Nat Commun. 2025 Mar 12;16(1):2479. doi: 10.1038/s41467-025-56628-w.

ABSTRACT

Predicting and quantifying phenotypic consequences of genetic variants in rare disorders is a major challenge, particularly pertinent for 'actionable' genes such as thyroid hormone transporter MCT8 (encoded by the X-linked SLC16A2 gene), where loss-of-function (LoF) variants cause a rare neurodevelopmental and (treatable) metabolic disorder in males. The combination of deep phenotyping data with functional and computational tests and with outcomes in population cohorts, enabled us to: (i) identify the genetic aetiology of divergent clinical phenotypes of MCT8 deficiency with genotype-phenotype relationships present across survival and 24 out of 32 disease features; (ii) demonstrate a mild phenocopy in ~400,000 individuals with common genetic variants in MCT8; (iii) assess therapeutic effectiveness, which did not differ among LoF-categories; (iv) advance structural insights in normal and mutated MCT8 by delineating seven critical functional domains; (v) create a pathogenicity-severity MCT8 variant classifier that accurately predicted pathogenicity (AUC:0.91) and severity (AUC:0.86) for 8151 variants. Our information-dense mapping provides a generalizable approach to advance multiple dimensions of rare genetic disorders.

PMID:40075072 | DOI:10.1038/s41467-025-56628-w

FEMS Yeast Res. 2025 Mar 12:foaf010. doi: 10.1093/femsyr/foaf010. Online ahead of print.

ABSTRACT

Komagataella phaffii has gained recognition as a versatile platform for recombinant protein production, with applications covering biopharmaceuticals, industrial enzymes, food additives, etc. Its advantages include high-level protein expression, moderate post-translational modifications, high-density cultivation, and cost-effective methanol utilization. Nevertheless, it still faces challenges for the improvement of production efficiency and extension of applicability. This review highlights the key strategies used to facilitate productivity in K. phaffii, including systematic advances in genetic manipulation tools, transcriptional and translational regulation, protein folding and secretion optimization. Glycosylation engineering is also concerned as it enables humanized glycosylation profiles for the use in therapeutic proteins and functional food additivities. Omics technologies and genome-scale metabolic models provide new insights into cellular metabolism, enhancing recombinant protein expression. High-throughput screening technologies are also emphasized as crucial for constructing high-expression strains and accelerating strain optimization. With advancements in gene-editing, synthetic and systems biology tools, the K. phaffii expression platform has been significantly improved for fundamental research and industrial use. Future innovations aim to fully harness K. phaffii as a next-generation cell factory, providing efficient, scalable, and cost-effective solutions for diverse applications. It continues to hold promise as a key driver in the field of biotechnology.

PMID:40074550 | DOI:10.1093/femsyr/foaf010

J Genet Eng Biotechnol. 2025 Mar;23(1):100471. doi: 10.1016/j.jgeb.2025.100471. Epub 2025 Feb 18.

ABSTRACT

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. This study aimed to explore the role of hsa-miR-101-3p in HCC pathogenesis by identifying key genes and pathways. A comprehensive bioinformatics analysis revealed twelve hub genes (ETNK1, BICRA, IL1R1, KDM3A, ARID2, GSK3β, EZH2, NOTCH1, SMARCA4, FOS, CREB1, and CASP3) and highlighted their involvement in crucial oncogenic pathways, including PI3K/Akt, mTOR, MAPK, and TGF-β. Gene expression analysis showed significant overexpression of ETNK1, KDM3A, EZH2, SMARCA4, and CASP3 in HCC tissues, correlating with poorer survival outcomes. Drug screening identified therapeutic candidates, including Tazemetostat for EZH2 and lithium compounds for GSK3β, underscoring their potential for targeted treatment. These findings provide novel insights into the complexity of HCC pathogenesis, suggesting that the identified hub genes could serve as diagnostic or prognostic biomarkers and therapeutic targets. While bioinformatics-driven, this study offers a strong basis for future clinical validation to advance precision medicine in HCC.

PMID:40074445 | DOI:10.1016/j.jgeb.2025.100471

J Med Ethics. 2025 Mar 12:jme-2024-110652. doi: 10.1136/jme-2024-110652. Online ahead of print.

