bims-toxgon Biomed News
on Toxoplasma gondii metabolism
Issue of 2025–11–30
thirty-two papers selected by
Lakesh Kumar, BITS Pilani
  1. Mitochondria of a human skeletal muscle cell line associate with the parasitophorous vacuoles of three archetypal lineages of Toxoplasma gondii and influence fatty acid import.
  2. RNG2 tethers the conoid to the apical polar ring in Toxoplasma gondii to enable parasite motility and invasion.
  3. Therapeutic effect of baicalein as an antiparasitic agent against Toxoplasma gondii in vitro and in vivo.
  4. Clustering of host N-glycans licenses Toxoplasma rhoptry discharge.
  5. An apical ring protein essential for conoid complex assembly and daughter cell formation in Toxoplasma gondii.
  6. A novel targeting domain directs essential components of the cytosolic iron-sulfur cluster assembly pathway to the mitochondrion of Toxoplasma parasites.
  7. The inner membrane complex protein, IMC55, is dispensable for intra-erythrocytic development of Plasmodium falciparum.
  8. Trem2-MICAL1-P-ERK Axis in Macrophages Confers Protection Against Toxoplasma gondii-Induced Adverse Pregnancy Outcomes.
  9. Early upregulation of immune suppressors dominates the macrophage response to Toxoplasma gondii.
  10. Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection.
  11. Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.
  12. Single-cell analysis of brain-derived Toxoplasma bradyzoites reveals a novel cell cycle regulated by AP2XI-6.
  13. An ApiAP2 Family Transcriptional Factor PfAP2-06B Regulates Erythrocyte Invasion Indirectly in Plasmodium falciparum.
  14. The histone modification regulator, SIN3, plays a role in the cellular response to changes in glycolytic flux.
  15. Molecular Architecture of the human Citrate Synthase-Malate Dehydrogenase 2 metabolon.
  16. Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.
  17. Unusual replication dynamics during Plasmodium falciparum schizogony.
  18. An essential adaptor for apicoplast fission and inheritance in malaria parasites.
  19. MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages.
  20. Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays.
  21. AMPK: an enzyme that may be effective in cancer and metabolic diseases.
  22. Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome.
  23. Mass Spectrometry for Lysine Methylation: Principles, Progress, and Prospects.
  24. An RPA-CRISPR/Cas12a-based rapid and sensitive nucleic acid method for detection of Toxoplasma gondii in tissue and blood samples.
  25. Expanding the plant epigenetic code: histone short-chain acylation.
  26. HDAC11 Deacetylates BRAF to Regulate Kinase Activity and Cell Proliferation.
  27. Regulation and Roles of Metacyclogenesis and Epimastigogenesis in the Life Cycle of Trypanosoma cruzi.
  28. Cdk5 regulates glutamine metabolism in colorectal cancer via the EZH2-GLS1 axis.
  29. The Mitochondrial F-box protein 1 and DJ-1 homolog HSP31 support cellular proteostasis during mitochondrial protein import clogging.
  30. Reciprocal control of metabolic and chromatin regulators improves rice tolerance to heat.
  31. CNPY4 is a Lipid-Binding Regulator of Sphingolipid Homeostasis.
  32. Glutamine synthetase modulates YAP activation by stabilizing LATS under glutamine homeostasis.
  1. FEMS Microbes. 2025 ;6 xtaf013
    Mitochondria of a human skeletal muscle cell line associate with the parasitophorous vacuoles of three archetypal lineages of Toxoplasma gondii and influence fatty acid import.
    Céline Christiansen, Michael Laue, Martin Blume.
      Toxoplasma gondii, an obligate intracellular parasite, acquires host nutrients to sustain its intracellular replication. A key interaction involves host mitochondrial association (HMA) with the parasitophorous vacuole membrane, previously thought to be strain- and cell-type-dependent, and notably absent in type 2 strains in fibroblasts. Here, we report that in human skeletal muscle KD3 myotubes, all three archetypal T. gondii strains-including type 2-demonstrate significant HMA. This association was confirmed by mitotracker staining and transmission electron microscopy. Notably, HMA appears to correlate inversely with the parasite's uptake of exogenous 13C-labeled fatty acids, suggesting a competitive nutrient environment shaped by host mitochondrial proximity. These findings highlight host cell-type specificity in mitochondrial interactions and suggest that HMA may function as a modulator of nutrient acquisition in a context-dependent manner. This work revises the understanding of strain-specific HMA and underscores the complexity of host-parasite metabolic interactions in muscle tissue, a physiologically relevant niche for chronic T. gondii infection.
    Keywords:  T. gondii; Toxoplasma gondii; host mitochondrial adhesion; human; mitochondria; skeletal muscle
    DOI:  https://doi.org/10.1093/femsmc/xtaf013
  2. PLoS Biol. 2025 Nov 24. 23(11): e3003506
    RNG2 tethers the conoid to the apical polar ring in Toxoplasma gondii to enable parasite motility and invasion.
    Romuald Haase, Bingjian Ren, Albert Tell I Puig, Alessandro Bonavoglia, Jean-Baptiste Marq, Rémy Visentin, Nicolas Dos Santos Pacheco, Bohumil Maco, Ricardo Mondragón-Flores, Oscar Vadas, Dominique Soldati-Favre.
      The conoid is a dynamic, tubulin-based structure conserved across the Apicomplexa that undergoes extrusion during egress, gliding motility, and invasion in Toxoplasma gondii. This organelle traverses the apical polar ring (APR) in response to calcium waves and plays a critical role in controlling parasite motility. While the actomyosin-dependent extrusion of the conoid is beginning to be elucidated, the mechanism by which it remains apically anchored to the APR is still unclear. RNG2, a protein localized to both the conoid and the APR, has emerged as a strong candidate for mediating this connection. Biochemical analysis revealed that RNG2 is an unstable protein, undergoing extensive proteolytic cleavage both in the parasite and in heterologous expression systems. Its biochemical properties, with the presence of large coiled-coil domains, likely facilitate the formation of concatenated assemblies, enabling RNG2 to serve as a dynamic and resilient bridge between the conoid and the APR. Using a combination of iterative ultrastructure expansion microscopy and immunoelectron microscopy, we confirmed the localization of RNG2 to the 22 tethering elements bridging the APR and the conoid. Conditional depletion of RNG2 led to the striking detachment of the intact conoid organelle from the APR, supporting an essential role for RNG2 as a tether. Cryo-electron tomography of conoid-less parasites revealed that, in the absence of RNG2, the apical vesicle remains anchored to the plasma membrane, while the rhoptries follow the detached conoid. Although RNG2 depletion only mildly reduces microneme secretion, the parasites are immotile and exhibit impaired rhoptry discharge, highlighting the critical role of proper conoid anchorage in motility and host cell invasion. Comprehensive mutagenesis of RNG2 identified distinct regions responsible for binding to the conoid and the APR, and demonstrated that the full-length, intact protein is essential for bridging these two structures and for its functional activity. Altogether, RNG2 emerges as a pivotal protein that ensures conoid functionality and coordination in Coccidia.
