Lysine Research Articles (Page 1)

Background: Bicuspid aortic valve (BAV) is a common congenital heart defect associated with serious cardiovascular complications, including thoracic aortic aneurysm and dissection (TAAD). Despite high heritability (~90%) and autosomal dominant inheritance, the genetic basis of BAV remains largely unknown. Methods: To investigate the genetic architecture of BAV, we leveraged electronic health record data linked to imputed genotyping from the VA Million Veteran Program (MVP). We developed and validated a Natural Language Processing (NLP) algorithm to extract valve leaflet morphology from echocardiographic reports and identify MVP participants with definitive BAV. We then conducted a multi-population genome-wide association study (GWAS) comparing individuals with BAV (n = 9,571) to all other MVP participants (n = 631,091) across European, African, Admixed American, and East Asian populations. Lead variants were mapped to nearby genes, followed by pathway enrichment analysis. To assess shared genetic architecture between BAV and TAAD, we calculated genetic correlation using LD score regression and performed colocalization analysis to identify shared causal loci. Results: Our NLP algorithm achieved high recall (0.955) and precision (0.984), identifying 655,762 reports (4.5%) and 83,704 patients (2.4%) with definitive BAV among 3.5 million Veterans. Of these, 9,571 had genotyping data and were included in the GWAS. Meta-analysis revealed seven loci reaching genome-wide significance (P < 5 × 10 -8 ), including two known ( PALMD, TEX41 ) and five novel loci ( PRDM6, LECT2, LPA, ADAMTSL1, ATXN2 ) (Figure 1). Enriched pathways included extracellular matrix organization, O-linked glycosylation, smooth muscle cell differentiation, and lysine degradation. BAV showed significant genetic correlation with TAAD (rg = 0.45; P = 5.64 × 10 -6 ). Colocalization analysis revealed seven shared loci between BAV and TAAD, with the strongest shared signal near PRDM6 (posterior probability ≈ 0.52). Notably, PRDM6 , which regulates smooth muscle cell differentiation, was previously implicated in a TAAD GWAS, reinforcing the possible genetic overlap between these conditions. Conclusions: Our findings identify novel candidate genes associated with BAV and support a shared genetic architecture with TAAD, providing new insights into the pathogenesis of BAV and related aortopathies while highlighting targets for future investigation.

Interactome quantitation reveals non-energetic mitochondrial roles in cell type specialization in murine kidney.

High temperatures during grain filling degrade rice quality, yet the metabolite-level basis of varietal tolerance—particularly root contributions—remains unclear. We compared the heat-tolerant ‘Fusaotome’ and the widely grown ‘Akitakomachi’ under control and high-temperature conditions. Panicles and roots were sampled at heading and profiled by capillary electrophoresis–mass spectrometry (CE–MS), followed by PCA, univariate testing, and KEGG pathway analysis. PCA resolved treatment and cultivar differences in an organ-specific manner. In panicles, ‘Fusaotome’ showed 8 increased metabolites (≥1.5-fold) and 11 decreased (≤1/1.5), whereas ‘Akitakomachi’ showed 19 increases and 6 decreases (p < 0.05). In roots, 12 metabolites increased in ‘Fusaotome’ and 9 in ‘Akitakomachi’; no significant decreases were detected. Pathway analysis indicated activation in ‘Fusaotome’ panicles of tryptophan, nicotinate/nicotinamide, arginine/proline, glycolysis/TCA, pyruvate, and vitamin B6 pathways, while ‘Akitakomachi’ emphasized phenylpropanoid, isoquinoline alkaloid, caffeine, and ubiquinone/terpenoid–quinone biosynthesis. In roots, ‘Fusaotome’ prioritized phenylalanine/phenylpropanoid, aromatic amino acids, lysine degradation, branched-chain amino acids, glycerophospholipids, and alkaloids, whereas ‘Akitakomachi’ favored nitrogen- and antioxidant-related routes. Collectively, the tolerant cultivar maintained antioxidant capacity and energy supply while coordinating root–panicle metabolism, whereas the susceptible cultivar shifted toward secondary defenses. These signatures nominate candidate metabolic markers and targets for breeding and management to stabilize rice production under warming climates.