ABSTRACT

Informed consent in surgical settings requires not only the accurate communication of medical information but also the establishment of trust through empathic engagement. The use of large language models (LLMs) offers a novel opportunity to enhance the informed consent process by combining advanced information retrieval capabilities with simulated emotional responsiveness. However, the ethical implications of simulated empathy raise concerns about patient autonomy, trust and transparency. This paper examines the challenges of surgical informed consent, the potential benefits and limitations of digital tools such as LLMs and the ethical implications of simulated empathy. We distinguish between active empathy, which carries the risk of creating a misleading illusion of emotional connection and passive empathy, which focuses on recognising and signalling patient distress cues, such as fear or uncertainty, rather than attempting to simulate genuine empathy. We argue that LLMs should be limited to the latter, recognising and signalling patient distress cues and alerting healthcare providers to patient anxiety. This approach preserves the authenticity of human empathy while leveraging the analytical strengths of LLMs to assist surgeons in addressing patient concerns. This paper highlights how LLMs can ethically enhance the informed consent process without undermining the relational integrity essential to patient-centred care. By maintaining transparency and respecting the irreplaceable role of human empathy, LLMs can serve as valuable tools to support, rather than replace, the relational trust essential to informed consent.

PMID:40074323 | DOI:10.1136/jme-2024-110652

Curr Biol. 2025 Feb 27:S0960-9822(25)00188-5. doi: 10.1016/j.cub.2025.02.025. Online ahead of print.

ABSTRACT

Sporulation is the most widespread means of reproduction and dispersal in fungi and, at the same time, an industrially important trait in crop mushrooms. In the Basidiomycota, sexual spores are produced on specialized cells known as basidia, from which they are forcibly discharged with the highest known acceleration in nature. However, the genetics of sporulation remains poorly known. Here, we identify a new, highly conserved transcription factor, sporulation-related regulator 1 (srr1), and systematically address the genetics of spore formation for the first time in the Basidiomycota. We show that Srr1 regulates postmeiotic spore morphogenesis, but not other aspects of fruiting body development or meiosis, and its role is conserved in the phylogenetically distant, but industrially important, Pleurotus spp. (oyster mushrooms). We used RNA sequencing to understand genes directly or indirectly regulated by Srr1 and identified a strongly supported binding motif for the protein. Using an inferred network of putative target genes regulated by Srr1 and comparative genomics, we identified genes lost in secondarily non-ballistosporic taxa, including a novel sporulation-specific chitinase gene. Overall, our study offers systematic insights into the genetics of spore morphogenesis in the Basidiomycota.

PMID:40073868 | DOI:10.1016/j.cub.2025.02.025

Talanta. 2025 Mar 10;292:127921. doi: 10.1016/j.talanta.2025.127921. Online ahead of print.

ABSTRACT

The detection of glycosylation alterations is essential for elucidating the roles of glycan functions in biological processes and identifying potential disease biomarkers. Stable isotopic chemical labeling, coupled with mass spectrometry (MS), represents a powerful approach in quantitative glycomics. In this study, we synthesized a novel isotopic hydrazide pair, 2,6-Dimethyl-4-chinolincarbohydrazid (DMQCH) and its deuterium isomer DMQCH-d4, via an efficient and cost-effective method, and applied it for the first time in MALDI-MS-based quantitative glycomics. The hydrazide tags, DMQCH/DMQCH-d4, enabled stable mass shifts through reductive-terminal reactions with glycans, allowing for differential mass tagging of two samples without additional purification after derivatization. This DMQCH/DMQCH-d4 pair exhibited high derivatization efficiency (including on-target derivatization), substantial improvements in MS signal intensity (a 15-fold increase for maltoheptaose, high reproducibility (CV < 13.6 %), and excellent linearity (R2 > 0.99) over two orders of magnitude in dynamic range for the relative quantitative analysis of maltoheptaose. Furthermore, this isotopic hydrazide pair was validated by successfully measuring changes in serum N-glycan profiles from individuals with healthy human serum control and ovarian cancer, highlighting its potential in quantitative glycomics for clinical applications.

PMID:40073825 | DOI:10.1016/j.talanta.2025.127921

Bioinformatics. 2025 Mar 12:btaf103. doi: 10.1093/bioinformatics/btaf103. Online ahead of print.

ABSTRACT

MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognisable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, for example, to the cancer evolution study.

RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved thanks to the hybridisation of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Echerichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.

AVAILABILITY: GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E.coli https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile https://github.com/qBioTurin/EpiCell_CDifficile.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:40073274 | DOI:10.1093/bioinformatics/btaf103

Elife. 2025 Mar 12;13:RP95802. doi: 10.7554/eLife.95802.