    DOI:  https://doi.org/10.1371/journal.pbio.3003506
  3. J Zhejiang Univ Sci B. 2025 Oct 25. pii: 1673-1581(2025)11-1086-17. [Epub ahead of print]26(11): 1086-1102
    Therapeutic effect of baicalein as an antiparasitic agent against Toxoplasma gondii in vitro and in vivo.
    Songrui Wu, Yingmei Lai, Zhong'ao Zhang, Jianzu Ding, Shaohong Lu, Huayue Ye, Haojie Ding, Xunhui Zhuo.
      The most common medications for the treatment of zoonotic toxoplasmosis are pyrimethamine and sulfadiazine, which may cause serious undesirable side effects. Thus, there is an urgent need to develop novel therapeutics. Baicalein (BAI, C15H10O5) has been shown to perform well against protozoan parasites including Leishmania and Cryptosporidium. In this study, the inhibition efficacy of BAI on Toxoplasma gondii was evaluated using plaque, invasion, and intracellular proliferation assays. BAI effectively inhibited T. gondii (half-maximum inhibitory concentration (IC50)=6.457×10-5 mol/L), with a reduced invasion rate (33.56%) and intracellular proliferation, and exhibited low cytotoxicity (half-maximum toxicity concentration (TC50)=5.929×10-4 mol/L). Further investigation using a mouse model shed light on the inhibitory efficacy of BAI against T. gondii, as well as the potential mechanisms underlying its anti-parasitic effects. The survival time of T. gondii-infected ICR mice treated with BAI was remarkably extended, and their parasite burdens in the liver and spleen were greatly reduced compared with those of the negative control group. Histopathological examination of live sections revealed effective therapeutic outcomes in the treatment groups, with no notable pathological alterations observed. Furthermore, alterations in cytokine levels indicated that BAI not only effectively suppressed the growth of T. gondii but also prevented excessive inflammation in mice. Collectively, these findings underscore the significant inhibitory efficacy of BAI against T. gondii, positioning it as a promising alternative therapeutic agent for toxoplasmosis.
    Keywords:  Antiparasitic; Baicalein (BAI); Immunity regulation; Toxoplasma gondii
    DOI:  https://doi.org/10.1631/jzus.B2400235
  4. bioRxiv. 2025 Oct 21. pii: 2025.10.16.682961. [Epub ahead of print]
    Clustering of host N-glycans licenses Toxoplasma rhoptry discharge.
    Dylan Valleau, Mudita Goyal, Justin M Roberts, Frances Male, Gary Ward, Sebastian Lourido.
      Apicomplexan parasites must discharge the contents of specialized organelles called rhoptries into host cells to initiate the process of invasion. This process requires the prior recognition and binding of the host cell by proteins released from another set of parasite organelles, the micronemes. However, the host-parasite interactions required for rhoptry discharge are largely unknown. Here we performed a host-cell directed genome-wide screen for host factors required for rhoptry discharge from Toxoplasma gondii, the causative agent of toxoplasmosis. The screen identified host N-glycosylation and cholesterol biosynthesis as pathways required for normal rhoptry discharge. A trimeric microneme complex, MIC1/4/6, interfaces with both pathways by binding host N-glycans to cluster proteins in a process dependent on host plasma membrane cholesterol. The process can be inhibited by depletion of host cholesterol or competition with exogenous glycans. This clustering of host factors by MIC1/4/6 likely prepares the host membrane for rhoptry discharge, delineating a new step in the Toxoplasma invasion process.
    DOI:  https://doi.org/10.1101/2025.10.16.682961
  5. Nat Commun. 2025 Nov 28. 16(1): 10149
    An apical ring protein essential for conoid complex assembly and daughter cell formation in Toxoplasma gondii.
    Wei Li, Oliwia Koczy, Peipei Qin, Ignasi Forné, Simon Gras, Jennifer Grünert, Andreas Klingl, Simone Mattei, Elena Jimenez-Ruiz, Markus Meissner.
      In Toxoplasma gondii, the conoid complex consists of intraconoidal microtubules (ICMTs), preconoidal rings (PCRs), apical polar ring (APR), and the conoid. This organelle plays an important role for initiation of gliding motility, required for host cell invasion and egress. The molecular mechanisms governing stepwise assembly of the conoid complex remain poorly understood. We previously identified CGP, an essential protein required for motility initiation. Here, we demonstrate that CGP is crucial for anchoring FRM1 and other PCR components to mature PCRs, while the initial assembly in daughter cells is unaffected. Cryo-electron tomography of CGP-depleted parasites reveals the absence of the PCRs in the mature parasites, demonstrating that CGP is essential for stabilising the PCRs after replication. Using CGP as bait, we identify a protein required for the early assembly of the nascent conoid complex. The APR scaffold assembly factor (ASAF1) defines the position of the conoid complex before tubulin polymerisation. Depletion of ASAF1 results in failure of conoid complex assembly, disorganised microtubules, and lack of daughter cell formation. Collectively, our findings reveal two essential proteins that play critical roles in the early and late stages of conoid complex formation, providing insight into the mechanisms of conoid complex assembly.
    DOI:  https://doi.org/10.1038/s41467-025-65382-y
  6. PLoS Biol. 2025 Nov 25. 23(11): e3003520
    A novel targeting domain directs essential components of the cytosolic iron-sulfur cluster assembly pathway to the mitochondrion of Toxoplasma parasites.
    Evie R Hodgson, Jenni A Hayward, Rachel A Leonard, F Victor Makota, Giel G van Dooren.
      The assembly of iron-sulfur (FeS) clusters for cytosolic and nuclear proteins is essential for eukaryotic cell biology. This assembly is mediated by the Cytosolic Iron-sulfur Assembly (CIA) pathway, which localizes to the cytosol of most eukaryotes. We showed previously that the scaffold protein on which cytosolic FeS clusters assemble localizes to the mitochondrion of the apicomplexan parasite Toxoplasma gondii. The localization and importance of the remainder of the pathway in these parasites, however, remained unclear. Here, we undertake a comprehensive analysis of the CIA pathway in T. gondii parasites. We present evidence that the CIA pathway localizes predominantly to the mitochondrion of the parasite and is essential for parasite survival. We show that the three proteins that make up the CIA Targeting Complex (CTC), which facilitates the transfer of FeS clusters to cytosolic and nuclear client proteins, exhibit dual localization to the mitochondrion and cytosol. We reveal that mitochondrial targeting of the CTC is mediated by a novel loop on the CIA1 protein of the complex, and that this loop is critical for parasite survival. We show that an aromatic amino acid motif in the loop facilitates mitochondrial targeting, and that this loop is functionally conserved in apicomplexans and their closest free-living relatives. Our study provides a comprehensive analysis of the CIA pathway in an important group of intracellular parasites, and elucidates pivotal differences in an otherwise ancient and highly conserved biosynthetic pathway that may reflect an evolutionary fitness advantage conferred on Toxoplasma and related organisms.
