Search Results (3,056)

Antibiotic-resistant bacteria are widely distributed and threaten public health. Photocatalytic antimicrobial technology can effectively inactivate multidrug-resistant bacteria without readily inducing resistance. We previously showed that oxygen-rich vacancy Bi₂MoO₆ (OBM) exhibits excellent activity against methicillin-resistant Staphylococcus aureus (MRSA), but the underlying molecular mechanisms remain poorly understood. Here, we employed integrated transcriptomics and metabolomics, with qRT-PCR validation, to systematically elucidate the antibacterial mechanism of OBM against MRSA. OBM treatment induced profound transcriptional and metabolic alterations: 231 differentially expressed genes and 206 differentially abundant metabolites were identified. Functional enrichment analysis revealed cooperative involvement in multiple critical pathways, including inhibition of amino acid biosynthesis and protein translation, disruption of cell wall and membrane integrity, induction of oxidative stress, collapse of energy metabolism (suppression of oxidative phosphorylation and impaired ATP synthesis), and imbalance in nucleotide metabolism (down-regulation of DNA helicase and mismatch repair genes, dysregulation of purine/pyrimidine metabolism). These findings demonstrate that OBM photocatalytically inactivates MRSA through a multi-target systemic attack at both the transcriptional and metabolic levels, providing a novel theoretical foundation for the development of photocatalytic materials aimed at controlling MRSA and other drug-resistant bacteria. Full article

Flavonoids are essential secondary metabolites that predominantly affect flower pigmentation in plants. Understanding the molecular mechanisms underlying flower color divergence is crucial for ornamental plant breeding. This study aimed to elucidate the factors responsible for the differences in color between white-petaled Cosmos bipinnatus and orange-petaled Cosmos sulphureus. We employed an integrated approach combining untargeted LC–MS/MS metabolomics and high-throughput transcriptome sequencing of fresh petals to analyze pigment composition and differential gene expression. Petal pigment extraction, total flavonoid quantification, and metabolomic profiling consistently revealed that differences in flavonoid abundance are responsible for flower color divergence between the two species. In contrast, carotenoids, previously considered potential contributors to flower coloration, were neither evident in the oil phase of the pigment extracts nor detected by metabolomic analysis. Flavonoid compounds accumulated at relatively high levels in the orange petals of C. sulphureus, reaching 11.36 times that of C. bipinnatus, contributing to its bright appearance. Transcriptomic analysis revealed differences in gene expression patterns between the two species, highlighting key candidate genes involved in the flavonoid biosynthesis pathway, such as chalcone synthase. These findings indicate that the orange coloration of C. sulphureus may be associated with CHS-regulated accumulation of naringenin chalcone and downstream compounds in the flavonoid metabolic pathway after CHS, providing valuable theoretical support for a deeper understanding of the causes underlying the differences in flower color between C. bipinnatus and the orange-petaled C. sulphureus. Full article

Background: Human breast milk (HBM), as the initial food for humans, is quite essential for infant development and also for health throughout the lifespan. Exosomes are bioactive components in HBM, yet their nutritional role remains poorly recognized. Objectives: This study investigates how HBM exosomes change with lactation and their potential role in infant growth and development. Methods: HBM samples were obtained at 2 and 6 months postpartum from a well-established birth cohort. Purified exosomes were detected using transcriptomic, lipidomic, and proteomic approaches. Then, multi-omics data were analyzed to compare differentially expressed miRNAs, lipids, and proteins along with different lactation periods and their association with the infant growth process. Results: Compared with the 2-month postpartum group, the expression levels of miR-214-3p, miR-199a-5p, miR-126-3p, miR-127-5p, miR-144-3p, and miR-4787-5p were down-regulated in the 6-month postpartum group. In addition, 190 lipids and 269 proteins were up-regulated in the 6-month postpartum group, whereas 15 lipids and 244 proteins were down-regulated. Enrichment analysis revealed that the predicted target genes of differentially expressed miRNAs were primarily involved in cell communication and axon guidance. In parallel, the differentially expressed proteins were enriched in biosynthesis of unsaturated fatty acids and fatty acid metabolism pathway, implying a potential role in adipogenesis and neurodevelopment. Conclusions: This study reveals that the cargo contents of HBM exosomes change with the lactation period and may adapt to the needs of infant growth and development, particularly adipogenesis and neurodevelopment. HBM exosomes may play an important role in transferring genetic information from mothers to infants and be related to infants’ development. The underlying mechanisms warrant further investigation and validation. Full article