ABSTRACT

Fiber photometry has become a popular technique to measure neural activity in vivo, but common analysis strategies can reduce the detection of effects because they condense within-trial signals into summary measures, and discard trial-level information by averaging across-trials. We propose a novel photometry statistical framework based on functional linear mixed modeling, which enables hypothesis testing of variable effects at every trial time-point, and uses trial-level signals without averaging. This makes it possible to compare the timing and magnitude of signals across conditions while accounting for between-animal differences. Our framework produces a series of plots that illustrate covariate effect estimates and statistical significance at each trial time-point. By exploiting signal autocorrelation, our methodology yields joint 95% confidence intervals that account for inspecting effects across the entire trial and improve the detection of event-related signal changes over common multiple comparisons correction strategies. We reanalyze data from a recent study proposing a theory for the role of mesolimbic dopamine in reward learning, and show the capability of our framework to reveal significant effects obscured by standard analysis approaches. For example, our method identifies two dopamine components with distinct temporal dynamics in response to reward delivery. In simulation experiments, our methodology yields improved statistical power over common analysis approaches. Finally, we provide an open-source package and analysis guide for applying our framework.

PMID:40073228 | DOI:10.7554/eLife.95802

Sci Adv. 2025 Mar 14;11(11):eadt4548. doi: 10.1126/sciadv.adt4548. Epub 2025 Mar 12.

ABSTRACT

Carbohydrate-responsive element binding protein (ChREBP) and Max-like protein X (MLX) form a heterodimeric transcription factor complex that couples intracellular sugar levels to carbohydrate and lipid metabolism. To promote the expression of target genes, two ChREBP-MLX heterodimers form a heterotetramer to bind a tandem element with two adjacent E-boxes, called carbohydrate-responsive element (ChoRE). How the ChREBP-MLX hetero-tetramerization is achieved and regulated remains poorly understood. Here, we show that MLX phosphorylation on an evolutionarily conserved motif is necessary for the heterotetramer formation on the ChoRE and the transcriptional activity of the ChREBP-MLX complex. We identified casein kinase 2 (CK2) and glycogen synthase kinase 3 (GSK3) as MLX kinases. High intracellular glucose-6-phosphate accumulation inhibits MLX phosphorylation and heterotetramer formation on the ChoRE, impairing ChREBP-MLX activity. Physiologically, MLX phosphorylation is necessary in Drosophila to maintain sugar tolerance and lipid homeostasis. Our findings suggest that MLX phosphorylation is a key mechanism for the ChREBP-MLX heterotetramer formation to regulate carbohydrate and lipid metabolism.

PMID:40073115 | DOI:10.1126/sciadv.adt4548

STAR Protoc. 2025 Mar 11;6(1):103657. doi: 10.1016/j.xpro.2025.103657. Online ahead of print.

ABSTRACT

Colostrum and milk from dairy sources consist of whey, casein, and fat, which have notable pharmacological properties due to their proteins and peptides. Here, we present a protocol for isolating, simulating in vitro gastrointestinal digestion, and fractionating colostrum and milk hydrolysates from any dairy source. We also describe steps for nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS/MS) identification of proteins and peptides and in silico system biology-based profiling of the proteins and peptides present in the hydrolysates.

PMID:40073020 | DOI:10.1016/j.xpro.2025.103657

PLoS Comput Biol. 2025 Mar 12;21(3):e1012109. doi: 10.1371/journal.pcbi.1012109. Online ahead of print.

ABSTRACT

Advancements with cost-effective, high-throughput omics technologies have had a transformative effect on both fundamental and translational research in the medical sciences. These advancements have facilitated a departure from the traditional view of human red blood cells (RBCs) as mere carriers of hemoglobin, devoid of significant biological complexity. Over the past decade, proteomic analyses have identified a growing number of different proteins present within RBCs, enabling systems biology analysis of their physiological functions. Here, we introduce RBC-GEM, one of the most comprehensive, curated genome-scale metabolic reconstructions of a specific human cell type to-date. It was developed through meta-analysis of proteomic data from 29 studies published over the past two decades resulting in an RBC proteome composed of more than 4,600 distinct proteins. Through workflow-guided manual curation, we have compiled the metabolic reactions carried out by this proteome to form a genome-scale metabolic model (GEM) of the RBC. RBC-GEM is hosted on a version-controlled GitHub repository, ensuring adherence to the standardized protocols for metabolic reconstruction quality control and data stewardship principles. RBC-GEM represents a metabolic network is a consisting of 820 genes encoding proteins acting on 1,685 unique metabolites through 2,723 biochemical reactions: a 740% size expansion over its predecessor. We demonstrated the utility of RBC-GEM by creating context-specific proteome-constrained models derived from proteomic data of stored RBCs for 616 blood donors, and classified reactions based on their simulated abundance dependence. This reconstruction as an up-to-date curated GEM can be used for contextualization of data and for the construction of a computational whole-cell models of the human RBC.