    DOI:  https://doi.org/10.1371/journal.pbio.3003520
  7. bioRxiv. 2025 Nov 10. pii: 2025.11.07.687246. [Epub ahead of print]
    The inner membrane complex protein, IMC55, is dispensable for intra-erythrocytic development of Plasmodium falciparum.
    Grace W Vick, Manuel A Fierro, Lenna Park, Carrie Brooks, Vasant Muralidharan.
      Plasmodium falciparum , an obligate intracellular Apicomplexan parasite and the causative agent of malaria must reside and replicate within a host cell during the intra-erythrocytic stage. The parasite utilizes a specialized double-membraned organelle, called the inner membrane complex for schizont-stage segmentation and merozoite motility during subsequent re-invasion. In this study, we investigate the function of IMC55, a multi-transmembrane inner membrane complex protein, which we identified as a putative interacting partner of the P. falciparum ER-resident calcium binding protein, PfERC. We have previously shown that PfERC is essential for parasite egress and our data shows that PfERC may also function in parasite invasion into the RBC. The whole genome transposon mutagenesis screen predicts that IMC55 is essential for the intra-erythrocytic asexual cycle. In this work, we show that IMC55 is not required for asexual replication. Following inducible expression of this gene using two conditional systems, we find there is no defect in replicative fitness during the asexual blood stage. Taken together, these data demonstrate that the function of IMC55 is either dispensable or redundant for the Plasmodium falciparum asexual blood stage.
    DOI:  https://doi.org/10.1101/2025.11.07.687246
  8. Pathogens. 2025 Oct 30. pii: 1105. [Epub ahead of print]14(11):
    Trem2-MICAL1-P-ERK Axis in Macrophages Confers Protection Against Toxoplasma gondii-Induced Adverse Pregnancy Outcomes.
    Xiaoyu Geng, Haochen Yang, Zihan Wang, Ziqian Chen, Jinling Chen, Mei Yang.
      Toxoplasma gondii (T. gondii) infection during pregnancy can cause severe placental damage and fetal impairment. Although triggering the receptor expressed on myeloid cells 2 (Trem2) confers protection against T. gondii infection, the precise molecular mechanisms underlying this immunoregulatory role remain incompletely understood. Using a mouse model, this study identifies a novel Trem2-MICAL1-P-ERK axis in macrophages that protects against T. gondii-induced adverse pregnancy outcomes (APO). RNA-seq of Trem2-overexpressing macrophages revealed significant upregulation of 1857 genes, with MICAL1 among the most markedly altered, highlighting its potential role in Trem2-mediated signaling. Mechanistically, correlation analysis, molecular docking, fluorescence co-localization, and immunoprecipitation assays demonstrate that Trem2 directly interacts with MICAL1, which modulates downstream phosphorylated ERK (P-ERK) signaling. In a T. gondii-infected murine pregnancy model, genetic ablation of Trem2 exacerbated pathogen-induced suppression of MICAL1 and P-ERK, whereas macrophage-specific overexpression of Trem2-DAP12 restored this signaling axis. Conversely, MICAL1 overexpression rescued P-ERK activation but failed to regulate Trem2 expression. Further studies in bone marrow-derived macrophages (BMDMs) revealed that Trem2 deficiency potentiated the inhibitory effects of soluble T. gondii antigens (TgAg) on MICAL1 and P-ERK. These findings elucidate how T. gondii disrupts placental immunity through targeted suppression of Trem2-mediated signaling and establish the Trem2-MICAL1-P-ERK cascade as a core regulatory pathway in immune homeostasis during pregnancy.
    Keywords:  Toxoplasma gondii; Trem2; placental immunity; soluble T. gondii antigens
    DOI:  https://doi.org/10.3390/pathogens14111105
  9. PLoS One. 2025 ;20(11): e0336849
    Early upregulation of immune suppressors dominates the macrophage response to Toxoplasma gondii.
    Dominykas Murza, Filip Lastovka, George Wood, Matthew P Brember, Oliver Chan, James W Ajioka, Betty Y W Chung.
      The apicomplexan parasite Toxoplasma gondii is a master manipulator, subverting its host through secreted proteins, hormone disruption, and even behavioural changes. Macrophages, the immune system's first responders, play a pivotal role in determining infection outcomes, yet the initial triggers shaping these complex responses remain elusive. This study unveils the earliest transcriptional shifts in a mouse macrophage-like cell line RAW264.7-T. gondii infection model. Using time-resolved transcriptomic profiling, we captured host and parasite gene expression dynamics within the critical 15-120 minute window - when the host mounts its first line of defence and the parasite secures its foothold. By leveraging inactivated parasites, we disentangled responses to active invasion from general immune activation. By 60 minutes, macrophages exhibited a trend of increased suppressor of cytokine signalling expression - uniquely tied to live infection - while stress and pro-growth genes became dysregulated. Meanwhile, T. gondii responded with a slow but strategic transcriptional shift: an early increase in transcription and growth capacity, followed by a delayed activation of secreted proteins. These findings reveal a tug-of-war at the transcriptional level, where macrophages show rapid upregulation, while T. gondii employs a measured, delayed strategy to carve out its replicative niche.
    DOI:  https://doi.org/10.1371/journal.pone.0336849
  10. Nat Microbiol. 2025 Nov 25.
    Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection.
    Chahat Mehra, Jesús Alvarado Valverde, Ana Margarida Nogueira Matias, Francesca Torelli, Tânia Catarina Medeiros, Julian Straub, James D Asaki, Peter J Bradley, Katja Luck, Steffen Lawo, Moritz Treeck, Lena Pernas.
      Membrane contact sites (MCS) are essential for organelle communication in eukaryotic cells. Pathogens also establish MCS with host organelles, but the mechanisms underlying these interactions and their role in infection remain poorly understood. Here, using a fluorescence sensor and CRISPR-based loss-of-function screening, together with imaging and proteomics, we identify the parasite effector mediating MCS between host endoplasmic reticulum (ER) and the vacuole containing the intracellular parasite Toxoplasma gondii. TgROP1 acts as a tether and mimics a canonical FFAT motif to bind the host ER proteins VAPA and VAPB. The loss of VAPA/B abolished host ER-Toxoplasma MCS and decreased pathogen growth. These findings indicate that targeting of host MCS tethers is a strategy exploited by pathogens during infection, which could inform future treatment design.
    DOI:  https://doi.org/10.1038/s41564-025-02193-3
  11. PLoS Negl Trop Dis. 2025 Nov 25. 19(11): e0013768
    Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.
    Ji-Xin Zhao, Wen-Bin Zheng, Shi-Chen Xie, He Ma, Xiao-Tong Chen, Ying-Qian Gao, Lu-Yao Tang, Meng-Ting Yang, Fu-Long Nan, Jing Jiang, Hany M Elsheikha, Xiao-Xuan Zhang.
