolism of cancer cells offers a unique target for pharmacological intervention. The mitochondrial pyruvate carrier (MPC) plays important roles in cancer progression by transporting cytosolic pyruvate into the mitochondria for use in the TCA cycle. In the current study, a series of novel fluoro-substituted aminocarboxycoumarin derivatives have been evaluated for their mitochondrial pyruvate carrier (MPC) inhibition properties. Our studies indicate that the aminocarboxycoumarin template elicits potent MPC inhibitory characteristics, and specifically, structure activity relationship studies show that the N-methyl-N-benzyl structural template provides the optimal inhibitory capacity. Further respiratory experiments demonstrate that candidate compounds specifically inhibit pyruvate driven respiration without substantially affecting other metabolic fuels, consistent with MPC inhibition. Further, computational inhibitor docking studies illustrate that aminocarboxycoumarin binding characteristics are nearly identical to that of classical MPC inhibitor UK5099 bound to human MPC, recently determined by cryoEM. The lead candidate C5 elicits cancer cell proliferation inhibition specifically in monocarboxylate transporter 1 (MCT1) expressing murine breast cancer cells 4T1 and 67NR, consistent with its ability to accumulate intracellular lactate. In vivo tumor growth studies illustrate that C5 significantly reduces the tumor burden in two syngeneic murine tumor models with 4T1 and 67NR cells. These studies provide novel MPC inhibitors with potential for anticancer applications in MCT1 expressing breast cancer tumor models.

Keywords:  aminocarboxycoumarin; breast cancer; mitochondrial pyruvate carrier; tumor metabolism

DOI:  https://doi.org/10.1016/j.jbc.2025.110486
J Med Chem. 2025 Jul 25.

Design, Synthesis, and Cellular Characterization of a New Class of IPMK Kinase Inhibitors.

Yubai Zhou, Pratima Chapagain, Desmarini Desmarini, Dilipkumar Uredi, Michael A Stashko, Hundaol Huluka, Lucia E Rameh, Julianne T Djordjevic, Raymond D Blind, Xiaodong Wang.

The kinase activity of human inositol phosphate multikinase (IPMK) is required for the synthesis of higher-order inositol phosphate signaling molecules, regulation of gene expression, and control of the cell cycle. Here, we report a novel series of highly potent IPMK inhibitors. The first-generation IPMK inhibitor 1 (UNC7437) decreased cellular proliferation and tritiated inositol phosphate levels in metabolically labeled human U251-MG glioblastoma cells. It also impacted the transcriptome of these cells, selectively regulating 993 genes enriched in cancer, epithelial-to-mesenchymal transition (EMT), and inflammatory and viral infection pathways, consistent with anticancer growth activity. Extensive optimization of 1 led to 14 (UNC9750) with improved pharmacokinetic properties. Compound 14 inhibited cellular accumulation of InsP5, the direct product of IPMK kinase activity, while having no effect on either InsP6 or InsP7 levels. These studies suggest that rapid chemical inhibition of IPMK induces a novel InsP5 metabolic signature, providing new biological insights into inositol phosphate metabolism and signaling.

DOI: https://doi.org/10.1021/acs.jmedchem.5c00015
Nat Commun. 2025 Jul 21. 16(1): 6700

Structure of human mitochondrial pyruvate carrier MPC1 and MPC2 complex.

Yingyuan Sun, Yaru Wang, Zheng Xing, Dongyu Li, Rong Wang, Baozhi Chen, Ning Zhou, Alyssa Ayala, Benjamin P Tu, Xiaofeng Qi.