IntroductionMicroorganisms exist and survive in complex and variable environments. Bacteria communities response and adapt to the changing conditions. The Mechanisms underlying bacterial survival can be elucidated through the use of multi-omics techniques.MethodsIn this study, we test an approach for measuring how different temperatures (4°C, 25°C, and 37°C) affected bacterial physiological functions. Proteomic and metabolomic analyses were conducted on Vibrio parahaemolyticus LF1113 under different temperatures.Results and discussionA total of 2,899 proteins and 396 metabolites were identified. The differentially expressed proteins (DEPs) and differentially metabolites (DMs) were involved in Lysine degradation, metabolic pathways, ABC transporters, and microbial metabolism in diverse environments pathways. An integrated metabolomics/proteomics analysis approach was employed in this study. The analysis of both types of data information (proteins and metabolites) aids to reveal the microbial adaptive regulation in response to temperature stimuli. The study can further help clinical research of V. parahaemolyticus from the perspective of metabolomics and proteomics.

Simple SummaryHeat stress (HS) severely jeopardizes thermoregulation in dairy cows, significantly reducing productivity. The present study revealed 29 differentially expressed proteins and 338 differential metabolites by using TMT-based proteomes and an untargeted metabolomics approach in the heat-stressed (n = 6) and heat-resistant (n = 6) groups, respectively. Combined analysis revealed four key pathways underlying protein–metabolite interactions, where up-regulated PLOD1 and ACTN4 and down-regulated EXT1 and GSN interacting with the down-regulated N6-Acetyl-L-lysine, citric acid, 4-Pyridoxic acid, uracil, and uric acid and the up-regulated arachidonic acid were enriched. Interference of the ACTN4 gene could induce dairy cow mammary epithelial cells apoptosis, which could be regarded as a potential biomarker for HS in Chinese Holstein. These findings provide new insights into the molecular mechanisms underlying HS in Chinese Holstein.Heat stress (HS) severely significantly reduces milk yield and causes substantial economic losses of dairy cows. TMT-based proteomes and an untargeted metabolomics approach were used to conduct the proteomics and metabolomics in heat-stressed (HS, n = 6) and heat-resistant (HR, n = 6) Chinese Holstein. The proteomics showed that 29 differentially expressed proteins (DEPs), with SERPINA3-7, ACTN4, and PLOD1 up-regulated, and GSN down-regulated in HR cows. The metabolomics showed that 168 differential positive metabolites and 170 differential negative metabolites were identified, with HR cows exhibiting lower levels of anti-inflammatory compounds, such as N6-Acetyl-L-lysine. In addition, 29 DEPs and 338 metabolites revealed four key pathways, including the lysine degradation (ko00310) and metabolic pathway (ko01100) with underlying protein–metabolite interactions, where up-regulated PLOD1 and ACTN4 and down-regulated EXT1 and GSN were observed to be interacting with the down-regulated N6-Acetyl-L-lysine, citric acid, 4-Pyridoxic acid, uracil, and uric acid, and the up-regulated arachidonic acid was enriched, which could be used for rapid and noninvasive screening of heat-tolerant cows. Functional validation through cell experiments, qPCR, and Western blot analyses showed that the interference of the ACTN4 gene could induce dairy cow mammary epithelial cell apoptosis, which could be regarded as a potential biomarker for HS in Chinese Holstein. Our results facilitate a better understanding of the molecular mechanism underlying the HS issue in dairy cows and provide a crucial insight into the alternative strategies to enhance animal welfare and productivity under high-temperature conditions.

BackgroundThe PLOD gene family, involved in extracellular matrix (ECM) remodeling, plays a role in tumor progression, but its comprehensive role and clinical significance in clear cell renal cell carcinoma (ccRCC) remains unclear.MethodsWe integrated multi-omics bioinformatics analyses from public databases (TCGA, GEO) with experimental validation using RT-qPCR, western blotting, and functional assays to systematically evaluate the expression patterns, prognostic value, immune microenvironment associations and drug resistance of PLOD genes in ccRCC. Computational approaches, including the comparative toxicogenomics database and molecular docking, were further employed to identify potential chemical modulators.ResultsPLOD1, PLOD2, and PLOD3 were consistently overexpressed at both mRNA and protein levels in ccRCC tissues and cell lines. High PLOD expression was significantly correlated with reduced overall survival, and poor disease-free survival. Functional enrichment analysis revealed the involvement of PLOD gene family in collagen biosynthesis, ECM-receptor interaction, and lysine degradation pathways. PLOD expression was also linked to an immunosuppressive microenvironment and resistance to conventional therapeutics. Through toxicogenomics screening and molecular docking, acetaminophen was identified as a potential regulator of all three PLOD proteins.ConclusionsThis study underscores the pivotal role of the PLOD family in ccRCC pathogenesis through ECM remodeling, immune modulation, and therapy resistance. Our results support their utility as diagnostic and prognostic biomarkers, and acetaminophen may serve as a candidate for targeting PLOD-mediated pathways, providing a foundation for future preclinical and therapeutic investigations.