      Toxoplasma gondii infection disrupts the gut microbiota and host systemic metabolism, which plays a key role in the pathophysiology of toxoplasmosis. To investigate these interactions, we conducted metagenomic sequencing and untargeted serum metabolomics on 18 Sprague-Dawley rats across control, acute, and chronic stages of infection. De novo assembly of 148 Gb of high-quality reads produced a comprehensive non-redundant microbial gene catalog comprising over 5.7 million genes. Infection led to a marked reduction in microbial diversity and significant shifts in community structure. Chronic infection, in particular, was characterized by the enrichment of Lactobacillus johnsonii, Lactobacillus intestinalis, and Limosilactobacillus reuteri, alongside a marked depletion of Akkermansia muciniphila and Rothia nasimurium. These compositional changes coincided with reduced abundance of carbohydrate-active enzymes, suggesting impaired microbial metabolic capacity. Pathway analysis revealed distinct, stage- and gut-region-specific metabolic disruptions, including suppressed amino acid and energy metabolism, and enhanced glycan and carbohydrate pathways during chronic infection. Untargeted LC-MS/MS profiling uncovered 883 differentially abundant serum metabolites, enriched in pathways related to amino acid metabolism, bile acid transformation, and aromatic compound processing. Importantly, L. johnsonii and L. reuteri were positively correlated with metabolites implicated in immune modulation and oxidative stress response, whereas A. muciniphila showed negative associations. These findings demonstrate that T. gondii infection orchestrates a coordinated host-microbiota-metabolome network, advancing our understanding of disease mechanisms and pointing to novel microbial and metabolic targets for therapy.
    DOI:  https://doi.org/10.1371/journal.pntd.0013768
  12. bioRxiv. 2025 Oct 20. pii: 2025.10.20.683543. [Epub ahead of print]
    Single-cell analysis of brain-derived Toxoplasma bradyzoites reveals a novel cell cycle regulated by AP2XI-6.
    Emma Franklin, Argenis Arriojas Maldonado, Kyra Lee, Grace Hilliard, Bruno Martorelli Di Genova, Gary E Ward, Kourosh Zarringhalam, Robyn Kent.
      Toxoplasma gondii prevalence is due, in part, to its ability to persist in hosts while retaining the capacity to transmit and recrudesce. A process that is poorly understood. Through single-cell RNA profiling of in vivo-derived bradyzoites, we discovered that they are heterogeneous and not G1-arrested, as expected from in vitro studies. Instead, they progress through two cell cycles that branch from a single G1. While in G1b, in vivo -derived bradyzoites express cyst wall proteins predicted to replenish the wall that shields cysts. One cell cycle is common amongst tachyzoites and in vitro- and in vivo-derived bradyzoites; the other is unique to in vivo-derived bradyzoites (BCC). We demonstrated that AP2XI-6, expressed in G1 in vivo, is dispensable for tachyzoite growth and cyst formation in vitro but necessary for encystation in vivo. We propose that AP2XI-6 is a driver of replication through the BCC that is required for cyst maturation and persistence.
    DOI:  https://doi.org/10.1101/2025.10.20.683543
  13. Pathogens. 2025 Oct 22. pii: 1076. [Epub ahead of print]14(11):
    An ApiAP2 Family Transcriptional Factor PfAP2-06B Regulates Erythrocyte Invasion Indirectly in Plasmodium falciparum.
    Qiyang Shi, Kai Wan, Yifei Gong, Jiayao Pang, Yaobao Liu, Jianxia Tang, Qingfeng Zhang, Jun Cao, Li Shen.
      Obligate intracellular parasites must efficiently invade host cells to complete their life cycle and facilitate transmission. For the malaria-causing parasite Plasmodium falciparum, the invasion of an erythrocyte is a critical process, and thereby a key target for intervention strategies. In this study, we investigate the role of the ApiAP2 family transcription factor PfAP2-06B (PF3D7_0613800) in the intraerythrocytic developmental cycle of P. falciparum and focus on its regulation of genes involved in erythrocyte invasion. Conditional knockdown of PfAP2-06B resulted in a defect in asexual growth and impaired erythrocyte invasion. Bulk RNA sequencing (RNA-seq) analysis revealed that PfAP2-06B modulates the expression of invasion-related genes during the schizont stage. Single-cell RNA sequencing indicated that PfAP2-06B influences invasion gene expression and contributes to stochastic variations in expression of cell-to-cell genes. These results underscore the critical function of PfAP2-06B in the process of erythrocyte invasion and suggest its potential as a target for novel malaria control strategies. Importance: Understanding gene regulation in Plasmodium falciparum is essential for uncovering mechanisms of parasite development and pathogenicity. The research underscores the pivotal role of PfAP2-06B in regulating critical aspects of Plasmodium intraerythrocytic development and host cell invasion, demonstrating that PfAP2-06B plays a key role in orchestrating stage-specific gene expression. These findings provide new insights into the transcriptional networks of P. falciparum and highlight PfAP2-06B as a potential target for therapeutic intervention. This work advances our understanding of malaria pathogenesis and developing effective interventions.
    Keywords:  ApiAP2 transcription factor; Plasmodium falciparum; erythrocyte invasion; malaria
    DOI:  https://doi.org/10.3390/pathogens14111076
  14. PLoS One. 2025 ;20(11): e0335411
    The histone modification regulator, SIN3, plays a role in the cellular response to changes in glycolytic flux.
    Imad Soukar, Anindita Mitra, Linh Vo, Melanie Rofoo, Miriam L Greenberg, Lori A Pile.
      Epigenetic regulation and metabolism are connected. Epigenetic regulators, like the SIN3 complex, affect the expression of a wide range of genes, including those encoding metabolic enzymes essential for central carbon metabolism. The idea that epigenetic modifiers can sense and respond to metabolic flux by regulating gene expression has long been proposed. In support of this cross-talk, we provide data linking SIN3 regulatory action on a subset of metabolic genes with the cellular response to changes in metabolic flux. Furthermore, we show that loss of SIN3 is linked to decreases in mitochondrial respiration and the cellular response to mitochondrial and glycolytic stress. Data presented here provide evidence that SIN3 is important for the cellular response to metabolic flux change.
    DOI:  https://doi.org/10.1371/journal.pone.0335411
  15. bioRxiv. 2025 Oct 14. pii: 2025.10.13.681887. [Epub ahead of print]
    Molecular Architecture of the human Citrate Synthase-Malate Dehydrogenase 2 metabolon.
    Angela J Kayll, Umanga Rupakheti, Renee St John, Joseph J Provost, Christopher E Berndsen.
      Metabolons are transient biomolecular complexes that enhance the efficiency of metabolic pathways through substrate channeling. These complexes are difficult to study because of the transient nature, thus limiting our understanding of how they are formed and regulated. The citric acid cycle is proposed to contain many such complexes although few have been characterized structurally. Here, we provide direct structural evidence for the complex of human Citrate Synthase and human mitochondrial Malate Dehydrogenase 2, which is part of the larger proposed citric acid cycle metabolon. Our structural model supports previous crosslinking studies and suggests that hMDH2 can interact with each subunit of the hCS dimer, forming up to a hexameric complex. However, this complex appears transient as titration of hMDH2 into hCS in activity assays does not saturate. We further show that the interaction site with hCS is non-specific, as hCS could also stimulate oxaloacetate formation by cytosolic and plant MDH enzymes. This structural model will provide a base for understanding the structure and regulation of the broader citric acid cycle metabolon.