Global warming exacerbates high-temperature stress, disturbing the growth, metabolic homeostasis and quality formation of tea plants (Camellia sinensis L.). Trehalose, a multifunctional osmolyte, can enhance abiotic stress tolerance, but its systematic metabolic mechanism against heat damage in tea remains unclear. Here, we applied integrated gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS) non-targeted metabolomics to compare control (CK), heat-stressed (T), and trehalose-treated heat-stressed (TT) tea leaves. We identified 163 differential volatile metabolites in GC-MS and 1619 differential non-volatile metabolites in LC-MS. Metabolite classification showed that organic oxygen compounds dominated differential volatile metabolites, while lipids and lipid-like molecules dominated differential non-volatile metabolites. The Kyoto Encyclopedia of Genes and Genomes enrichment showed that alanine, aspartate and glutamate metabolism, arginine biosynthesis, aminoacyl-tRNA biosynthesis, and flavone and flavonol biosynthesis were core shared pathways. Quantitatively, exogenous trehalose under heat stress significantly increased carbohydrate accumulation, restored lipid homeostasis, and elevated alanine, arginine, and related intermediates, thereby maintaining carbon–nitrogen balance. Trehalose also remodeled the amino acid substrate pool for aminoacyl-tRNA biosynthesis. In flavonoid metabolism, trehalose enhanced high-antioxidant flavonoid aglycones while reducing most glycosides and inhibiting excessive hydroxylation of flavonols. Although total flavonoid content decreased in TT relative to T, this reflected alleviated oxidative damage and reduced dependence on flavonoid-based defense. Combined with total amino acid and flavonoid quantifications, we conclude that exogenous trehalose enhances tea plant thermotolerance by coordinately regulating primary amino acid metabolism and secondary flavonoid metabolism. These findings provide a theoretical basis for using trehalose in heat-resistance cultivation and quality improvement of tea plants. Full article

Strigolactones (SLs), as a class of novel plant hormones, play important roles in the regulation of plant branching. However, their function in branch development of wintersweet remains unclear. In this study, a gene involved in SLs biosynthesis, CpD27, was identified and isolated from wintersweet. The sequence characteristics, expression patterns, subcellular localization, and functional analysis through heterologous expression in Arabidopsis thaliana were investigated. Multiple sequence alignment showed that CpD27 contains the conserved D27 protein domain DUF4033. Quantitative real-time PCR analysis revealed that CpD27 is expressed in various vegetative organs of wintersweet, with the highest expression in leaves, followed by axillary buds. It is also expressed in all floral organs, with the highest expression level in the outer petals. CpD27 expression is induced by hormones (ABA and ACC) and low temperature (4 °C). Subcellular localization analysis indicated that CpD27 is localized in the chloroplasts of Arabidopsis. Heterologous expression of CpD27 in Arabidopsis delayed bolting. The number of both rosette branches and cauline branches in transgenic plants was reduced compared with wild-type plants. In addition, the expression of AtBRC1 was significantly upregulated in transgenic lines, suggesting that CpD27 has a function similar to that of its homolog in Arabidopsis. Overall, these results indicate that CpD27 plays a conserved role in the SLs-mediated branching pathway, which regulates branch development in wintersweet. This study provides a molecular and theoretical basis for further understanding branch development in wintersweet. Full article

Nervonic acid (NA, C24:1 Δ15) is a vital extra-long-chain monounsaturated fatty acid essential for neural development, myelin sheath formation, and neurological health. As the most abundant natural source of NA, Malania oleifera Chun & S.K.Lee has become a key model for studying NA biosynthesis and regulation. This review systematically summarizes the metabolic pathways of nervonic acid biosynthesis in M. oleifera, including plastidial de novo fatty acid synthesis, endoplasmic reticulum (ER)-based very-long-chain fatty acid elongation, and Δ15 desaturation. We focus on the catalytic mechanisms and rate-limiting roles of the elongase complex (KCS, KCR, HCD, ECR) and Δ15 desaturase. Additionally, we integrate recent multi-omics data to analyze key enzyme KCS gene families, their phylogenetic relationships, and syntenic distribution patterns. Furthermore, transcriptional regulatory networks (MYB, bZIP, WRI1, ABI3, FUS3) and epigenetic regulation underlying NA accumulation are also discussed. Finally, we highlight advances, challenges, and prospects in metabolic engineering and synthetic biology for sustainable NA production. This review provides a theoretical basis for the conservation, molecular breeding, and biotechnological utilization of M. oleifera. Full article