The Mitochondrial Pyruvate Carrier (MPC) bridges cytosolic and mitochondrial metabolism by transporting pyruvate into mitochondria for ATP production and biosynthesis of various essential molecules. MPC functions as a heterodimer composed of MPC1 and MPC2 in most mammalian cells. Here, we present the cryogenic electron microscopy (cryo-EM) structures of the human MPC1-2 complex in the mitochondrial intermembrane space (IMS)-open state and the inhibitor-bound in the mitochondrial matrix-open state. Structural analysis shows that the transport channel of MPC is formed by the interaction of transmembrane helix (TM) 1 and TM2 of MPC1 with TM2 and TM1 of MPC2, respectively. UK5099, a potent MPC inhibitor, shares the same binding site with pyruvate at the matrix side of the transport channel, stabilizing MPC in its matrix-open conformation. Notably, a functional W82F mutation in MPC2 leads to the complex in an IMS-open conformation. Structural comparisons across different conformations, combined with yeast rescue assays, reveal the mechanisms of substrate binding and asymmetric conformational changes in MPC during pyruvate transport across the inner mitochondrial membrane (IMM) as well as the inhibitory mechanisms of MPC inhibitors.

DOI: https://doi.org/10.1038/s41467-025-61939-z
Proc Natl Acad Sci U S A. 2025 Jul 29. 122(30): e2511507122

Modulation of histone tail electrostatic potentials in nucleosome core particles by acetylation and PARylation.

Nicolas Bolik-Coulon, Philip Rößler, Michael L Nosella, Tae Hun Kim, Lewis E Kay.

  Cellular DNA is wrapped about an octamer composed of four histone proteins forming the fundamental unit of chromatin structure, the nucleosome core particle (NCP). The intrinsically disordered tails of the histones serve as scaffolds for binding an array of proteins that regulate the fidelity of the genome and gene expression. A variety of posttranslational modifications (PTMs) on the tails have been characterized, including some that alter their overall charge; however, per-residue changes in tail electrostatic potentials for different PTMs have not been reported. Here, using a solution NMR approach in which enhancements of transverse relaxation rates of tail amide and methyl group protons are quantified through the addition of paramagnetic cosolutes, we examine how acetylation and PARylation modulate histone tail electrostatic potentials. Notably, even though both PTMs decrease the net positive charge carried by each tail, their electrostatic potentials either increase or decrease in a tail-specific manner relative to an unmodified NCP. A simple model of tail-DNA interactions is presented to explain these results.

Keywords:  NMR; histone tail–DNA interactions; post-translational modifications; solvent paramagnetic relaxation enhancement

DOI:  https://doi.org/10.1073/pnas.2511507122
Nat Commun. 2025 Jul 22. 16(1): 6736

PFKM phosphorylates histone H3 and promotes mitotic progression by sensing the levels of citrate.

Pianpian Lin, Yijun Qi, Huiying Chu, Hongyu Wu, Yajuan Zhang, Xiaolan Huang, Chen Li, Xiaoyan Xu, Hong Gao, Rong Zeng, Guohui Li, Weiwei Yang.

Emerging evidence indicates that metabolic signals-including nutrient availability, biosynthetic intermediates, and energy balance-are linked to cell cycle progression. However, how these signals are sensed by the cell cycle machinery remains unclear. Citrate, a key intermediate in the TCA cycle, peaks during mitosis (M phase) and is detected by the glycolytic enzyme ATP-dependent 6-phosphofructokinase 1 muscle isoform (PFKM), accelerating mitotic progression. Mechanistically, citrate binds PFKM, disrupting its tetrameric structure into dimers. Dimeric PFKM interacts with nucleosomes and phosphorylates histone H3 at serine 10 (H3S10), functioning as a protein kinase to promote mitosis and cell proliferation. Structural simulations reveal that PFKM binds nucleosomes optimally when H3S10 aligns with its catalytic site. Disrupting citrate-PFKM or PFKM-H3 interactions reduces H3S10 phosphorylation, delays mitosis, and suppresses tumor growth and T-cell proliferation. Our findings demonstrate that PFKM acts as a citrate sensor, coupling metabolic signals to cell cycle regulation.

DOI: https://doi.org/10.1038/s41467-025-62111-3
NPJ Vaccines. 2025 Jul 24. 10(1): 167

Precocious Eimeria magna transgenically expressing RHDV P2 subdomain induces immune responses in rabbits.