Chickpea (Cicer arietinum L.), a vital cool-season pulse crop, experiences significant yield losses when exposed to heat stress during its reproductive stages, a vulnerability exacerbated by weather extremes. Chickpea plants synthesize numerous metabolites when subjected to heat stress; however, the underlying metabolomic mechanisms of heat tolerance remain poorly understood. In this study, we employed widely targeted metabolomics to identify key metabolites and potential biomarkers in the flower buds of two contrasting chickpea genotypes: the heat-tolerant PI518255 and the heat-sensitive PI598080. The tolerant genotype showed improved chlorophyll index, photochemical efficiency, antioxidant activity, along with low electrolyte leakage and malondialdehyde content. In contrast, the sensitive genotype exhibited low chlorophyll index, photochemical efficiency and low antioxidant activity, and high electrolyte leakage and malondialdehyde content, under heat stress conditions (35/20 °C day/night). Volcano plot analysis identified 86 up-regulated and 230 down-regulated metabolites in response to heat stress. Heatmap analysis revealed that elevated levels of specific flavonoids, phenolic acids, lignans, coumarins, alkaloids, quinones, and terpenoids characterized the heat-tolerant genotype, suggesting their potential as biomarkers for screening heat stress tolerance. KEGG enrichment and pathway analysis highlighted isoflavonoid biosynthesis, flavonoid metabolism, lysine degradation, and butanoate metabolism as key pathways affected by heat stress. Future targeted metabolomics studies may provide deeper insights into the biochemical mechanisms underlying chickpea acclimation to heat stress.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-21697-w.

Abstract Haemonchus contortus poses a significant threat to sustainable sheep production in the southern United States. The Florida Cracker, a heritage sheep breed, demonstrates remarkable resistance to parasites, yet the molecular mechanisms underlying this resistance remain poorly understood. The objective of this study was to assess the impact of H. contortus infection on the plasma metabolomic profile of Florida Cracker ewes during the peripartum period. A total of 20 pregnant Florida Cracker ewes were allocated into two groups: infected (INF, n=10) and control (CTL, n=10), at 90 days of pregnancy. Ewes were housed in pens with covered concrete floors of similar dimensions and characteristics, with ad libitum access to shelter, feed, and water. At 110 days of pregnancy, animals were dewormed with a combination of Cydectin (0.2 mg/kg) and Prohibit (8 mg/kg). A fecal egg reduction test confirmed the absence of parasite eggs prior to infection. At 120 days of pregnancy, the INF group was orally infected with 10,000 L3 larvae of H. contortus, while the CTL group received 3 mL of distilled water. Fecal egg counts (FECs) were measured at 0 and 3 hours, and at 2, 7, 14, and 28 days post-infection (dpi). Blood samples were collected by jugular venipuncture at the same time points, and plasma was extracted for targeted metabolomic analysis. Nuclear Magnetic Resonance (NMR) spectroscopy was employed to analyze 50 metabolites, including organic acids, amino acids, hexoses, lipids, and carnitines. The Shapiro-Wilk test assessed normality of the FEC data, and Box-Cox and logarithmic transformations (log(x+1)) were applied to the FEC values. The highest FEC (p < 0.05) was observed at 28 dpi in the INF group (3.11 ± 0.65), compared to the control group (0 ± 0). Significant differentially abundant metabolites were detected at 3hpi (1 downregulated metabolite), and at 7 (3 upregulated metabolites), 14 (16 downregulated and 6 upregulated metabolites), and 28dpi (14 upregulated metabolites). Key metabolic pathways identified included the metabolism of glycerolipids (3hpi), galactose (3hpi), purine (7dpi), pyrimidine (7dpi), propanoate (7dpi), biotin (7 and 14dpi), nitrogen (7dpi), glutathione (14dpi), primary bile acid biosynthesis (14dpi), pantothenate and CoA biosynthesis (14dpi), porphyrin (14dpi), lysine degradation (14dpi), lipoic acid (14 and 28dpi), beta-alanine (14 and 28dpi), glyoxylate and dicarboxylate (28dpi), and arginine and proline (28dpi). These pathways may be crucial in the ewe’s response to H. contortus infection during the peripartum period. Our findings indicate that H. contortus infection significantly alters the metabolomic profile of Florida Cracker ewes. Understanding these metabolic changes could help in the development of management strategies to mitigate gastrointestinal parasitism in sheep.