    DOI:  https://doi.org/10.1101/2025.10.13.681887
  16. Mol Metab. 2025 Nov 24. pii: S2212-8778(25)00195-4. [Epub ahead of print] 102288
    Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.
    Orion S Willoughby, Anna S Nichenko, Matthew H Brisendine, Niloufar Amiri, Shelby N Henry, Daniel S Braxton, John R Brown, Braeden J Kraft, Kalyn S Jenkins, Adele K Addington, Alexey V Zaitsev, Steven T Burrows, Ryan P McMillan, Haiyan Zhang, Spencer A Tye, Charles P Najt, Siobhan E Craige, Timothy W Rhoads, Junco S Warren, Joshua C Drake.
      Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses suggest a compensatory reliance on autophagy-derived amino acids in Ulk1(S555A) mice. These findings suggest Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching. This work highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility, with implications for metabolic dysfunction.
    DOI:  https://doi.org/10.1016/j.molmet.2025.102288
  17. Malar J. 2025 Nov 28. 24(1): 432
    Unusual replication dynamics during Plasmodium falciparum schizogony.
    Rosie Berners-Lee, Terry K Smith.
      Plasmodium falciparum causes the most severe form of malaria in humans, and disease severity is directly linked to parasite proliferation during the erythrocytic cycle. During this cycle, P. falciparum replicates via schizogony. This is an unusual form of asexual replication in which the parasite undergoes alternating asynchronous rounds of DNA replication and nuclear division within a shared cytoplasm, followed by a mass cytokinesis event that produces numerous daughter cells. Despite recent advances in high-throughput, single-molecule techniques, clarity on P. falciparum replication dynamics remains elusive. These dynamics are likely shaped by its highly AT-rich genome and the unique pressures of schizogony. Clarifying the pressures that shape schizogony and DNA replication may reveal parasite-specific vulnerabilities and inform the development of new antimalarials.
    Keywords:  DNA replication; Malaria; Nuclear divisions; Plasmodium falciparum; Replication dynamics; Schizogony
    DOI:  https://doi.org/10.1186/s12936-025-05610-4
  18. Nat Commun. 2025 Nov 27.
    An essential adaptor for apicoplast fission and inheritance in malaria parasites.
    James A Blauwkamp, Krithika Rajaram, Sophia R Staggers, Oliver Harrigan, Emma H Doud, Wei Xu, Hangjun Ke, Sean T Prigge, Stella Y Sun, Sabrina Absalon.
      Blood-stage Plasmodium falciparum parasites rely on a non-photosynthetic plastid, the apicoplast, for survival, making it an attractive target for antimalarial intervention. Like the mitochondrion, the apicoplast cannot be generated de novo and must be inherited by daughter parasites during cell division. This inheritance relies on coordinated apicoplast positioning and fission, but the molecular mechanisms controlling these processes remain poorly understood. Here, we identify a previously uncharacterized P. falciparum protein (Pf3D7_0613600), which we name PfAnchor, as a key regulator of apicoplast fission. Using Ultrastructure Expansion Microscopy (U-ExM), we show that PfAnchor localizes to the apicoplast throughout the asexual blood-stage. Conditional depletion disrupts apicoplast fission, leading to incomplete cytokinesis and parasite death. Notably, loss of the apicoplast's elongated branched structure via azithromycin treatment rescues these defects, underscoring Anchor's specific role in apicoplast fission. Immunoprecipitation identified an interaction with the dynamin-like GTPase PfDyn2, a key mediator of both apicoplast and mitochondrial fission, establishing PfAnchor as the first apicoplast-specific dynamin adaptor protein. Our findings define PfAnchor as an essential factor for apicoplast fission and inheritance in P. falciparum blood-stage parasites, highlighting parasite-specific organelle division as a potential vulnerability for therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41467-025-66393-5
  19. Nat Microbiol. 2025 Nov 28.
    MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages.
    Samuel Pazicky, Seth Tjia, Guilherme B Farias, Nick Piwon, Nisha Philip, Radoslaw M Sobota, Andrew P Waters, Tim-Wolf Gilberger, Zbynek Bozdech.
      The malaria parasite Plasmodium falciparum undergoes a complex intraerythrocytic developmental cycle (IDC) that relies on a dynamic network of protein-protein interactions. These are usually mapped ex vivo, limiting our understanding of their dynamics and composition in natural environments. Here we introduce the meltome-assisted profiling of protein complexes (MAP-X) that maps the complexome through thermal proteome profiling in intact cells. We applied MAP-X across seven timepoints in the P. falciparum IDC. MAP-X predicted more than 20,000 interactions, resolving conserved protein complexes, reproducing previously identified interactions and finding previously unreported associations. We found that malaria protein complexes undergo distinct dynamic alterations, and we predicted their moonlighting subunits that dissociate from their native complex to assume different biological functions. Altogether, our findings provide a resource for uncovering Plasmodium biology and show that MAP-X can characterize protein complexes in intact cells to reveal cellular physiology at a proteome-wide level.
    DOI:  https://doi.org/10.1038/s41564-025-02173-7
  20. Nat Commun. 2025 Nov 27. 16(1): 10672
    Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays.
    Jia Gao, Hongyun Li, Song Tan, Ruobo Zhou, Tae-Hee Lee.
      Chromatin condensation is dynamically regulated throughout the cell cycle and plays key roles in modulating gene accessibility. The DNA-histone dynamics in the nucleosome are central to the regulation mechanisms of chromatin condensation, which remain poorly understood. Employing fluorescence recovery after photobleaching, optical super-resolution imaging, and microrheology with optical tweezers, we investigated the roles of various parameters in regulating phase-separation of 12-mer nucleosome arrays. Here, we show that histone H4 tail lysine residues are the main drivers of liquid-liquid phase separation of nucleosome arrays. We also show that the condensed liquid-like droplets comprise a mobile fraction and a relatively immobile structural scaffold. Histone chaperone Nap1 and histone H3 tail acetylation enhance DNA-histone dynamics within this scaffold, thereby lowering the overall viscosity of the droplets. These results suggest that histone chaperone and histone H3/H4 tails play critical roles in regulating chromatin condensation and gene accessibility in condensed chromatin.
    DOI:  https://doi.org/10.1038/s41467-025-65701-3
  21. Discov Oncol. 2025 Nov 27.
    AMPK: an enzyme that may be effective in cancer and metabolic diseases.
    Sümeyye Güney Kalkan, Meltem Ceylan Ünlüsoy.