Granulosa cells (GCs), an element of the ovarian follicle, are crucial for oocyte maturation, folliculogenesis, and steroidogenesis. Granulosa cells play a crucial role in fertilization by providing metabolic and hormonal support to the oocyte, maintaining its quality and regulating its meiotic arrest. Oocyte quality and fertilization efficiency depend on the proper activity of GCs, especially their mutual communication, providing metabolic support and protecting against oxidative stress. When interrupted, they may take part in the pathogenesis of polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, and diminished ovarian reserve. GCs are enclosed in the antrum where they communicate with surrounding cells, create a dynamic microenvironment, and regulate hormone biosynthesis. To analyze molecular mechanisms regulating endogenous signaling, it is important to consider the dynamic transcriptomic response of porcine GCs during in vitro culturing over 48, 96, and 144 h. Transcriptomic analysis revealed a variable and dynamic transcriptional upregulation of genes associated with cellular response to endogenous and external stimuli, chemical compound metabolism, vascular development, and GCs migration. Also, proven by Gene Ontology (GO) enrichment analysis, the following terms were highlighted: “cellular response to chemical stimulus” and “cellular response to organic substance”. Specific genes, such as HSD3B1, POSTN, LOX, SERPINB2, ITGB3, ANKRD1, SLC1A1, and SFRP2, exhibited significant expression changes, suggesting extensive GCs self-regulation and metabolism changes. Further analysis indicates improvements in cellular response to a cytokine stimulus, growth factor response, hormone response, enzyme-linked receptor protein signaling, and positive regulation of cell migration. These findings suggest interweaving of regulatory mechanisms underlying intercellular communication in GCs during in vitro culturing, despite the lack of signals from the native ovarian environment. Further investigating interplays of detecting pathways will provide a more comprehensive understanding and even insights into the potential clinical use of the knowledge about the role of GCs in folliculogenesis, oocyte maturation and ovulation. Full article

Anthocyanin-rich dark pigmentation is increasingly recognized as more than a simple consequence of flavonoid accumulation. Here, we define the anthocyanin-driven dark phenotype (ADP) as a coordinated stress-responsive state characterized by intense anthocyanin accumulation coupled with cellular and regulatory reprogramming. Recent studies show that reactive oxygen species, sugar signaling, temperature stress, and hormonal crosstalk converge on MYB–bHLH–WD40-centered regulatory networks that integrate pigment biosynthesis with vacuolar organization, transport activity, and stress adaptation. Epigenetic remodeling, chromatin dynamics, and post-transcriptional regulation further influence pigment intensity and persistence. Importantly, ADPs do not represent an alternative biosynthetic pathway or merely pigment abundance, but instead reflect a systems-level regulatory state governed by coordinated transcriptional, hormonal, and epigenetic control of the canonical anthocyanin machinery. However, several important questions remain unresolved, including how plants retain phenotypic stability under various environmental and developmental settings, whether ADPs contribute to long-term stress memory, and how anthocyanin accumulation is balanced with growth and energy expenditures. To translate ADP-associated features into crop development techniques, these gaps must be filled. We also emphasize spatial omics and CRISPR-based engineering as new methods for analyzing and modifying stress-resilient phenotypes. Full article

Seasonal changes in leaf coloration are a key ecological and ornamental characteristic of Liquidambar formosana. To clarify the molecular basis of this process, we performed an integrated transcriptomic and metabolomic investigation comparing wild-type L. formosana (FX) with the autumn-red cultivar ‘Jinyu’ (JY). Leaves were sampled before and after the color transition. Analyses revealed distinct metabolic pathways driving coloration in each genotype. In JY, the red phenotype was primarily attributed to the activation of anthocyanin biosynthesis, characterized by coordinated upregulation of key structural genes (LfDFR, LfANS, LfBZ1) and significant accumulation of anthocyanins, especially pelargonidin derivatives. Conversely, FX exhibited enhanced flavonol biosynthesis and carotenoid/terpenoid metabolism, leading to greater yellow pigment accumulation and an orange-yellow hue. Weighted gene co-expression network analysis (WGCNA) identified a core module strongly correlated with anthocyanin content in JY, which was significantly enriched with transcription factors from the MYB, bHLH, and WRKY families. These results demonstrate that different L. formosana genotypes employ divergent metabolic strategies for autumn coloration, governed by specific transcriptional regulatory networks. This study provides crucial insights into pigment regulation in woody plants and offers valuable candidate genes for the molecular breeding of ornamental L. formosana cultivars. Full article

