Periprostatic adipose tissue secretes chemokines and lipid mediators that, particularly in the context of obesity, enhance prostate cancer cell (PCa) migration and invasion. Treating 3 T3-F442A pre-adipocytes with condit...Periprostatic adipose tissue secretes chemokines and lipid mediators that, particularly in the context of obesity, enhance prostate cancer cell (PCa) migration and invasion. Treating 3 T3-F442A pre-adipocytes with conditioned medium (CM) from M1-like RAW264.7 cells resulted in a significant upregulation of TG-interacting factor 1 (Tgif1) expression. Using a Tgif1 promoter reporter assay, we showed that the tumor necrosis factor (TNF) transcriptionally upregulates Tgif1 promoter activity, consistent with increased mRNA and protein expression. We also demonstrated that Tgif1 contributes to the modulation of TNF-driven Il-6 and Ccl2 cytokine mRNA expression in Tgif1-knockout and Tgif1-overexpressing 3 T3-F442A pre-adipocytes. CM from Tgif1-overexpressing cells showed a positive correlation between Tgif1 expression and PCa cell migration. We conclude that Tgif1 mediates TNF-induced Ccl2 expression in pre-adipocytes, thereby promoting PCa progression.
Intrinsically disordered regions (IDRs) constitute a substantial portion of eukaryotic proteomes but are less prevalent in prokaryotes. Nevertheless, accumulating evidence reveals that IDRs play crucial roles in bacteria...Intrinsically disordered regions (IDRs) constitute a substantial portion of eukaryotic proteomes but are less prevalent in prokaryotes. Nevertheless, accumulating evidence reveals that IDRs play crucial roles in bacterial virulence, niche adaptation, and host interactions. In this review, we focus on human bacterial pathogens and discuss recent advances in understanding the distribution, evolution, and functional characterization of IDRs. We begin by briefly summarizing their biological properties, conformational ensembles, and representation within bacterial proteomes. We then highlight the diverse mechanisms through which bacterial IDRs interact with and manipulate host cell machineries. These include hijacking host pathways, mediating protein-protein interactions, sensing nutrients and environmental cues, accommodating short linear motifs that mimic eukaryotic signaling elements, and sequestering antimicrobial peptides. Finally, we examine current knowledge and outstanding questions concerning the evolution and antigenicity of bacterial IDRs. Drawing on recent research advances, we provide a focused and accessible overview on how IDRs contribute to the shaping of host-bacteria interactions.
Tuberculosis (TB) remains a major health threat, while the increasing occurrence of drug-resistant strains underscores the need for new antitubercular drugs. A promising strategy to combat TB is based on disrupting the m...Tuberculosis (TB) remains a major health threat, while the increasing occurrence of drug-resistant strains underscores the need for new antitubercular drugs. A promising strategy to combat TB is based on disrupting the mycobacterial redox homeostasis by inhibiting an NADPH-dependent oxidoreductase, mycothione reductase (Mtr). Using high-throughput screening, we recently identified potent and selective Mtr inhibitors. Here we report high-resolution X-ray structures of Mtr from Mycobacterium tuberculosis and Mycobacterium xenopi, including the M. tuberculosis enzyme complexed with a novel inhibitor, Respiri-1093. Our findings demonstrate that Respiri-1093 competes with the NADP(H) binding rather than mycothione binding. Analysis of the binding site explains the observed selectivity of the inhibitor towards the M. tuberculosis enzyme. These results provide a structural basis for rational drug design.
The finding of the pyruvate generator ('mitochondrial gas pedal') arose from the observation that cytosolic Ca accelerates glutamate-driven respiration. Here, we show that glutamate respiration of isolated rat brainstem...The finding of the pyruvate generator ('mitochondrial gas pedal') arose from the observation that cytosolic Ca accelerates glutamate-driven respiration. Here, we show that glutamate respiration of isolated rat brainstem mitochondria appears to be insensitive to extra-mitochondrial Ca . This raises the question: Do these mitochondria lack a pyruvate generator, or is its detection masked? By reconstituting the complete malate-aspartate shuttle (MAS), we demonstrate that brainstem mitochondria possess a pyruvate generator, just like mitochondria from other brain regions. Direct measurement, however, is hindered by the high rate of Ca-insensitive glutamate utilization by glial mitochondria. We therefore conclude that the pyruvate generator is a universal mechanism in all tissues that contain a functional MAS and pyruvate-generating enzymes.