PMID:40072998 | DOI:10.1371/journal.pcbi.1012109

Biol Chem. 2025 Mar 13. doi: 10.1515/hsz-2025-0101. Online ahead of print.

ABSTRACT

The disruption of protein homeostasis leads to the increased un- and misfolding of proteins and the formation of toxic protein aggregates. Their accumulation triggers an unfolded protein response that is characterized by the transcriptional upregulation of molecular chaperones and proteases, and aims to restore proteome integrity, maintain cellular function, suppress the cause of perturbation, and prevent disease and death. In the green microalga Chlamydomonas reinhardtii, the study of this response to proteotoxic stress has provided insights into the function of chaperone and protease systems, which are, though simpler, closely related to those found in land plants. In addition, there has been considerable progress in understanding the triggers and regulation of compartment-specific unfolded protein responses. This review provides an overview on how the dysfunction of protein homeostasis is sensed in the different compartments of Chlamydomonas, and summarizes the current knowledge on the pathways that are triggered to restore equilibrium in the cell, while also highlighting similarities and differences to the unfolded protein responses of other model organisms.

PMID:40072221 | DOI:10.1515/hsz-2025-0101

Scand J Med Sci Sports. 2025 Mar;35(3):e70034. doi: 10.1111/sms.70034.

ABSTRACT

High cardiorespiratory fitness (CRF) is associated with better overall health. This study aimed to find a metabolic signature associated with CRF to identify health-promoting effects. CRF based on cardiopulmonary exercise testing, targeted and untargeted metabolomics approaches based on mass spectrometry, and clinical data from two independent cohorts of the Study of Health in Pomerania (SHIP) were used. Sex-stratified linear regression models were adjusted for age, smoking, and height to relate CRF with individual metabolites. A total of 132 (SHIP-START-2: 483 men with a median age of 58 years and 450 women with a median age of 56 years) and 118 (SHIP-TREND-0: 341 men and 371 women both with a median age of 51 years) metabolites were associated with CRF. Lipids showed bidirectional relations to CRF independent of sex. Specific subsets of sphingomyelins were positively related to CRF in men (SM (OH) C14:1, SM(OH)C22:2 SM C16:0, SM C20:2 SM(OH)C24:1) and inversely in women (SM C16:1, SM C18:0, SM C18:1). Metabolites involved in energy production (citrate and succinylcarnitine) were only associated with CRF in men. In women, xenobiotics (hippurate, stachydrine) were related to CRF. The sex-specific metabolic signature of CRF is influenced by sphingomyelins, energy substrates, and xenobiotics. The greater effect estimates seen in women may emphasize the important role of CRF in maintaining metabolic health. Future research should explore how this profile changes with different types of exercise interventions or diseases in diverse populations and how these metabolites could be implemented in primary prevention settings.

PMID:40072034 | DOI:10.1111/sms.70034

J Exp Bot. 2025 Mar 12:eraf116. doi: 10.1093/jxb/eraf116. Online ahead of print.

ABSTRACT

Plant metabolism is profoundly affected by various abiotic stresses. Consequently, plants must reconfigure their metabolic networks to sustain homeostasis while synthesizing compounds that mitigate stress. This aspect, with the current intensified climate impact results in more frequent abiotic stresses on a global scale. Advances in metabolomics and systems biology in the last decades have enabled both a comprehensive overview and a detailed analysis of key components involved in the plant metabolic response to abiotic stresses. This review addresses metabolic responses to altered atmospheric CO2 and O3, water deficit, temperature extremes, light intensity fluctuations including the importance of UV-B, ionic imbalance, and oxidative stress predicted to be caused by climate change, long-term shifts in temperatures and weather patterns. It also assesses both the commonalities and specificities of metabolic responses to diverse abiotic stresses, drawing on data from the literature. Classical stress-related metabolites such as proline, and polyamines are revisited, with an emphasis on the critical role of branched-chain amino acid metabolism under stress conditions. Finally, where possible, mechanistic insights into the regulation of metabolic processes and further outlook on combinatory stresses are discussed.