Pseudomonas aeruginosa (P. aeruginosa) is a multidrug-resistant opportunistic pathogen that causes both acute and chronic infections and is known for its ability to form biofilms. In the current study, we applied a hypothesis-generating framework primarily based on integrating four different datasets and applying batch correction. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed in parallel with differential expression analysis using limma. Therefore, we aimed to identify potential biofilm-associated gene candidates. Significant candidate genes were subjected to functional analysis and gene ontology, followed by the construction of a protein–protein interaction network using STRING. The Pseudomonas Genome Database was used to highlight the candidate genes. A total of 271, 687, 533, and 277 significantly up-regulated differentially expressed genes (DEGs), as well as 306, 985, 472, and 312 significantly down-regulated DEGs, resulted from the exploratory analysis. Through WGCNA/limma integration, 223 common significantly up-regulated/positively correlated gene candidates were identified. Functional analysis results showed significant enrichment in virulence-related pathways, such as biofilm formation (PA0083, PA0084, hcp1, hcpC, pilH, pilI, pilJ, vfr, pqsA, pqsB, pqsC, pqsE, PA1657, and PA1658). In addition, other virulence-related pathways, such as quorum sensing, phenazine biosynthesis, the bacterial secretion system, and secondary metabolite biosynthesis, were enriched. In conclusion, our hypothesis-generating integrative analysis identifies candidate genes and potential pathways associated with biofilm formation, virulence, and other processes in P. aeruginosa. In light of this, we point out that all candidate genes presented in this study remain hypothesis-generating. Further validation is recommended, including large-scale in silico analyses and in vitro experimental studies. Full article

While Peribacillus simplex has been reported to alleviate abiotic stress-induced damage in diverse plant species, its precise functional mechanism in mediating salt tolerance in asparagus remains unclear. The present study sought to uncover the molecular regulatory mechanisms through which strain P10 enhances the salt adaptability of asparagus seedlings. We investigated physiological responses, as well as transcriptomic and metabolomic alterations, in P10-inoculated asparagus seedlings grown under saline conditions. The results demonstrated that P10 inoculation alleviated salt-induced physiological damage by enhancing antioxidant enzyme activities and promoting the accumulation of osmotic regulatory substances. Comparative transcriptomic and metabolomic analyses identified 1659 differentially expressed genes (DEGs) and 128 differentially accumulated metabolites (DAMs) between P10-inoculated and non-inoculated seedlings under salt stress. These DEGs were primarily associated with multiple biological pathways, including phenylpropanoid biosynthesis, nitrogen metabolism, and flavonoid biosynthesis pathways (flavone, flavonol, and total flavonoid synthesis). Metabolomic profiling indicated that organic acids constituted the most abundant class of DAMs, followed by amino acids and their derivatives, and flavonoids. Integrated transcriptomic and metabolomic analyses suggested that P10 optimized the amino acid metabolic network under salt stress by upregulating genes involved in nitrogen assimilation, glutathione biosynthesis, and polyamine biosynthesis, thereby promoting amino acid accumulation and enhancing glutathione and polyamine levels. In addition, P10 markedly stimulated flavone and flavonol biosynthesis while maintaining elevated anthocyanin levels. Overall, P10 mitigated salt stress injury in asparagus by regulating amino acid metabolism to improve osmotic balance and growth stability, while simultaneously redirecting phenylpropanoid flux toward flavone and flavonol biosynthetic pathways to fine-tune stress responses. Full article

The molecular mechanisms of mycelial degeneration during subculturing of Auricularia heimuer strain ‘HWS1908’ were investigated across generations G1 to G20. With successive subculturing, mycelial growth rate and compactness declined, cellulase and laccase activities decreased significantly, whereas antioxidant enzyme activities increased. Comparative transcriptome analysis between G1 and G20 identified 2643 differentially expressed genes (DEGs). Gene Ontology (GO) analysis indicated that the DEGs were significantly enriched in terms associated with protein refolding, response to reactive oxygen species, and ferroxidase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed significant enrichment of DEGs in pathways including phenylpropanoid biosynthesis, peroxisome, fatty acid degradation, and longevity-regulating pathways. Key DEGs, including transcription factors, glycoside hydrolases, lignin-modifying enzymes, chitin synthases, chitinases, ornithine decarboxylase, and Ras/Rho signaling pathway components (Sos, Ras, Rac1), were identified. These genes may be associated with the progressive decline of mycelial vigor, cell wall integrity, and substrate utilization capacity. These findings provide a basis for further exploration of the molecular mechanisms of strain degeneration in A. heimuer, and a practical recommendation to limit subcultures to within 20 generations for maintaining high vitality. Full article