Andrographis paniculata (Burm. F.) Nees (AP) is a phytomedicinal plant traditionally used for colds, infections, and diabetes in Southeast Asia. The bioactive diterpenoids such as andrographolide, 14-deoxyandrographolide, and neoandrographolide has anti-inflammatory, antimicrobial, and glucose-lowering effects. Although widely used, clinical studies integrating AP's drug composition with its pharmacometabolomics responses remain limited. This study integrated pharmacokinetics (PK) and pharmacometabolomics (PMx) to understand dose-response relationships and pharmacological effects of orally administered AP capsules (1000mg and 2000mg) to 12 healthy volunteers under fasting conditions. Three biomarkers were measured from five AP brands to determine the highest-concentration AP capsule for dosing. PK analysis used 75 plasma samples while PMx analysis involved 96 plasma and urine samples. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used for both analyses. Statistical analysis included multivariate analyses (PCA, PLS-DA), followed by peaks-to-pathway analysis via MetaboAnalyst 5.0. Time to reach maximum plasma concentration (Tmax) for andrographolide, 14-deoxyandrographolide, and neoandrographolide was 1.5h, with maximum plasma concentration (Cmax) of 10.15ngmL-1, 7.02ngmL-1 and 58.45ngmL-1, respectively. At 1000mg, AP enhanced steroid hormone biosynthesis, while 2000mg induced broader metabolic shifts, enriching pathways such as biosynthesis of unsaturated fatty acids, alanine/aspartate/glutamate metabolism, and lysine degradation. No free bioactive compounds were detected in urine, indicating metabolism into conjugated forms. Clinical PK guided PMx revealed metabolic responses supporting AP's potential as a therapeutic agent for inflammation and glucose lowering effect. Further clinical research could optimize dosing and advance AP as a precision medicine candidate.

Lysine potentiates insulin secretion via AASS-dependent catabolism and regulation of GABA content and signaling.

Therapeutic AASS inhibition by AAV-miRNA rescues glutaric aciduria type I severe phenotype in mice.

As a major source of high-quality protein in China, duck meat such as the renowned Beijing Duck plays a critical role in the poultry industry. Sansui duck, a prized native breed, is valued for its tender meat and rich flavor, yet molecular mechanisms underlying its meat quality remain poorly studied. This study employed metabolomics and proteomics techniques to conduct a comprehensive comparative analysis of the breast and thigh muscles from 90-day-old (90X, 90T) and 468-day-old (468X, 468T) Sansui ducks. The meat quality traits indicated that the shear force and redness (a*) were significantly higher in the 468T and 468X groups compared to the 90X and 90T groups (p < 0.05). Similarly, the shear force values of the 90T and 468T groups were significantly higher than those of the 90X and 468X groups (p < 0.05). Quantitative proteomics analysis revealed differentially expressed proteins (DEPs) significantly enriched in oxidative phosphorylation and ribosomal biogenesis pathways. Non-targeted metabolomics identified differentially expressed metabolites (DEMs) concentrated in amino acid and lipid metabolism pathways. Correlation analysis indicated that in the comparison between 90X and 468X, 18 DEPs and 10 DEMs were closely associated with fleshiness, whereas in the comparison between 468X and 468T, 23 DEPs and 19 DEMs were closely associated with fleshiness. Integrating proteomics and metabolomics data analysis, proteins such as A0A8B9TTI1, R0JRM6, and A0A8B9SQI5, along with metabolites including L-lysine, L-pyrrolidone, and γ-aminobutyric acid from lysine degradation, butanoate metabolism, and 2-oxocarboxylic acid metabolism pathways, can be proposed as key factors influencing meat quality through pathways including lysine degradation, butanoate metabolism, and 2-oxocarboxylic acid metabolism in older ducks. In contrast, the protein R0JXJ3 and metabolites choline and L-glutamine may determine meat quality differences between anatomical sites through the ABC transporter pathway. These findings provide molecular insights and potential biomarkers for genetic breeding and meat quality improvement in Sansui ducks.

