Jiushi Liu

Schisandra chinensis (Turcz.) Baill. (S. chinensis) is a traditional Chinese medicinal plant whose fruits are rich in bioactive constituents, including lignans, organic acids, and flavonoids. Nevertheless, the biochemical dynamics underlying fruit development remain insufficiently characterized, limiting the effective cultivation, harvest, and utilization of S. chinensis. Here, we applied widely targeted metabolomics, together with a dynamic assessment of fruit growth, to profile temporal changes in major metabolites and to identify the optimal harvest window. The results show that the morphological changes in fruit mainly occurred from 70 to 110 days after fruit set; fresh fruit mass peaked at 110 days after fruit set. During the harvest period, the fruits are deep red and firm, showing no signs of softening. Meanwhile, fruit cluster weight, single fruit weight, and fruit longitudinal diameter all reached their peak values. Over the course of maturation, lignan levels declined markedly, whereas terpenoids, organic acids and flavonoids increased significantly. The most pronounced shifts were observed for schizandrin, gomisin N, shikimic acid, citric acid, gamma-terpinene and cyanidin 3-sophoroside, key marker compounds of S. chinensis fruit. Network pharmacology predicts that ESR1, RXRA, GATM, NCOA2, and SONEA are core targets. These findings provide a basis for determining timely harvest and for establishing quality evaluation criteria for S. chinensis.

Schisandraceae, an early-diverging angiosperm lineage, produces dibenzocyclooctadiene (DBCOD) lignans, unique bioactive compounds with liver-protecting properties. Although DBCOD lignan chemodiversity is well documented, their biosynthesis and evolution remain unclear. Here, we present a high-quality Schisandra chinensis genome, completing genomic representation of early angiosperms. Phylogenetic analysis confirms Austrobaileyales as sister to monocots, magnoliids, and eudicots, clarifying their evolutionary position. We identified an Austrobaileyales-specific whole-genome duplication postdiversification from Amborellales and Nymphaeales. Integrating coexpression networks and biochemical assays, we delineated five key steps in DBCOD lignan biosynthesis, including dimerization, hydroxylation, methylation, and C─C phenol coupling. Notably, we found SchCYP719G1b, a previously unidentified enzyme catalyzing C─C linkage to form the signature DBCOD scaffold. Substrate selectivity assays and quantum mechanical/molecular mechanics calculations suggested that the para -hydroxyl diradical electronic properties preferentially drive selective C2─C2′ coupling over alternative pathways. Our findings illuminate early angiosperm evolution and the molecular basis of specialized lignan diversity.

Astragalus membranaceus var. mongholicus (AMM) is a widely used medicinal plant in China, primarily cultivated in the northern regions; however, the selection and breeding of superior varieties remains underdeveloped. To scientifically assess the germplasm resources of AMM and facilitate its breeding, this study collected 33 germplasm samples from five provinces and conducted a comprehensive evaluation of their botanical traits, agronomic traits, quality traits, and powdery mildew resistance. The results indicated that, among the 18 botanical and agronomic traits, the Shannon–Wiener diversity index (H′) for quantitative traits was higher than that for qualitative traits, with the coefficient of variation ranging from 6.82% to 34.14%. The characterization of five flavonoids and eight saponins based on the established UPLC-Q-TOF/MS technique revealed that 13 compounds showed significant abundance variations across germplasms. Correlation analysis revealed that plants with robust above-ground growth usually have higher yields. Moreover, the number of compound leaflets was positively correlated with flavonoid content in the roots, whereas germplasms with smaller above-ground biomass and thinner roots exhibited higher saponin content. Based on the comprehensive scores (F-value), the top three germplasms were An-31, An-26, and An-28, which may serve as promising breeding materials. Cluster analysis grouped the 33 germplasms into five categories, including high-content and high-yield groups. Five germplasms exhibiting strong disease resistance were identified, with An-26 demonstrating the best performance in yield, quality, and resistance. Furthermore, a negative correlation was observed between powdery mildew resistance and flavonoid content in roots. This study will provide a foundation for the AMM breeding and selection.