Von Willebrand factor (vWF) is central to hemostasis, yet its ultralarge multimers promote arterial thrombosis. Nattokinase, a natto-derived serine protease, reduces plasma vWF levels, but the underlying mechanism remain...Von Willebrand factor (vWF) is central to hemostasis, yet its ultralarge multimers promote arterial thrombosis. Nattokinase, a natto-derived serine protease, reduces plasma vWF levels, but the underlying mechanism remains unclear. Here, we show that nattokinase directly cleaves the unstructured vWF73 peptide and the folded vWF A2 domain under static conditions. Mass spectrometry identified Thr1608-Gly1609 as the primary cleavage site, located three residues downstream of the ADAMTS13-targeted Tyr1605-Met1606 bond. Kinetic analysis revealed that nattokinase exhibits a catalytic efficiency (k/K) ~200-fold higher than that of ADAMTS13. Unlike ADAMTS13, which requires shear stress to expose its scissile bond, nattokinase functions independently of substrate unfolding. These results provide molecular evidence for direct vWF A2 domain cleavage by nattokinase, providing mechanistic support for its potential contribution to the antithrombotic effects reported for oral nattokinase.
Across the human lifespan, the gut microbiome exhibits considerable inter-individual variation. However, individuals within the same age group often share characteristic compositional and functional patterns shaped by fa...Across the human lifespan, the gut microbiome exhibits considerable inter-individual variation. However, individuals within the same age group often share characteristic compositional and functional patterns shaped by factors such as early microbial seeding, lifelong environmental exposures, and age-related physiological changes. Birth and early feeding establish the initial gut microbiome, with maternal transmission and milk-derived substrates typically favoring Bifidobacterium. As infants transition to solid foods and experience increasing social and environmental exposures, the microbiome undergoes substantial restructuring throughout childhood and adolescence. In adulthood, functional redundancy underpins stability despite routine perturbations; later life brings greater compositional uniqueness, with some profiles losing core taxa and accommodating opportunistic species, whereas others, particularly healthy older adults and centenarians, retain distinctive metabolic capacities that may buffer inflammaging. Efforts to build microbiome "aging clocks" highlight potential to index biological age, but progress remains constrained by technical and methodological limitations and is still maturing. This review synthesizes current evidence and identifies priorities for developing microbiome-informed, life-stage-tailored interventions.
Embryo-like structures, or stembryos, complement embryo research in innovative ways and provide an alternative when embryo utilization is ethically or technically limited. These models, however, are hindered by experimen...Embryo-like structures, or stembryos, complement embryo research in innovative ways and provide an alternative when embryo utilization is ethically or technically limited. These models, however, are hindered by experimental variability and limited developmental potential, whose causes are still not fully understood. Establishment of appropriate DNA methylation patterns is crucial for mammalian development but characterization of DNA methylation in stembryo models has been largely overlooked. This Perspective manuscript highlights this knowledge gap and suggests that characterization of DNA methylation, and in the future also of other epigenetic modifications, should become standard practice in stembryo model characterization. Available datasets indicate that differences in DNA methyltransferase expression between stembryos and embryos exist, thus suggesting an avenue of investigation to further improve these models.
Left-right (L-R) symmetry is a fundamental feature of bilaterian body plans, yet how it is actively maintained and corrected during development remains poorly understood. In the ascidian Ciona, embryos transiently exhibi...Left-right (L-R) symmetry is a fundamental feature of bilaterian body plans, yet how it is actively maintained and corrected during development remains poorly understood. In the ascidian Ciona, embryos transiently exhibit clockwise tail twisting that is progressively reduced but stabilizes at a residual angle of approximately 10°. Inhibition of retinoic acid signaling or neuromuscular activity eliminated this residual twist, restoring full bilateral symmetry. Myofibrils in both left and right muscles adopted the same left-handed helical orientation, and mechanical modeling showed that this architecture generates net torque sufficient to stabilize residual twisting against full symmetry restoration. These findings reveal how bilaterian embryos balance symmetry restoration with morphogenetic asymmetry.
AAA+ ATPases safeguard proteostasis by harnessing ATP hydrolysis to unfold misfolded or damaged proteins. Depending on their specific structural motifs and partners, they either channel substrates to peptidases for degra...AAA+ ATPases safeguard proteostasis by harnessing ATP hydrolysis to unfold misfolded or damaged proteins. Depending on their specific structural motifs and partners, they either channel substrates to peptidases for degradation or disentangle aggregates for refolding. This conserved mechanism across all life domains relies on the conversion of chemical energy into mechanical force. Although structural, biochemical and single-molecule studies have provided valuable insights into ATP-driven unfolding, the precise threading mechanism remains unresolved. This review synthesises current knowledge on three classes of AAA+ unfoldases: (a) self-contained proteases with both ATPase and peptidase domains, (b) ATPases cooperating with separate peptidases and (c) ATPases dedicated to disaggregation and refolding without proteolysis. We discuss existing models, underline technological limitations and outline experimental approaches to address these challenges. Gaining a clearer picture of substrate threading will enhance our grasp of basic protein quality control and also enable modulation of proteostasis in eukaryotic cells, relevant to neurodegenerative diseases and antibiotic targeting of bacterial unfoldases. Like the mythological Moirai, AAA+ enzymes govern the fate of proteins, though their exact decision-making and handling of their protein substrates remains elusive.