Wenxuan Chen, Jingxia Suo, Jiahua Kong, Chunxia Lu, Xiaomin Ge, Fang Yu, Xinming Tang, Xun Suo, Xianyong Liu.

Rabbit coccidiosis and rabbit haemorrhagic disease (RHD) pose major threats to the rabbit industry, causing significant economic losses. Developing a multivalent vaccine to concurrently protect rabbits against Eimeria and RHDV infections would provide dual protection through a single immunization protocol. Here, we utilized a precocious line of E. magna (EmagPWT) as a vaccine vector to express P2 subdomain of RHDV capsid protein VP60. We constructed three transgenic parasites expressing (i) RHDV1-P2 subdomain, (ii) RHDV2-P2 subdomain, and (iii) 2 copies of P2 subdomains from both RHDV1 and RHDV2. We found that all transgenic parasites elicited detectable neutralizing antibodies and robust mucosal immune response following secondary immunization. In conclusion, our results indicate genetically manipulated precocious Eimeria parasite expressing heterologous antigens, such as P2 subdomain, holds promise as a vector for developing a multivalent vaccine against RHD and Eimeria infections in rabbits.

DOI: https://doi.org/10.1038/s41541-025-01223-9
Protein Expr Purif. 2025 Jul 16. pii: S1046-5928(25)00121-4. [Epub ahead of print]235 106779

Modulation of Glutamine Synthetase adenylylation by nitrogen availability enables one-step purification in distinct post-translational states.

Larissa Fonseca Tomazini, Eduardo Sabatine Lopes, Bárbara Barizão Nogueira, Gabriela Carvalho Calsavara, Ana Paula Santos Silva, Naiara Cristina Lucredi, Edileusa Cristina Marques Gerhardt, Luciano Fernandes Huergo, Marco Aurelio Schuler Oliveira.

  The glutamine synthetase (GS) enzyme pathway promotes ammonium assimilation in bacteria and is a metabolic hub for glutamine and glutamate homeostasis. Bacterial GS can be reversibly inhibited through adenylylation as a response to nitrogen availability, carried out by the GlnE enzyme. The adenylylation changes GS catalytic and regulatory properties, such as the sensitivity to negative feedback by allosteric modulators and the preferred cofactor usage. In this way, the purification of GS in different modification states can be useful during the investigation of its regulatory properties. Here we show that just by changing nitrogen availability during cell growth it is possible to obtain adenylylated or unmodified GS enzymes after heterologous expression followed by a one-step purification. As a model, we expressed GS enzymes from the diazotrophic bacteria Herbaspirillum seropedicae and Azospirillum brasilense in the M9 media supplemented with ammonium or glutamine. The enzymes were purified by Ni2+-affinity chromatography. The data showed that just by varying the nitrogen source during protein expression it was possible to obtain GS in different adenylation status. The different adenylated isoforms of GS obtained were confirmed by electrophoretic mobility shifts and showed unique responses to Mg2+ and Mn2+ ions and feedback inhibition by amino acids. Finally, we show the unmodified GS can only bind the glutamate substrate when ATP is present. The method to purify GS on different adenylylation states in a single step described here will facilitate the characterization of this key metabolic enzyme in the future.

Keywords:  Adenylylation; Glutamine synthetase; Nitrogen metabolism; Protein purification; Protein-ligand interaction

DOI:  https://doi.org/10.1016/j.pep.2025.106779
mBio. 2025 Jul 21. e0167525

Host sphingolipids support Plasmodium berghei liver stage development.

Erin A Schroeder, Isabel C Colón, Porter E Petruzziello, Emily R Derbyshire.