Astragali Radix (AR), a traditional food and medicinal herb used for thousands of years, is widely recognized for its role in enhancing immunity, particularly when combined with adjuvant chemotherapy. The two primary types of AR available in the market are imitation wild AR (grown for seven years) and cultivated AR (grown for two years). However, whether differences exist in their immune-enhancing effects and chemical constituents remains unclear. In this study, a comparative analysis was performed to evaluate the immune activity and chemical composition of cultivated and imitation wild AR. Immune activity was assessed through in vivo animal studies, while metabolomic analysis was used to characterize their chemical profiles. The results demonstrate that AR possesses significant antitumor and immune-enhancing activities, with imitation wild AR showing superior efficacy compared with cultivated AR. Following 16 days of daily AR treatment, both the thymus and spleen coefficients were significantly increased, effectively reversing the immune dysfunction induced by cyclophosphamide (CTX). Moreover, the administration of AR showed no significant toxicity, as evidenced by the stable liver and kidney function indicators, including ALT, UREA, and CRE levels. To investigate chemical differences, a customized chemotaxonomic-based in-house library containing 215 compounds was developed and integrated with the Progenesis QI informatics platform for metabolite annotation. Using multivariate analysis, 48 constituents were identified in total: 46 unique to the imitation wild AR and 45 specific to the cultivated AR. The correlation between chemical constituents and the pharmacological effects of AR was evaluated. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA) and S-plot analysis, five potential biomarkers were identified, including Calycosin-7-glucoside, Rhamnocitrin-3-O-β-D-glucopyranoside, Ononin, 3,5-Dicaffeoylquinic acid, and Acetylastragaloside I. These biomarkers likely account for the differences in immune-enhancing effects between the two AR types. This study provides a scientific foundation for the rational use of Astragali Radix.

The fruits of Schisandra chinensis (SCF) and Schisandra sphenanthera (SSF) are traditional Chinese herbal medicines classified as medicinal and food homologous materials, known for their significant neuroprotective efficacy. However, the differences in their therapeutic effects and active components for the treatment of vascular cognitive impairment (VCI) remain unclear. This study aimed to elucidate the neuroprotective activities of SCF and SSF on VCI and investigate the compositional disparities between the two. The lipopolysaccharide-induced and oxygen-glucose deprivation/reoxygenation (OGD/R)-induced BV2 cell models were used to evaluate the protective effects of SCF and SSF against neuroinflammation and mitochondrial damage, respectively. The therapeutic effects were further validated using a bilateral common carotid artery stenosis mouse model. Compositional differences were analyzed using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS), and drug-like properties of their constituents were assessed. In vitro experiments showed that SCF and SSF at concentrations of 6.4, 16, and 40 μg/mL reduced nitric oxide, tumor necrosis factor-alpha, and interleukin-6 levels in a dose-dependent manner. Notably, at the same concentrations, SCF significantly mitigated OGD/R-induced mitochondrial damage, whereas SSF showed no significant effect. Compared with SSF, SCF exhibited stronger anti-neuroinflammatory and antioxidant properties. In vivo experiments further demonstrated that SCF, administered at 400 mg/kg, was more effective in improving learning ability, spatial learning and memory, cerebral blood flow, and nerve fiber repair than SSF. Moreover, 71 and 64 compounds were identified in SCF and SSF, respectively, using UPLC-Q-TOF/MS. Drug-like property analysis of these compounds revealed that the superior therapeutic effects of SCF may be attributed to differences in biphenylcyclooctene-type lignans. Our data support the conclusion that SCF possesses significantly superior neuroprotective activity compared to SSF, providing a theoretical basis for its clinical application in VCI.