Cells rely on metabolic control; the mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability, particularly amino acids. Lysosomes maintain amino acid homeostasis through recycling. SLC38A9, a lyso...Cells rely on metabolic control; the mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability, particularly amino acids. Lysosomes maintain amino acid homeostasis through recycling. SLC38A9, a lysosomal amino acid transporter, functions as a critical sensor in the mTORC1 pathway. Here, we investigate how pH regulates SLC38A9 activity. We show that arginine uptake is pH-dependent, with His544 residue serving as the pH sensor. Mutating His544 abolishes pH dependence without impairing overall transport, indicating His544 influences transport through protonation/deprotonation, instead of involving in the substrate binding. We propose a working model for pH-induced activation, through comparing two determined SLC38A9 structures at different pH. These findings reveal how local ionic shifts regulate lysosomal transporters and fine-tune SLC38A9 function to control mTORC1 signaling.
Although the mechanism of action of the tripeptide-like herbicide bialaphos is well understood, its cellular uptake process remains elusive. We report that a peptide transporter mediates its uptake in Saccharomyces cerev...Although the mechanism of action of the tripeptide-like herbicide bialaphos is well understood, its cellular uptake process remains elusive. We report that a peptide transporter mediates its uptake in Saccharomyces cerevisiae. The Japanese sake yeast strain Kyokai 7 (K7) was supersensitive to bialaphos compared to S288C. Disruption of PTR2, which encodes a peptide transporter, alleviated bialaphos sensitivity in K7. PTR2 mRNA and protein levels were higher in K7 than in S288C. Higher expression levels were observed in the S288C strain when Ptr2 was expressed using the K7-derived genomic promoter of PTR2. We identified single-nucleotide polymorphisms (SNPs) in the PTR2 promoter responsible for the increased expression levels. One of the critical SNPs was specifically found in sake strains of K7-lineage.
Z. Hu , X. Guo , Q. Yu , L. Qiu , J. Li , K. Ying , C. Guo and J. Zhang , "Down-Regulation of Adenine Nucleotide Translocase 3 and Its Role in Camptothecin-Induced Apoptosis in Human Hepatoma QGY7703 Cells," FEBS Letters...Z. Hu , X. Guo , Q. Yu , L. Qiu , J. Li , K. Ying , C. Guo and J. Zhang , "Down-Regulation of Adenine Nucleotide Translocase 3 and Its Role in Camptothecin-Induced Apoptosis in Human Hepatoma QGY7703 Cells," FEBS Letters 583, no. 2 (2009): 383-388, https://doi.org/10.1016/j.febslet.2008.12.029. The above article, published online on 25 December 2008 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors; the journal Editor-in-Chief, Michael Brunner; the Federation of European Biochemical Societies; and John Wiley & Sons Ltd. The retraction has been agreed upon following concerns raised by a third party. An investigation identified several unexpected similarities between the FACS 6h and 12h panels shown in Figure 1A. Duplication of the β-actin bands between Figures 2 and 3A, and between Figures 2 and 4A, was also identified. Due to the time that has elapsed since publication, the authors were unable to provide any original data and stated that the duplications resulted from unintentional errors. In light of these issues, the editors consider the results and conclusions to be unreliable.
Plasma membranes are organized into dynamic nanoscale domains that regulate lipid and protein distribution, diffusion, and receptor availability. Because viruses act on similar length scales, this organization shapes ear...Plasma membranes are organized into dynamic nanoscale domains that regulate lipid and protein distribution, diffusion, and receptor availability. Because viruses act on similar length scales, this organization shapes early infection steps, including attachment, membrane exploration, receptor engagement, and entry. This review summarizes how pre-existing receptor nanoplatforms promote viral capture and how virus binding can remodel plasma membrane nanoarchitecture. Using influenza A virus and human immunodeficiency virus 1 as examples, we discuss how multivalent, low-affinity glycoprotein-glycan interactions exploit clustered attachment factors to increase avidity and tune receptor dynamics. We also address transbilayer lipid asymmetry and how its perturbation-particularly phosphatidylserine exposure and apoptotic mimicry-is exploited by enveloped viruses.