IntroductionAlthough existing studies have shown that radiofrequency electromagnetic fields (RF-EMFs) have a variety of effects on living organisms, the specific impact of RF-EMFs on the metabolism of reproductive cells and their underlying mechanisms remain unclear.This study aims to explore the effects of RF-EMFs on the metabolism of mouse Leydig cells (TM3) and spermatogonia cells (GC-1) through metabolomics analysis, revealing the potential mechanisms by which RF-EMFs affect reproductive health.MethodsWe employed liquid chromatography-mass spectrometry (LC-MS) to analyze the metabolomic profiles of TM3 and GC-1 cells under two irradiation modalities: continuous and intermittent RF-EMF exposure. The data were further analyzed using KEGG pathway analysis to identify significantly enriched metabolic pathways. The ELISA (Enzyme-Linked Immunosorbent Assay) was used to detect glutathione levels.ResultsOur results showed that continuous irradiation had a more pronounced impact on the metabolism of TM3 cells, primarily affecting amino acid metabolism, the citric acid cycle, ABC transporters, bile secretion, and glutathione metabolism. In contrast, intermittent irradiation mainly altered the levels of fatty acyls and purine nucleosides, with significant enrichment in purine metabolism, biosynthesis of unsaturated fatty acids, and fatty acid metabolism. Compared to TM3 cells, GC-1 cells exhibited lower sensitivity to RF-EMF irradiation. Both irradiation modalities affected purine metabolism and lysine degradation pathways in TM3 cells, suggesting that changes in ADP levels may serve as a key metabolic signature in the cellular response to RF-EMF exposure.ConclusionContinuous irradiation significantly impacts TM3 cell metabolism, particularly amino acid and glutathione pathways, while intermittent irradiation mainly affects fatty acyls and purine metabolism. GC-1 cells show lower sensitivity to RF-EMF. ADP level changes may be a key metabolic signature of RF-EMF exposure.

BACKGROUNDMetabolomics sequencing technology was used to investigate the changes of intestinal flora and metabolites in gastric cancer patients in plateau areas.AIMTo investigate changes in gut microbiota and their metabolites in patients with gastric cancer from plateau regions using untargeted metabolomic sequencing.METHODSFresh morning fecal samples were collected from 30 gastric cancer patients diagnosed at a tertiary hospital in Qinghai Province and 30 healthy individuals (controls). Liquid chromatography-tandem mass spectrometry based untargeted metabolomic sequencing was used to analyze metabolite changes and predict metabolic function.RESULTSMetabolomic analysis identified 281 metabolites in samples from both groups. These metabolites were categorized into eight major classes, listed in descending order of abundance: Lipids and lipid-like molecules (35.443%); organic acids and derivatives (29.114%); organic oxygen compounds (15.19%); nucleosides, nucleotides, and analogs (13.924%); organoheterocyclic compounds (2.532%), amino acids and peptides (1.266%); benzenoids (1.266%); and fatty acids (1.266%). Compared with the control group, the top 10 metabolites elevated in the gastric cancer group included: Dethiobiotin, glycylproline, glycine, hydroxyisocaproic acid, tyramine, methionine sulfoxide, 5-aminopentanoic acid, citrulline, betonicine, and formiminoglutamic acid and the top 10 decreased were: Cytidine, 5'-methylthioadenosine, trehalose, melibiose, lotaustralin, adenosine, inosine, ribothymidine, raffinose, and galactinol. Functional prediction analysis revealed that these differential metabolites were primarily enriched in 12 metabolic pathways, including purine metabolism, cysteine and methionine metabolism, galactose metabolism, lysine degradation, glycine, serine, and threonine metabolism, biotin metabolism, pyrimidine metabolism, arginine and proline metabolism, histidine metabolism, primary bile acid biosynthesis, starch and sucrose metabolism, and tyrosine metabolism.CONCLUSIONSignificant differences in intestinal microbial metabolites and associated metabolic pathways were observed between gastric cancer patients and healthy controls residing in plateau regions.