Berberine is an effective antimicrobial and antidiabetic alkaloid, primarily extracted from divergent botanical lineages, specifically Coptis (Ranunculales, early-diverging eudicot) and Phellodendron (Sapindales, core eudicot). In comparison with its known pathway in Coptis species, its biosynthesis in Phellodendron species remains elusive. Using chromosome-level genome assembly, coexpression matrix, and biochemical assays, we identified six key steps in berberine biosynthesis from Phellodendron amurense , including methylation, hydroxylation, and berberine bridge formation. Notably, we discovered a specific class of O -methyltransferases (NOMT) responsible for N -methylation. Structural analysis and mutagenesis of PaNOMT9 revealed its unique substrate-binding conformation. In addition, unlike the classical FAD-dependent berberine bridge formation in Ranunculales, Phellodendron uses a NAD(P)H-dependent monooxygenase (PaCYP71BG29) for berberine bridge formation, originating from the neofunctionalization of tryptamine 5-hydroxylase. Together, these findings reveal the convergence of berberine biosynthesis between Coptis and Phellodendron and signify the role of the convergent evolution in plant specialized metabolisms.

Phenylpropenes, such as isoeugenol and eugenol, are produced as defend compounds, floral attractants, and flavor constituents by phenylpropene synthases belonging to the PIP reductase family. Moreover, isoeugenol is proposed to be involved in the biosynthesis of dibenzocyclooctadiene lignans, the main active compounds of Schisandra chinensis (Turcz.) Baill. fruits (SCF). S. chinensis, a woody vine plant, is widely used for its medicinal, horticultural, edible, and economic values. In this study, nine ScPIP genes were identified and characterized from the transcriptome datasets of SCF. The expression profiles revealed that ScPIP genes were differentially expressed during different developmental stages of SCF. Three ScPIPs were selected and cloned as candidate genes encoding phenylpropene synthases according to phylogenetic analysis. ScPIP1 was proved to function as isoeugenol synthase (IGS) and designated as ScIGS1 through in vivo functional characterization in Escherichia coli. Subcellular localization analysis demonstrated that ScIGS1 was localized in both the cytoplasm and nucleus. The three-dimensional (3D) model of ScIGS1 was obtained using homology modeling. Site-directed mutagenesis experiments revealed that the substitution of residues at positions 110 and 113 impacted the product specificity of ScIGS1 and the mutation of Lys157 to Ala abolishing catalytic function. Moreover, the k_cat values of mutants were lower than that of ScIGS1 using a deep learning approach. In conclusion, this study provides a basis for further research on PIP reductases and the biosynthetic pathway of dibenzocyclooctadiene lignans.

Main conclusion The hierarchical architecture of chromatins affects the gene expression level of glandular secreting trichomes and the artemisinin biosynthetic pathway-related genes, consequently bringing on huge differences in the content of artemisinin and its derivatives of A. annua. Abstract The plant of traditional Chinese medicine "Qinghao" is called Artemisia annua L. in Chinese Pharmacopoeia. High content and the total amount of artemisinin is the main goal of A. annua breeding, nevertheless, the change of chromatin organization during the artemisinin synthesis process has not been discovered yet. This study intended to find the roles of chromatin structure in the production of artemisinin through bioinformatics and experimental validation. Chromosome conformation capture analysis was used to scrutinize the interactions among chromosomes and categorize various scales of chromatin during artemisinin synthesis in A. annua. To confirm the effect of the changes in chromatin structure, Hi-C and RNA-sequencing were performed on two different strains to find the correlation between chromatin structure and gene expression levels on artemisinin synthesis progress and regulation. Our results revealed that the frequency of intra-chromosomal interactions was higher in the inter-chromosomal interactions between the root and leaves on a high artemisinin production strain (HAP) compared to a low artemisinin production strain (LAP). We found that compartmental transition was connected with interactions among different chromatins. Interestingly, glandular secreting trichomes (GSTs) and the artemisinin biosynthetic pathway (ABP) related genes were enriched in the areas which have the compartmental transition, reflecting the regulation of artemisinin synthesis. Topologically associated domain boundaries were associated with various distributions of genes and expression levels. Genes associated with ABP and GST in the adjacent loop were highly expressed, suggesting that epigenetic regulation plays an important role during artemisinin synthesis and glandular secreting trichomes production process. Chromatin structure could show an important status in the mechanisms of artemisinin synthesis process in A. annua.