      Diseases are processes that feed on the interaction and triggering of impairments in cellular metabolism. The fact that AMPK has arresting and initiating effects on anabolic-catabolic processes shows that it plays a key role in the functioning of metabolism and especially energy metabolism. The effects of AMPK on fat, carbohydrate, and protein metabolism, as wel as on growth, and autophagy have made AMPK an important target in chronic diseases such as Type 2 diabetes, metabolic syndrome, obesity, inflammation, cancer treatment, and even anti-aging. Considering the other effects of AMPK, the possibility that it can exhibit an anticancer effect through a mechanism other than just suppressing the cell growth and division cycle and activating autophagic pathways is within the realm of possibility. It has been stated that suppression of AMPK will trigger glycolysis in some cancer cells and increase the Warburg effect, which is effective in the energy production of cells. Besides, it has been reported recently that inflammation is a major factor in the development of tumors and that chronic inflammation raises the risk of cancer. This enzyme, that is known to be effective in all metabolic pathways, has attracted attention in the treatment of metabolic diseases. Therefore, this study aims to provide some information about the AMPK enzyme, the role of AMPK in cancer, metabolic disorders, and developed AMPK activators.
    Keywords:  AMPK; AMPK activators; Cancer; Inflammation; Metabolic syndrome
    DOI:  https://doi.org/10.1007/s12672-025-02229-4
  22. bioRxiv. 2025 Nov 03. pii: 2025.11.01.686011. [Epub ahead of print]
    Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome.
    Birgit Schilling, Leonard Rorrer, Lauren Royer, Anne Silva-Barbosa, Katherine Pfister, Eric Goetzman, Sunder Sims-Lucas, Daniel DeBord, Joanna Bons.
      Protein post-translational modifications (PTMs) dynamically regulate essential biological and cellular processes. Lysine succinylation changes the amino acid charge, potentially affecting protein structures and functions, and dysregulation of protein succinylation may lead to metabolic disorders. Proteome-wide succinylation quantification using proteomic tools remains challenging, especially due to the low abundance of succinylated peptides and the frequent presence of isomeric PTM forms. Ion mobility spectrometry workflows that can differentiate peptidoforms with different PTM distributions represent a powerful strategy to alleviate these challenges. Recently, a new Parallel Accumulation with Mobility Aligned Fragmentation (PAMAF™) operating mode for high-resolution ion mobility-mass spectrometry (HRIM-MS) analysis based on the structures for lossless ion manipulation (SLIM) technology was introduced. Here, we first assessed the performance of PAMAF mode for protein succinylation analysis using synthetic succinylated peptides, demonstrating residue-level differentiation of co-eluting isomers and isobars and precise PTM site localization. We leveraged this novel approach to investigate succinylome remodeling in kidney tissues from wild-type and Sirtuin-5 (Sirt5) knock-out mice, a NAD + -dependent lysine de-succinylase. PAMAF acquisitions yielded ∼1,000 confidently identified and accurately quantified succinylated peptides and sites from mouse kidney. Sirt5 regulated succinylation of mitochondrial proteins involved in metabolic processes, including fatty acid oxidation, the tricarboxylic acid cycle, and propionate metabolism.
    DOI:  https://doi.org/10.1101/2025.11.01.686011
  23. Biomedicines. 2025 Nov 19. pii: 2825. [Epub ahead of print]13(11):
    Mass Spectrometry for Lysine Methylation: Principles, Progress, and Prospects.
    Mackenzie G Cumming, Kyle K Biggar.
      Lysine methylation is a regulatory post-translational modification with diverse roles across both histone and non-histone proteins. Despite its biological relevance, comprehensive characterization of lysine methylation remains analytically challenging due to its low stoichiometry, subtle mass changes, and the absence of standardized, robust enrichment strategies. Mass spectrometry (MS) has become the cornerstone of methylation analysis, supporting both targeted and proteome-wide investigations. In this review, we examine the evolution of MS-based workflows for lysine methylation, including advances in ionization and fragmentation techniques, high-resolution mass analyzers, and acquisition strategies such as data-independent acquisition (DIA) and parallel accumulation-serial fragmentation (PASEF). We evaluate bottom-up, middle-down, and top-down proteomic approaches and discuss enrichment methods ranging from immunoaffinity and chromatography to chemical derivatization. Particular attention is given to persistent challenges, including proteolytic constraints and isobaric interference, that complicate confident site-level resolution. Finally, we highlight emerging solutions and future directions aimed at improving the sensitivity, specificity, and reproducibility of lysine methylation profiling. Together, this synthesis provides a forward-looking roadmap for optimizing MS workflows in methyllysine proteomics.
    Keywords:  lysine methylation; mass spectrometry; methyllysine; proteomics
    DOI:  https://doi.org/10.3390/biomedicines13112825
  24. Microbiol Spectr. 2025 Nov 28. e0155025
    An RPA-CRISPR/Cas12a-based rapid and sensitive nucleic acid method for detection of Toxoplasma gondii in tissue and blood samples.
    Yilin Wang, Ziyang Qin, Qinglin Wang, Yurong Yang, Chunhao Gu, Fuchang Yu, Yayun Wu, Long Xian Zhang.
      Toxoplasma gondii is a zoonotic pathogen that can infect humans and a wide range of warm-blooded animals, posing a significant threat to human health and the livestock industry. The development of a time-saving, highly sensitive, and specific method for the detection of T. gondii in tissue and blood samples is crucial to the monitoring, prevention, and control of toxoplasmosis. In this study, we evaluated the efficiency of a previously described method, termed REPORT, that integrates recombinase polymerase amplification with CRISPR/Cas12a for the detection of T. gondii nucleic acids. We evaluated the limit of detection (LOD) and specificity of the extended REPORT method using prepared target DNA in addition to tissue and blood samples. Furthermore, we validated the accuracy of T. gondii detection in clinical samples using the REPORT-based method in comparison with nested PCR based on the B1 gene. Sensitivity tests showed that the LOD of the REPORT-based fluorescence method and the lateral flow strip method were 3.7 copies /μL for target DNA, 3.1 tachyzoites/g for tissue samples, and five tachyzoites/mL for blood samples. Specificity tests suggested that the REPORT method had good specificity and did not cross-react with several common parasites. The method performed well for clinical DNA samples, demonstrating its ability for use in on-site detection.IMPORTANCEToxoplasma gondii can infect over 200 species of warm-blooded animals, including humans, posing not only a significant threat to public health systems but also causing substantial economic losses to the global livestock industry. Current diagnostic methods are slow, equipment-dependent, and impractical for field use. This study addresses these limitations by developing REPORT, a rapid, ultrasensitive nucleic acid test combining recombinase polymerase amplification and CRISPR/Cas12a. The REPORT detects T. gondii in tissue and blood samples within 1 h at low cost, requiring only a portable heater. Its visual results (fluorescence or test strips) enable on-site use without specialized training, achieving 100% accuracy versus nested PCR. With a sensitivity of 3.1 parasites per gram of tissue and five parasites per milliliter of blood, this method revolutionizes toxoplasmosis screening in resource-limited clinics, farms, and food safety inspections, empowering timely interventions to curb transmission and improve public health outcomes.