The extensive use of the herbicide quinclorac has led to significant residues in agricultural soil, posing adverse effects on crop safety and high-quality production. In this study, using the tobacco variety CB-1 as material, we found that oxidizing agent K2S2O8 can significantly reduce quinclorac-induced phytotoxicity symptoms in tobacco. Furthermore, we integrated biochemical methods, metagenomics, metabolomics, and transcriptomics to investigate the effects of K2S2O8 on both quinclorac-contaminated soil and tobacco plants. Soil physicochemical properties analysis showed that the incorporation of K2S2O8-based remediation significantly mitigated the negative effects of quinclorac and largely restored the soil properties affected by quinclorac stress. Metagenomic analysis found that quinclorac significantly reduced soil species diversity, while K2S2O8-based remediation soil exhibited higher richness of microbial communities, with increased abundance of Sphingomonas and Bradyrhizobium, and decreased abundance of Alphaproteobacteria. Differential gene expression analysis showed significant up-regulation and down-regulation of genes under C10H5Cl2NO2 stress, which was partially mitigated by K2S2O8 treatment. Gene Ontology (GO) enrichment analysis indicated that these genes were mainly involved in cellular processes, metabolic pathways, and biological regulation. Metabolomic analysis further confirmed significant changes in metabolite profiles, with K2S2O8 treatment restoring many metabolites to near control levels. Integrated metabolomic-transcriptomic analysis revealed enrichment of differentially expressed genes (DEGs) and metabolites in six key pathways: (1) lysine degradation, (2) stilbenoid diarylheptanoid and gingerol biosynthesis, (3) arginine and proline metabolism, (4) phenylalanine biosynthesis, (5) tyrosine metabolism, and (6) flavonoid biosynthesis. Additionally, the levels of 4-hydroxyphenylacetylglutamic and 5-aminovaleric acid were down-regulated, along with the expression of genes associated with these metabolites, when quinclorac residual soil was treated by K₂SO8. The results of this study provide a theoretical basis for the remediation of pesticide residue soil in rice tobacco rotation areas, offering valuable insights for sustainable agricultural practices.

BackgroundLiver injury (LI) is responsible for a significant number of fatalities each year. In the context of Mongolian medicine, Rhododendron molle (Blume) G. Don (RM) is utilized for its properties to treatment of hepatic disorders. However, the underlying mechanisms of its action remain poorly understood.ObjectivesClarifying the process through which RM enhances LI.MethodsThe chemical constituents were subjected to analysis, and network pharmacology alongside molecular docking studies were conducted. Additionally, ELISA, staining techniques, metabolomic analyses, and 16S rDNA sequencing were performed.ResultsA total of 17 components have been identified from RM, including liver disease-related compounds such as kaempferol, emodin, quercetin. Network pharmacology has identified notable genes that exhibit a strong binding affinity to active compounds, including emodin, which interacts with IL6 and PPARG, and aloeemodin, which binds to IL6 and AKT1. In a rat model of LI induced by CCL4, low dose (0.07875 g/kg) of RM demonstrated a reduction in ALT and γ-GT levels (p < 0.05). Metabolomic analysis indicated that RM has an impact on the concentrations of 13-OxoODE, morphine, and niacinamide in rat models exhibiting LI, simultaneously several metabolic pathways, including steroid biosynthesis, linoleic acid metabolism, and tryptophan metabolism. By integrating the findings from metabolomics with KEGG pathways, it was determined that RM may ameliorate LI by activating specific pathways and modulating fatty acid metabolic processes, particularly linoleic acid and arachidonic acid metabolism. Furthermore, low-dose RM (RML) was found to enhance beneficial gut microbiota such as Lactobacillus, suggesting its potential role in the regulation of intestinal homeostasis and barrier integrity.ConclusionRML has the potential to enhance the composition of intestinal microbiota by through the differential regulation of various metabolized components, including 13-OxoODE, morphine, and niacinamide, it influences several metabolic pathways, notably steroid biosynthesis, lysine degradation, interconversions of pentose and glucuronate, as well as the metabolism of linoleic acid. Additionally, it may promote the proliferation of HT002 and Lactobacillus probiotics, thereby contributing to the amelioration of LI. It establishes a robust foundation for future applications and the development of associated pharmaceuticals.