  During the asymptomatic liver stage, Plasmodium resides within a parasitophorous vacuole (PV) that protects the parasite from immune clearance while also restricting nutrient exchange with its host cell. Although it is known that Plasmodium must scavenge resources from its environment, the specific nutrients sequestered and the mechanisms for transporting them to the PV are poorly understood, particularly during the liver stage. In this study, we investigated the role of host lipids and discovered that sphingolipids are critical for both Plasmodium berghei liver stage development and invasion. Specifically, exogenous C16-ceramide enhanced parasite development and nuclear replication, while sphingomyelin in the host cell membrane was essential for parasite invasion. Live microscopy studies using NBD labeled sphingolipids further found that exogenous lipids are actively transported into the PV with sphingolipid scavenging occurring at all tested time points throughout the liver stage. This was, in part, supported by the host ceramide transporter, CERT1. CERT1 was enriched at the PV and genetic disruption significantly reduced both P. berghei load and ceramide trafficking into the PV. Finally, we identified proteins of the host salvage pathway as critical for the Plasmodium liver stage using chemical and genetic approaches. In particular, depletion of CERS3 and SPHK1 affected PV size and infection rate, but not invasion. Our findings enhance our understanding of host-parasite lipid interactions and may offer novel therapeutic targets to reduce disease burden.IMPORTANCEPlasmodium, the causative agent of malaria, remains a significant global health challenge, placing approximately half the world's population at risk of infection. Despite the existence of antimalarial treatments, the emergence of drug-resistant parasites highlights the urgent need to identify novel therapeutic targets. The Plasmodium liver stage represents a promising avenue for drug discovery as inhibiting parasite development would prevent both symptomatic disease and transmission to the mosquito vector. In this study, we examined the role of host sphingolipids and found that members perform distinct functions, supporting parasite invasion and/or development. We also identified several host proteins that influence Plasmodium liver stage viability and contribute to sphingolipid acquisition. In addition to their role in the liver stage, sphingolipids are known to be critical for the asexual and sexual blood stages, suggesting that targeting host sphingolipid metabolism could offer a novel multistage therapeutic strategy against malaria.

Keywords:  CERT1; Plasmodium; host-parasite interactions; lipid trafficking; liver stage malaria; sphingolipid

DOI:  https://doi.org/10.1128/mbio.01675-25
Biochemistry. 2025 Jul 22.

Mechanistic Insights into Homoserine O-Acetyltransferase from Mycobacterium tuberculosis.

Wanting Jiao, Gerd Mittelstädt, Alistair T Richardson, Timothy M Allison, Michael Berney, Emily J Parker.

The enzyme MetX is a homoserine O-acetyltransferase that catalyzes the first step in methionine biosynthesis and is essential for survival and virulence of various pathogens. It is an attractive target for antifungal and antibacterial drug development. MetX catalyzes the acetyl transfer from acetyl-CoA (AcCoA) to homoserine via a ping-pong mechanism involving an acyl-enzyme intermediate. The active site contains a Ser-His-Asp catalytic triad, which constitutes its core catalytic machinery. Here we investigated the mechanistic details of MetX from Mycobacterium tuberculosis (MtbMetX) using a combination of quantum mechanics/molecular mechanics (QM/MM) calculations, mutagenesis, and mass spectrometry. QM/MM calculations suggest that D320 of the catalytic triad participates in the proton transfer during homoserine acetylation, but not during acyl-enzyme formation. Experiments showed that a D320N substitution, which removes the proton-accepting capability of D320 as well as the pKa modulation of H350 by D320, still allowed acyl-enzyme formation at a markedly reduced rate, but significantly impaired the production of acetyl-homoserine. To isolate the effect of D320's participation in proton transfer from its pKa modulation role, we used QM/MM calculations to simulate a system where D320 could modulate H350 pKa but not accept a proton. These calculations suggest that while D320's proton-accepting role is not required for the AcCoA reaction, it contributes thermodynamically in the homoserine reaction by lowering the energy of the forward pathway. Elucidating the mechanistic details of MtbMetX reactions offers valuable insights that will facilitate the development of mechanism-based inhibitors, contributing to future therapeutic strategies.

DOI: https://doi.org/10.1021/acs.biochem.5c00089
Cells. 2025 Jul 17. pii: 1100. [Epub ahead of print]14(14):

Histone Acetyltransferase MOF-Mediated AURKB K215 Acetylation Drives Breast Cancer Cell Proliferation via c-MYC Stabilization.