    Keywords:  CRISPR/Cas12a; On-site detection; Toxoplasma gondii; recombinase polymerase amplification; visualized detection
    DOI:  https://doi.org/10.1128/spectrum.01550-25
  25. Trends Plant Sci. 2025 Nov 25. pii: S1360-1385(25)00302-4. [Epub ahead of print]
    Expanding the plant epigenetic code: histone short-chain acylation.
    Xuelu Wei, Guiyu Xiao, Xiaoyang Chen, Jisen Zhang, Qiutao Xu.
      Gene expression regulation in plants involves complex epigenetic mechanisms. Historically, histone acetylation and methylation have been recognized as central determinants of chromatin dynamics and transcriptional regulation. However, recent studies have identified novel types of short-chain lysine acylation - including crotonylation, butyrylation, β-hydroxybutyrylation, 2-hydroxyisobutyrylation, succinylation, and lactylation - as emerging players in epigenetic control. Although these modifications have been extensively characterized in mammals, accumulating evidence now confirms their presence in plants. We focus on plant-specific findings related to histone acylation and analyze its metabolic sources, writers, and erasers, as well as its functional roles in plant development and stress adaptation. Investigation of these modifications in higher plants may unveil unique regulatory mechanisms that underlie developmental plasticity and resilience, and thereby open new avenues for crop improvement and sustainable agriculture.
    Keywords:  epigenetic regulation; gene transcription; histone code; lysine acetylation; post-translational modification; short-chain lysine acylation
    DOI:  https://doi.org/10.1016/j.tplants.2025.10.020
  26. ACS Chem Biol. 2025 Nov 22.
    HDAC11 Deacetylates BRAF to Regulate Kinase Activity and Cell Proliferation.
    Augustine C Madueke, Rafael Andrade, Mary Kay H Pflum.
      Histone acetylation, governed by histone deacetylase (HDAC) enzymes, plays a pivotal role in cell biology. Elevated HDAC expression is linked to a poor prognosis in various diseases, including cancer, making HDAC inhibitors clinically valuable. Among the 11 metal-dependent HDAC isoforms, the exceptional ability of HDAC11 to regulate both the deacetylation and defattyacylation of proteins suggests an expansive role in cellular processes. However, since HDAC11 is one of the least studied HDAC isoforms, the known roles for HDAC11 in cell biology are limited. In this study, proteomics-based mutant trapping was performed to identify nonhistone substrates of HDAC11 and link HDAC11 activity to specific cellular events. Proteomics revealed 64 putative substrates, with follow-up studies documenting that HDAC11 deacetylates the BRAF kinase on K680 to suppress kinase activity and cell proliferation. Given the established role of BRAF in cancer, HDAC11-mediated deacetylation likely influences signaling pathways in tumor progression, underscoring the diverse regulatory role of HDAC11 in cellular events.
    DOI:  https://doi.org/10.1021/acschembio.5c00631
  27. Pathogens. 2025 Nov 12. pii: 1149. [Epub ahead of print]14(11):
    Regulation and Roles of Metacyclogenesis and Epimastigogenesis in the Life Cycle of Trypanosoma cruzi.
    Abel Sana, Izadora Volpato Rossi, Marcel Ivan Ramirez.
      Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits remarkable developmental plasticity that enables its survival across distinct environments within the insect vector and mammalian host. This review focuses on two critical differentiation processes-metacyclogenesis and epimastigogenesis-emphasising their environmental triggers, metabolic regulation, and roles in parasite transmission and life cycle progression. Metacyclogenesis, occurring in the hindgut of triatomine vectors, transforms replicative epimastigotes into infective metacyclic trypomastigotes and is tightly controlled by factors such as nutrient starvation, pH, and temperature. In contrast, epimastigogenesis allows trypomastigotes to revert to epimastigote forms, primarily in the vector midgut, as part of the parasite's adaptation to vector colonisation. We compare these processes through the lens of stress-induced signalling and proteomic reprogramming, highlighting their metabolic divergence and ecological significance. Emerging evidence also suggests that extracellular vesicles (EVs) released by different parasite forms may actively modulate these transitions, supporting parasite communication and immune evasion strategies. A better understanding of these transitions provides novel insight into parasite adaptation and reveals potential molecular targets for disrupting the life cycle of T. cruzi.
    Keywords:  Trypanosoma cruzi; epimastigogenesis; insect vector; metacyclogenesis
    DOI:  https://doi.org/10.3390/pathogens14111149
  28. Cancer Metab. 2025 Nov 22.
    Cdk5 regulates glutamine metabolism in colorectal cancer via the EZH2-GLS1 axis.
    Qilong Wu, Xiaotong Zhu, Xinxin Wan, Xinjie Lu, Jiayan Chen, Zhe Ying, Yan Li, Xing Hu, Jiahai Lu, Yongliang Lou, Xiang Li.
      Colorectal cancer (CRC) is a globally prevalent malignancy that poses a substantial threat to human health. Despite advancements in prevention, diagnosis, and treatment, CRC remains a formidable clinical challenge due to the incomplete elucidation of its pathological mechanisms. Glutamine, an abundant amino acid, exerts pivotal roles in energy production, redox homeostasis, macromolecular biosynthesis, and signal transduction within cancer cells. Elucidating the role of glutamine in CRC pathogenesis is therefore of profound significance. In this study, we investigated the regulatory role of Cyclin-dependent kinase 5 (Cdk5) in glutamine metabolism in CRC, employing both human CRC cell models and murine models. Our findings demonstrated that Cdk5 knockdown accelerated glutamine uptake while suppressing the proliferation of CRC cells. Further exploration of the underlying molecular mechanisms revealed that Cdk5 physically interacts with EZH2. Besides, Cdk5 phosphorylates EZH2 at specific sites, and then the PRC2 complex (centered around EZH2) catalyzes the production of H3K27me3, an inhibitory marker, to regulate the expression of genes involved in glutamine metabolism. At the same time, we also found that modulation of the Cdk5-EZH2 axis alters the epigenetic landscape of genes associated with glutamine transporters and tricarboxylic acid cycle (TCA) enzymes, resulting in reduced mitochondrial activity, impaired glutamine utilization in the TCA cycle, and decreased ATP production-collectively impacting the global glutamine metabolic processes in CRC cells. In in vivo experiments utilizing a murine CRC model, we established five experimental groups. Results showed that Dinaciclib treatment suppressed tumor growth in the CRC model, with this inhibitory effect being further potentiated upon combination with glutamine deprivation. These findings not only uncover the intricate interplay between Cdk5, EZH2, and glutamine metabolism in CRC but also offer novel insights into the pathogenic mechanisms of CRC and identify potential therapeutic targets.
    Keywords:  Colorectal cancer; Cyclin-dependent kinase 5; Glutaminase; Glutamine; Mitochondria; Tricarboxylic acid cycle
    DOI:  https://doi.org/10.1186/s40170-025-00414-1
  29. bioRxiv. 2025 Oct 14. pii: 2025.10.13.682092. [Epub ahead of print]
    The Mitochondrial F-box protein 1 and DJ-1 homolog HSP31 support cellular proteostasis during mitochondrial protein import clogging.