PMID:40071778 | DOI:10.1093/jxb/eraf116

Rheumatology (Oxford). 2025 Mar 1;64(Supplement_1):i38-i41. doi: 10.1093/rheumatology/keae556.

ABSTRACT

Spatial transcriptomics enables the study of the mechanisms of disease through gene expression and pathway activity analysis in a spatial context. Originally mainly employed in oncology, the techniques developed use different methods of transcript identification, resolution (single cells vs regions), flexibility of target regions and the type of molecules that can be assessed (RNA and/or protein). Selection of regions of interest requires both knowledge of the underlying histopathological changes and limitations of the methods, like artefacts due to variation in pre-analytics, or the probes used to analyse them. Here we review techniques currently available, their opportunities and limitations and discuss results obtained using Digital Spatial Profiling in pauci-immune focal necrotizing (and crescentic) glomerulonephritis (piFNGN) and giant cells arteritis (GCA). Spatial profiling techniques are powerful tools to investigate defined regions of interest in autoimmune and inflammatory disorders and allow for the identification of genes differentially expressed between different types of lesions and different disease aetiologies. Spatial profiling provides an example of a powerful methodology to investigate disease pathways in tissue at a local level across a spectrum of human diseases and generates hypotheses about molecular mechanisms that can be further investigated in detail. When implemented in the setting of a systems biology approach it may ultimately reach the goal of predicting the course of disease from histopathological slides.

PMID:40071426 | DOI:10.1093/rheumatology/keae556

iScience. 2025 Feb 11;28(3):111994. doi: 10.1016/j.isci.2025.111994. eCollection 2025 Mar 21.

ABSTRACT

Brain endothelial cells (BECs) play an important role in maintaining central nervous system (CNS) homeostasis through blood-brain barrier (BBB) functions. BECs express low baseline levels of adhesion receptors, which limits entry of leukocytes. However, the molecular mediators governing this phenotype remain mostly unclear. Here, we explored how infiltration of immune cells across the BBB is influenced by the scaffold protein IQ motif containing GTPase-activating protein 2 (IQGAP2). In mice and zebrafish, we demonstrate that loss of Iqgap2 increases infiltration of peripheral leukocytes into the CNS under homeostatic and inflammatory conditions. Using single-cell RNA sequencing and immunohistology, we further show that BECs from mice lacking Iqgap2 exhibit a profound inflammatory signature, including extensive upregulation of adhesion receptors and antigen-processing machinery. Human tissue analyses also reveal that Alzheimer's disease is associated with reduced hippocampal IQGAP2. Overall, our results implicate IQGAP2 as an essential regulator of BBB immune privilege and immune cell entry into the CNS.

PMID:40071147 | PMC:PMC11894336 | DOI:10.1016/j.isci.2025.111994

QRB Discov. 2025 Feb 18;6:e11. doi: 10.1017/qrd.2025.1. eCollection 2025.

ABSTRACT

Metabolism is at the core of all functions of living cells as it provides Gibbs free energy and building blocks for synthesis of macromolecules, which are necessary for structures, growth, and proliferation. Metabolism is a complex network composed of thousands of reactions catalyzed by enzymes involving many co-factors and metabolites. Traditionally it has been difficult to study metabolism as a whole network and most traditional efforts were therefore focused on specific metabolic pathways, enzymes, and metabolites. By using engineering principles of mathematical modeling to analyze and study metabolism, as well as engineer it, that is, design and build, new metabolic features, it is possible to gain many new fundamental insights as well as applications in biotechnology. Here, we present the history and basic principles of engineering metabolism, as well as the newest developments in the field. We are using examples of applications in: (1) production of protein pharmaceuticals and chemicals; (2) basic studies of metabolism; and (3) impacting health care. We will end by discussing how engineering metabolism can benefit from advances in artificial intelligence (AI)-based models.

PMID:40070847 | PMC:PMC11894412 | DOI:10.1017/qrd.2025.1

Front Immunol. 2025 Feb 25;16:1494624. doi: 10.3389/fimmu.2025.1494624. eCollection 2025.