Background: Natto, a well-known fermented soybean product beneficial for bone health, remains unclear in its mechanism. Methods: This study investigated its effect on secondary osteoporosis (OP) in mice. Results: Natto significantly inhibited weight loss, bone quality deterioration, and bone morphological damage, and regulated OPG/RANKL pathway protein expression (p < 0.05) in OP mice. Analysis of 16S rRNA revealed that natto increased gut microbiota α-diversity and the abundance of Sutterella, Roseburia, and Coprococcus, while reducing harmful bacteria such as Streptococcus, Shigella, and Helicobacter. These microbial changes positively correlated with body weight, bone size, and serum osteogenic metabolism in OP mice. Serum metabolomics showed differential metabolites of the natto group enriched in PPAR signaling and primary bile acid biosynthesis. Verification by mRNA and ELISA indicated that the upregulated liver and circulating PPARα by natto may regulate downstream bile acid pathways, linking gut microbiota to multi-organ metabolic functions. Conclusions: In summary, natto may act on gut microbiota to alleviate bone loss via the “gut microbiota–bile acid–OPG/RANKL” network, targeting multiple organs including gut, liver, and bone. This provides a theoretical basis for natto dietary intervention in osteoporosis prevention through the gut–bone axis. Full article

Salt stress is a major abiotic stress that threatens citrus yield and quality. To elucidate the molecular mechanisms underlying differential salt tolerance in citrus rootstocks, we performed an integrative transcriptomic and metabolomic analysis of salt-sensitive trifoliate orange (Poncirus trifoliata) and salt-tolerant Goutoucheng (Citrus aurantium) under 60 mM NaCl treatment for 12 h and 24 h. Physiological observations confirmed that Goutoucheng exhibited less growth inhibition and leaf damage than trifoliate orange. Transcriptome sequencing identified 2081 and 1588 differentially expressed genes (DEGs) in trifoliate orange at 12 h and 24 h, respectively, compared with 1166 and 997 DEGs in Goutoucheng. Metabolome profiling revealed 217 and 173 differentially accumulated metabolites (DAMs) in trifoliate orange versus 162 and 239 DAMs in Goutoucheng at the two time points. KEGG pathway analysis showed that DEGs were mainly enriched in the Mitogen-activated protein kinase (MAPK) signaling pathway—plant, plant hormone signal transduction, and flavonoid biosynthesis—and DAMs were mainly enriched in flavonoid biosynthesis, starch and sucrose metabolism, and glutathione metabolism. Integrative nine-quadrant and two-way orthogonal partial least squares analyses further pinpointed flavonoid biosynthesis as a central hub in salt response. Notably, quercetin derivatives accumulated preferentially in the salt-tolerant rootstock Goutoucheng. Several transcription factor families—including HSF, MYB, NAC, HB-HD-ZIP, C2H2, bHLH, AP2/ERF, and Trihelix—may enhance antioxidant capacity under salt stress by regulating flavonoid accumulation. Collectively, these results indicated that coordinated regulation of flavonoids contributed critically to salt stress adaptation in citrus rootstocks. The identified DEGs, DAMs, and transcription factors provide candidate targets for genetic improvement of salt tolerance in citrus. Full article

This meta-analysis combined the results of 61 independent studies published in 2005–2025 to examine polyamine-mediated responses to aluminum, cadmium, lead, chromium, copper, manganese, and selenium stress in plants. The logarithm ratio of responses (lnRR) under the random-effects model was used to calculate the effect sizes. Polyamine application significantly (p < 0.001) enhanced plant growth, with strong increases in root elongation (lnRR = 0.490, 95% CI: 0.362–0.618), fresh weight (lnRR = 0.413, 95% CI: 0.347–0.480), and dry weight (lnRR = 0.475, 95% CI: 0.409–0.541). Oxidative stress was markedly reduced, as reflected by decreases in reactive oxygen species accumulation (lnRR = −0.585, 95% CI −0.682 to −0.487, p < 0.001), hydrogen peroxide content (lnRR = 0.005, 95% CI −0.244 to 0.254, p = 0.968), and lipid peroxidation (lnRR = −0.487, 95% CI −0.578 to −0.397, p < 0.001). The antioxidant defenses were strengthened, and the levels of superoxide dismutase (lnRR = 0.468, p < 0.001) and catalase activity (lnRR = 0.373, p < 0.001) increased significantly. Metal accumulation was consistently reduced in polyamine-treated plants (lnRR = −0.392, 95% CI −0.460 to −0.324, p < 0.001). Supplementary genetic-level data indicated that metal stress triggers polyamines to regulate metal transporters, polyamine biosynthesis genes, antioxidant-related genes, and hormone-signaling pathways. Collectively, these data points make polyamines a key controller of plant metal stress tolerance and offer a quantitative and mechanistic system to apply them to metal-impacted agroecosystems. Full article