The complexity of human neurobiology is influenced by its heterogeneity, reflected in both cell type diversity as well as genetic variations between individuals. Neural organoids are 3D developing neural tissues designed...The complexity of human neurobiology is influenced by its heterogeneity, reflected in both cell type diversity as well as genetic variations between individuals. Neural organoids are 3D developing neural tissues designed to mimic development of the nervous system; however, most currently fail to capture this diversity. Recent advances have focused on increasing complexity through self-organised multi-region organoids, assembloids and chimeroids. Here, we discuss these approaches, as well as the remaining lack of genetic and ethnic diversity in neural organoid research, its impact on the generalizability of findings, and strategies to address this gap. We provide a flowchart to guide the experimenter towards the choice of model and discuss applications of neural organoids that benefit from complexity or reliability.
Lysosomes play a critical role in the quality control of cellular organelles. However, lysosomal membranes can be damaged under a variety of conditions, leading to the onset of various diseases. Damaged lysosomes are sel...Lysosomes play a critical role in the quality control of cellular organelles. However, lysosomal membranes can be damaged under a variety of conditions, leading to the onset of various diseases. Damaged lysosomes are selectively cleared via a ubiquitin-dependent mechanism, but the molecular mechanisms underlying this process have not been adequately elucidated. In this study, we found that RNF115 is a lysosomal damage-responsive ubiquitin ligase that undergoes massive translocation from the cytosol to the p62/SQSTM1-positive puncta around ruptured lysosomes. In accordance with the changes in its distribution, the depletion of RNF115 delayed the removal of Gal3 from damaged lysosomes during the restoration process following lysosomal damage. These observations suggest that RNF115 is responsible for the clearance of damaged lysosomes.
The placenta plays a vital role in supporting and nourishing the fetus throughout pregnancy, yet the mechanisms governing its development remain poorly understood. Recent advances in 3D human trophoblast organoid systems...The placenta plays a vital role in supporting and nourishing the fetus throughout pregnancy, yet the mechanisms governing its development remain poorly understood. Recent advances in 3D human trophoblast organoid systems derived from both primary tissues and stem cells provide physiologically relevant platforms to investigate placental development in both health and disease. This 'In a Nutshell' review highlights how these models are transforming our ability to investigate human placental biology in pregnancy.
Recombinant NAD-dependent ribitol dehydrogenase derived from Klebsiella oxytoca (KoRdh) exhibits activity toward both ribitol and allitol. KoRdh catalyzes the NAD-dependent oxidation of allitol to d-allulose and the NADH...Recombinant NAD-dependent ribitol dehydrogenase derived from Klebsiella oxytoca (KoRdh) exhibits activity toward both ribitol and allitol. KoRdh catalyzes the NAD-dependent oxidation of allitol to d-allulose and the NADH-dependent reduction of d-allulose to allitol. Notably, the flexible loop of KoRdh undergoes conformational changes upon NAD and substrate binding. To elucidate the flexible loop's role in substrate recognition, we determined the X-ray structures of KoRdh alone and in complexes with NAD, d-allulose, or d-allose. Although d-allose is an aldose and not a substrate of KoRdh, it binds to KoRdh in the pyranose form, revealing the location of the substrate-binding site. Based on these structures, we propose a substrate recognition mechanism for KoRdh. Impact statement This research reveals an insight into a substrate recognition mechanism in the flexible region of ribitol dehydrogenase. Because ribitol dehydrogenase is a member of the short-chain reductases/oxidases (SDR) family, the current study will provide further insight into related enzymes that harbor the flexible region.
Cellular senescence, a state of irreversible cell cycle arrest, is implicated in age-related diseases. While it is well known that senescent cells resist apoptosis, studies on their resistance to ferroptosis are limited...Cellular senescence, a state of irreversible cell cycle arrest, is implicated in age-related diseases. While it is well known that senescent cells resist apoptosis, studies on their resistance to ferroptosis are limited and not fully understood. Senescent cells remain sensitive to ferroptosis induced by direct inhibition of glutathione peroxidase 4 (GPX4) but resist ferroptosis from cystine starvation, suggesting a role for mitochondrial metabolism. Here, we found that this resistance is mediated by peroxisome proliferator-activated receptor α (PPARα)-dependent upregulation of pyruvate dehydrogenase kinase 4 (PDK4), which inactivates pyruvate dehydrogenase (PDH) and suppresses mitochondria-derived reactive oxygen species, a key driver of ferroptosis. Our findings identify the PPARα-PDK4-PDH axis as a metabolic switch regulating ferroptosis sensitivity in senescent cells and provide insight into the senescence-ferroptosis interaction.