ABSTRACT

Antigen specific humoral immunity can be characterized by the analysis of serum antibodies. While serological assays for the measurement of specific antibody levels are available, these are not quantitative in the biochemical sense. Yet, understanding humoral immune responses quantitatively on the systemic level would need a universal, complete, quantitative, comparable measurement method of antigen specific serum antibodies of selected immunoglobulin classes. Here we describe a fluorescent, dual-titration immunoassay, which provides the biochemical parameters that are both necessary and sufficient to quantitatively characterize the humoral immune response. For validation of theory, we used recombinant receptor binding domain of SARS-CoV-2 as antigen on microspot arrays and varied the concentration of both the antigen and the serum antibodies from infected persons to obtain a measurement matrix of binding data. Both titration curves were simultaneously fitted using an algorithm based on the generalized logistic function and adapted for analyzing biochemical variables of binding. We obtained equilibrium affinity constants and concentrations for distinct antibody classes. These variables reflect the quality and the effective quantity of serum antibodies, respectively. The proposed fluorescent dual-titration microspot immunoassay can generate truly quantitative serological data that is suitable for immunological, medical and systems biological analysis.

PMID:40070838 | PMC:PMC11893856 | DOI:10.3389/fimmu.2025.1494624

Sci Rep. 2025 Mar 11;15(1):8394. doi: 10.1038/s41598-025-92618-0.

ABSTRACT

Gut dysbiosis plays an important role in cirrhosis, but the mechanism of its development was not established. The aim of the study was to test the hypothesis that portal hypertension can be the main factor in the development of gut dysbiosis in cirrhosis. This cross-sectional study included 25 patients with chronic non-cirrhotic portal hypertension due to extrahepatic portal vein obstruction after portal vein thrombosis (PVT) (NCPVT group), 29 cirrhotic patients without PVT (CirNoPVT), 15 cirrhotic patients with chronic PVT (CPVT), and 22 healthy controls. The fecal microbiota was assessed using 16S rRNA gene sequencing. The CirNoPVT and CPVT groups had largely similar differences in gut microbiota composition from the control group. Patients with NCPVT, as well as patients with cirrhosis, had a higher abundance of Streptococcus, Escherichia, Enterococcus, Enterobacteriaceae, Enterococcaceae, Streptococcaceae, Bacilli, Gammaproteobacteria, Proteobacteria, and a lower abundance of Roseburia, Faecalibacterium, Methanobrevibacter, Ruminococcaceae, Methanobacteriaceae, Clostridia, Methanobacteria, and Euryarchaeota as they were compared with healthy individuals. Patients with NCPVT had a higher abundance of Bifidobacterium, Bifidobacteriaceae, Actinobacteria, and a lower abundance of Gemmiger and Catenibacterium compared to healthy individuals, which was not observed in the cirrhosis groups. The abundance of Porphyromonadaceae with the genus Parabacteroides was reduced in both groups with PVT, but not in CirNoPVT. There were no significant differences in gut microbiota beta-diversity among the CirNoPVT, CPVT and NCPVT groups. All these groups had significant differences in beta-diversity from the control group. Portal hypertension seems be the main factor in the development of gut dysbiosis in cirrhosis.

PMID:40069378 | DOI:10.1038/s41598-025-92618-0

Nat Struct Mol Biol. 2025 Mar 11. doi: 10.1038/s41594-025-01516-6. Online ahead of print.

ABSTRACT

The metazoan tRNA ligase complex (tRNA-LC) has essential roles in tRNA biogenesis and unfolded protein response. Its catalytic subunit RTCB contains a conserved active-site cysteine that is susceptible to metal ion-induced oxidative inactivation. The flavin-containing oxidoreductase PYROXD1 preserves the activity of human tRNA-LC in a NAD(P)H-dependent manner, but its protective mechanism remains elusive. Here, we report a cryogenic electron microscopic structure of the human RTCB-PYROXD1 complex, revealing that PYROXD1 directly interacts with the catalytic center of RTCB through its carboxy-terminal tail. NAD(P)H binding and FAD reduction allosterically control PYROXD1 activity and RTCB recruitment, while reoxidation of PYROXD1 enables timed release of RTCB. PYROXD1 interaction is mutually exclusive with Archease-mediated RTCB guanylylation, and guanylylated RTCB is intrinsically protected from oxidative inactivation. Together, these findings provide a mechanistic framework for the protective function of PYROXD1 that maintains the activity of the tRNA-LC under aerobic conditions.

PMID:40069351 | DOI:10.1038/s41594-025-01516-6