Yujuan Miao, Na Zhang, Fuqing Li, Fei Wang, Yuyang Chen, Fuqiang Li, Xueli Cui, Qingzhi Zhao, Yong Cai, Jingji Jin.

  Aurora kinase B (AURKB), a serine/threonine protein kinase, is essential for accurate chromosome segregation and cytokinesis during mitosis. Dysregulation of AURKB, often characterized by its overexpression, has been implicated in various malignancies, including breast cancer. However, the mechanisms governing its dysregulation remain incompletely understood. Here, we identify a pivotal role for the MOF/MSL complex-which includes the histone acetyltransferase MOF (KAT8)-in modulating AURKB stability through acetylation at lysine 215 (K215). This post-translational modification inhibits AURKB ubiquitination, thereby stabilizing its protein levels. MOF/MSL-mediated AURKB stabilization promotes the proper assembly of the chromosomal passenger complex (CPC), ensuring mitotic fidelity. Notably, inhibition of MOF reduces AURKB K215 acetylation, leading to decreased AURKB expression and activity. Consequently, this downregulation suppresses expression of the downstream oncogene c-MYC, ultimately attenuating the malignant proliferation of breast cancer cells. Collectively, our findings reveal a novel mechanism by which lysine acetylation regulates AURKB stability, highlight the significance of the MOF-AURKB-c-MYC axis in breast cancer progression, and suggest potential therapeutic strategies targeting this pathway in clinical settings.

Keywords:  AURKB; MOF; acetylation; cell proliferation; histone acetyltransferase

DOI:  https://doi.org/10.3390/cells14141100
RSC Adv. 2025 Jul 21. 15(32): 26240-26252

Investigating the binding mechanism of AML inhibitors based on panobinostat with HDAC3 proteins using Gaussian accelerated molecular dynamics.

Xia Yu, Hengzheng Yang, Baiji Xue, Tong Liu, Xue Zhang, Yang Xu, Xueliang Zhao, Xianwen Yue.

Class I histone deacetylases (HDACs) play a crucial role in the transformation and survival of myeloid and lymphoid malignancies, with HDAC1, 2, and 3 (Class I HDACs) being potential molecular targets for acute myelogenous leukemia (AML) treatment. Among them, HDAC3 depletion or inhibition significantly reduces proliferation and promotes differentiation in leukemia, with inhibitors like Panobinostat and compound 13a showing promise in suppressing its activity. In this study, we utilized Gaussian accelerated molecular dynamics (GaMD) simulations to compare the inhibitory potency of 13a and Panobinostat against HDAC3. Our findings suggest that the superior inhibitory activity of 13a may be attributed to its stronger interactions with HDAC3. Distance analysis demonstrated that 13a maintains a closer and more consistent coordination with the zinc ion in the catalytic pocket, resulting in a more stable interaction compared to Panobinostat. Additionally, interaction analysis revealed that 13a forms more π-alkyl interactions, along with additional attractive charge and metal-acceptor interactions with HDAC3. Principal component analysis (PCA) further showed that the binding of 13a stabilizes HDAC3 in multiple distinct conformational states, suggesting that a more substantial conformational rearrangement is required upon 13a binding. This structural complexity may explain why 13a behaves as a slow-on/slow-off inhibitor and exhibits a superior IC50 compared to Panobinostat. Alanine scanning identified residues such as PRO23, HIS125, and PHE144 as potential sites for inhibitor binding, making significant contributions to binding affinity. These combined findings suggest that 13a not only has a higher inhibitory potency but also holds potential for further optimization, making it a promising candidate for targeted cancer therapy.

DOI: https://doi.org/10.1039/d5ra01129a
Plant Cell Environ. 2025 Jul 22.

SnRK1 as the Core Node Integrating Energy Homoeostasis, Stress Adaptation and Hormonal Crosstalk in Plants.

Qinzhen Xu, Fanjiang Kong, Wenqiang Yang.