Riboswitches are 5' untranslated regulators that control gene expression by specifically monitoring cellular metabolites. Metabolite binding to the riboswitch triggers the genetic regulation at the transcriptional or translational level. Riboswitches typically exhibit high affinities and strong discrimination against non-cognate metabolites, making them well suited to regulate gene expression. Importantly, despite the well characterized cellular processes ensuring metabolic conversion and recycling in bacteria, there is little information about how these processes influence riboswitch regulation mechanisms. Here, we characterize the regulation mechanisms of the lysine-sensing and thiamin pyrophosphate (TPP)-sensing riboswitches in E. coli. In agreement with previous results, our study indicates that the addition of lysine or TPP to the growth medium significantly reduces the expression of the respective riboswitch-regulated mRNAs. Surprisingly, we find that the addition of lysine also leads to a significant decrease in TPP-regulated mRNAs, suggesting that lysine indirectly affects TPP riboswitches. Using mutant strains from the Keio collection, we observe that the effect of lysine on TPP riboswitches is lost when perturbing the lysine degradation process. These data suggest that lysine degradation products may be used to generate TPP through metabolic conversion. In contrast, our results indicate that TPP does not modulate the regulation of the lysine riboswitch, suggesting that TPP does not indirectly affect the lysine riboswitch genetic control. Together, our results indicate that intracellular changes in lysine concentrations can be detected by TPP riboswitches, thus suggesting that riboswitches may be sensitive to cellular stress that are not directly related to their cognate metabolite.

BackgroundAntimony (Sb), with low biodegradability and high bioavailability in plants, poses significant health risks via the food chain due to its chronic toxicity and carcinogenicity. Modified biochar represents a promising amendment for ecological remediation of metal-contaminated croplands, yet the efficacy and mechanisms of its application in mitigating Sb accumulation and improving plant growth in Sb-polluted agricultural systems remain inadequately elucidated and require systematic investigation.ResultsIn this study, pristine biochar (BC) and iron-modified biochar (FeBC) were prepared from pomelo peel flesh (PPF; Citrus maxima), and their effects on rice root growth, Sb content, and metabolism under 30 mg/L Sb stress were evaluated. Treatment with 5 g/L BC and 5 g/L FeBC increased root length by 35.04% and 84.60%, respectively, while reducing Sb accumulation in roots by 25.79% and 28.03%, respectively. Root metabolite analysis showed that, compared to BC, FeBC significantly decreased levels of p-coumaroylagmatine, silibinin, and osmanthuside A by 75%, 37%, and 37%, respectively. Conversely, FeBC elevated levels of (S)-actinidine, phaeophorbide A, and 2-keto-6-acetamidocaproate by 187%, 156%, and 122%, respectively. These altered metabolites were enriched in five key metabolic pathways: phenylalanine, tyrosine, and tryptophan biosynthesis; phenylalanine biosynthesis; lysine degradation; tryptophan metabolism; and pantothenate and CoA biosynthesis. Correlation analysis demonstrated significant interrelationships among biochar-induced metabolites, root growth, and Sb accumulation dynamics under Sb stress.ConclusionsThe findings provided the insights that FeBC enhanced rice root metabolism and growth while reducing root Sb accumulation. This study provided a methodological foundation for developing eco-friendly remediation technologies in Sb-contaminated soils to enable safer and more sustainable rice production.Graphical abstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07071-y.

Abstract Irritable bowel syndrome (IBS) is a prevalent stress‐associated disorder characterised by gut barrier dysfunction and gut‐brain axis disturbances. However, the interplay between host metabolites and gut microbes in IBS pathogenesis remains incompletely understood. Here, through integrated microbiome and metabolome profiling of faecal sample from seafarers before and after long‐term voyages, we identify a reciprocal interaction between the essential amino acid l‐lysine and the gut bacterium Holdemanella biformis (H. biformis). l‐lysine was depleted in individuals with voyage‐induced IBS, whereas H. biformis abundance increased concurrently. In a mouse model of diarrhoea‐predominant IBS, l‐lysine supplementation restored intestinal barrier integrity, reduced visceral hypersensitivity, and alleviated anxiety‐like behaviours through modulation of tryptophan metabolism. In contrast, oral administration of H. biformis improved tight junction protein expression but paradoxically worsened anxiety‐like phenotypes. In vitro, both l‐lysine and H. biformis supernatant promoted epithelial wound healing and ZO‐1 expression. Mechanistically, H. biformis degrades l‐lysine via lysine degradation pathway, while l‐lysine suppresses H. biformis growth possibly by downregulating pathways involved in carbohydrate and energy metabolism. These findings reveal a stress‐sensitive, bidirectional metabolic loop in between l‐lysine and H. biformis, with complementary but opposing effects on gut and neurological function. Targeting this axis may offer new strategies for IBS and other gut‐brain axis disorders.

The spoilage characteristics and key metabolites of Lactobacillus brevis and Lactobacillus plantarum in ready-to-eat chicken feet.