    Gargi Mishra, Xiaowen Wang, Eamon Fitzpatrick, Auyon Ghosh, Xin Jie Chen.
      Mitochondrial biogenesis requires the import of ∼1,000-1,500 nuclear-encoded proteins across the Translocase of Outer Membrane (TOM) and the Translocase of Inner Membrane (TIM) 22 or 23 complexes. Protein import defects cannot only impair mitochondrial respiration but also cause mitochondrial Precursor Overaccumulation Stress (mPOS) in the cytosol. Recent studies showed that specific mutations in the nuclear-encoded Adenine Nucleotide Translocase 1 (ANT1) cause musculoskeletal and neurological diseases by clogging TOM and TIM22 and inducing mPOS. Here, we found that overexpression of MFB1 , encoding the mitochondrial F-box protein 1, suppresses cell growth defect caused by a clogger allele of AAC2 , the yeast homolog of Ant1. Disruption of MFB1 synergizes with a clogger allele of aac2 to inhibit cell growth. This is accompanied by increased retention of mitochondrial proteins in the cytosol, suggesting exacerbated defect in mitochondrial protein import. Proximity-dependent biotin identification (BioID) suggested that Mfb1 interacts with several mitochondrial surface proteins including Tom22, a component of the TOM complex. Loss of MFB1 under clogging conditions activates genes encoding cytosolic chaperones including HSP31 . Interestingly, disruption of HSP31 creates a synthetic lethality with protein import clogging under respiring conditions. We propose that Mfb1 functions to maintain mitochondrial protein import competency under clogging conditions, whereas Hsp31 plays an important role in protecting the cytosol against mPOS. Mutations in DJ-1, the human homolog of Hsp31, and mitochondria-associated F-box proteins (eg., Fbxo7) are known to cause early-onset Parkinson's disease. Our work may help to better understand how these mutations affect cellular proteostasis and cause neurodegeneration.
    DOI:  https://doi.org/10.1101/2025.10.13.682092
  30. Nat Commun. 2025 Nov 28. 16(1): 10698
    Reciprocal control of metabolic and chromatin regulators improves rice tolerance to heat.
    Yaping Yue, Biao Liu, Qiutao Xu, Zhengting Chen, Jing Wang, Yu Zhao, Dao-Xiu Zhou.
      Plant metabolic activities are regulated to adapt to the fluctuating environment for optimized growth, while interplay between metabolic and chromatin pathways plays an essential role in environmental adaptation. However, how metabolic and chromatin regulators cooperate to control metabolite accumulation and gene expression required for stress tolerance remains unclear. Here, we show that the pyruvate kinase 1 (PK1) has a function to integrate stress signals for metabolic and epigenetic controls of heat tolerance in rice. Over-expression of PK1 enhances plant tolerance to heat, while its loss-of-function decreases the recovery rate from heat stress. Heat stress induces PK1 production, nuclear enrichment, lysine acetylation and activity for pyruvate accumulation, H3T11 phosphorylation (H3T11p) and H3K9 acetylation (H3K9ac), and gene expression. In addition, PK1 phosphorylates General control non-repressed protein 5 (GCN5) and stimulates its activity for H3K9ac. Conversely, under heat stress GCN5 enhances PK1 lysine acetylation and enhances its activity for H3T11p and pyruvate production. The PK1 and GCN5-controlled H3T11p and H3K9ac are required for heat stress-responsive gene expression. These results establish PK1 as key player linking metabolic and chromatin pathways and uncover a mutually stimulating mechanism between metabolic and chromatin regulators for stress tolerance in rice.
    DOI:  https://doi.org/10.1038/s41467-025-66406-3
  31. bioRxiv. 2025 Oct 14. pii: 2025.10.13.682155. [Epub ahead of print]
    CNPY4 is a Lipid-Binding Regulator of Sphingolipid Homeostasis.
    Michael D Paul, Olga Zbodakova, Isabella S Glenn, Aleksandr Stotland, Ophir D Klein, Natalia Jura.
      Sphingolipids function both as signaling molecules and as organizers of cell membranes, and their dysregulation has been linked to cancer, metabolic disorders, and neurodegeneration. A central node in the sphingolipid metabolism network is ceramide, which is converted into numerous derivatives, including sphingomyelin (SM). Through interactions with cholesterol, SM forms liquid-ordered microdomains that influence membrane organization and signaling. Previously, we reported that the Saposin-like (SAPLIP) protein Canopy4 (CNPY4) negatively regulates the levels of free cholesterol in the plasma membrane. Although SAPLIPs commonly regulate lipid metabolism through direct lipid interactions, CNPY4 does not bind cholesterol directly. Here, we show that CNPY4 interacts with multiple sphingolipids in vitro , including ceramide and SM, and with ceramide in cells. We also demonstrate that CNPY4 knockdown elevates SM levels at the plasma membrane and disrupts cellular localization and abundance of ceramide, suggesting that the levels and consequently the homeostatic distribution of these sphingolipids is under control of CNPY4. Although the most pronounced effect of CNPY4 loss is on the ceramide/SM conversion pathway, it additionally impacts the levels of over 150 cellular lipids and modulates neutral sphingomyelinase activity, consistent with secondary disruptions in sphingolipid homeostasis. Collectively, our findings point to CNPY4 as a sphingolipid chaperone that regulates the abundance and localization of these lipids, modulating in turn cholesterol homeostasis and cellular signaling.
    DOI:  https://doi.org/10.1101/2025.10.13.682155
  32. Cell Rep. 2025 Nov 25. pii: S2211-1247(25)01392-0. [Epub ahead of print]44(12): 116620
    Glutamine synthetase modulates YAP activation by stabilizing LATS under glutamine homeostasis.
    Siyi Li, Ting Ling, Yuhan Wang, Jing Shi, Qiuping Wang, Jing Lv, Jinghan Li, Yu Liu, Yi Zhang, Changhao Liu, Tian Xia, Di Chen, Wenqi Wang, Hong-Xu Liu, Hai-Long Piao.
      Glutamine homeostasis plays a crucial role in fundamental cellular processes and is often dysregulated in cancer cells; however, the underlying mechanisms governing this homeostasis remain unclear. Here, we demonstrate that enriched glutamine activates the Hippo pathway. Mechanistically, glutamine synthetase (GS) interacts with LATS1, leading to its downregulation via increased ubiquitin degradation. Glutamine supplementation reduces the expression of GS and stabilizes LATS1, leading to YAP phosphorylation and inhibition. Clinically, GS expression is associated with clinical outcomes and inversely correlated with LATS1 expression and YAP1 phosphorylation. Taken together, these results not only uncover a previously undescribed mechanism by which glutamine homeostasis regulates the Hippo pathway but also suggest a potential therapeutic strategy by targeting glutamine metabolism and key growth-related signaling pathways for cancer treatment.
    Keywords:  CP: cancer; CP: metabolism; GS; Hippo pathway; LATS; cancer; glutamine
    DOI:  https://doi.org/10.1016/j.celrep.2025.116620
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