  The SnRK1 (sucrose nonfermenting 1-related protein kinase 1) plays a pivotal role in plant growth, development and stress responses. This review provides an overview of the structure, posttranslational regulation and diverse functions of SnRK1 in plants. SnRK1 is a heterotrimeric complex composed of α, β and βγ subunits, and its activity is regulated through phosphorylation, ubiquitination, SUMOylation, N-myristoylation and potentially acetylation. SnRK1 is expressed across various plant tissues and is involved in multiple cellular processes, including sugar signalling, energy homoeostasis and hormone regulation. It governs plant growth and development, ranging from seed germination to flowering and fruiting, by modulating gene expression, protein stability and metabolic pathways. Furthermore, SnRK1 plays a crucial role in the plant's response to abiotic and biotic stresses. SnRK1 also modulates plant hormone signals, thus coordinating growth and stress responses. Despite the established functional framework of SnRK1, questions regarding subunit interaction dynamics, subcellular localisation shifts and spatiotemporal specificity of posttranslational modifications remain. Future research should prioritise engineering SnRK1 signalling networks to develop stress-tolerant and energy-efficient crop germplasm. This would provide valuable insights into enhancing crop yield and stress tolerance.

Keywords:  SnRK1; energy homoeostasis; hormone signalling; metabolic regulation; stress response

DOI:  https://doi.org/10.1111/pce.70074
EMBO J. 2025 Jul 21.

mTORC1 senses glutamine and other amino acids through GCN2.

Gianluca Figlia, Sandra Müller, Fabiola Garcia-Cortizo, Marilena Neff, Glynis Klinke, Gernot Poschet, Aurelio A Teleman.

  mTORC1 promotes cell growth when nutrients such as amino acids are available. While dedicated sensors relaying availability of leucine, arginine and methionine to mTORC1 have been identified, it is still unclear how mTORC1 senses glutamine, one of its most potent inducers. Here, we find that glutamine is entirely sensed through the protein kinase GCN2, whose initial activation is not triggered by depletion of glutamine itself, but by the concomitant depletion of asparagine. In turn, GCN2 leads to a succession of events that additively inhibit mTORC1: within 1 h, GCN2 inhibits mTORC1 through the Rag GTPases, independently of its function as an eIF2α kinase. Later, GCN2-mediated induction of ATF4 upregulates Ddit4 followed by Sestrin2, which together cause additional mTORC1 inhibition. Additionally, we find that depletion of virtually any other amino acid also inhibits mTORC1 through GCN2. GCN2 and the dedicated amino acid sensors thus represent two independent systems that enable mTORC1 to perceive a wide spectrum of amino acids.

Keywords:  Amino Acid Sensors; Asparagine; GCN2; Glutamine; mTORC1

DOI:  https://doi.org/10.1038/s44318-025-00505-1
J Cell Sci. 2025 Jul 24. pii: jcs.263848. [Epub ahead of print]

Creation and validation of a proteome-wide yeast library for protein detection and analysis.

Din Baruch, Ioannis Tsirkas, Ehud Sass, Benjamin Dubreuil, Yeynit Asraf, Amir Aharoni, Maya Schuldiner, Ofir Klein.

  A significant challenge in cell biology is to uncover the function of uncharacterized proteins. Surprisingly a quarter of the proteome is still poorly understood even in the most well studied model organisms. Systematic methodologies, including the use of tagged protein collections, have emerged as a powerful approach to address this gap. Despite the availability of proteome-wide collections featuring various fused proteins, the impact of different tags on protein function highlights the need for diversifying the tags used for functional genomic studies. To rise to this challenge, we created a proteome-wide collection of yeast strains in which proteins are N-terminally tagged with the broadly utilized and compact Hemagglutinin (HA) epitope. We showcase the potential uses of our library for systematically evaluating protein size, abundance and localization using an in vivo labeling approach. Our characterization underscores the potential utility of a proteome-wide HA-tagged library in revealing novel aspects of cell biology, providing an additional powerful tool for functional genomics.

Keywords:  HA tag; Proteome wide library; SWAT approach; Saccharomyces cerevisiae; Single-chain fragment variable (scFv)

DOI:  https://doi.org/10.1242/jcs.263848