Search Results (13,820)

Coptis trifolia (threeleaf goldthread) offers a valuable comparative system for investigating the evolution and regulation of benzylisoquinoline alkaloid (BIA) synthesis. In this study, we analyzed the leaf and root transcriptomes of C. trifolia using both long-read and short-read RNA-Sequencing. We assembled 41,926 unigenes (≥500 bp) and identified 37 genes related to BIA biosynthesis, including two transcription factors, bHLH1 and WRKY1. The number of BIA genes identified in C. trifolia was comparable to that in other Coptis species. Transcriptome analysis revealed that most of these genes were more highly expressed in roots than leaves. Consistent with previous studies, C. trifolia contained a single (S)-stylopine synthase (SPS) gene homolog, potentially multifunctional for (S)-canadine synthase (CAS), (S)-cheilanthifoline synthase (CFS), and SPS. Transcriptome and untargeted metabolomic data indicated greater variation in root samples than leaf samples, although slightly more differentially expressed transcripts and metabolites were observed in leaves. Targeted metabolite profiling showed higher BIA accumulation in roots, with epiberberine being the most abundant, followed by coptisine, berberine, and columbamine. These results provide essential genomic resources for comparative analysis of the BIA pathway across Ranunculaceae, targeted gene function studies for metabolic bioengineering, and conservation strategies for C. trifolia, a member of an early-diverging clade within the genus with limited genetic resources. Full article

Background: Maple syrup urine disease (MSUD) is a genetic disorder caused by mutations in the branched-chain α-ketoacid dehydrogenase (BCKDH) complex, leading to toxic buildup of branched-chain amino acids (BCAAs) and their ketoacid derivatives. While newborn screening (NBS) and molecular testing are standard diagnostic tools, they face challenges such as delayed results and false positives. Untargeted metabolomics has emerged as a complementary approach, offering comprehensive metabolic profiling and potential for novel biomarker discovery. We previously applied untargeted metabolomics to neonates with MSUD, identifying distinct metabolic signatures. Objective: This follow-up study investigates metabolic changes and biomarkers in pediatric MSUD patients and explores shared dysregulated metabolites between neonatal and pediatric MSUD. Methods: Dried blood spot (DBS) samples from pediatric MSUD patients (n = 14) and matched healthy controls (n = 14) were analyzed using LC/MS-based untargeted metabolomics. Results: In pediatric MSUD, 3716 metabolites were upregulated and 4038 downregulated relative to controls. Among 1080 dysregulated endogenous metabolites, notable biomarkers included uric acid, hypoxanthine, and bilirubin diglucuronide. Affected pathways included sphingolipid, glycerophospholipid, purine, pyrimidine, nicotinate, and nicotinamide metabolism, and steroid hormone biosynthesis. Seventy-two metabolites overlapped with neonatal MSUD cases, some exhibiting inverse trends between age groups. Conclusion: Untargeted metabolomics reveals that the metabolic profiling of MCUD pediatric patients different from that of their controls. Also, there are valuable age-specific and shared metabolic alterations in MSUD, enhancing the understanding of disease progression in MSUD patients. This supports its utility in improving diagnostic precision and developing personalized treatment strategies across developmental stages. Full article

Dihydroorotase (DHOase) catalyzes the reversible cyclization of N-carbamoyl-L-aspartate to dihydroorotate, a key step in de novo pyrimidine biosynthesis. A flexible active site loop in DHOase undergoes conformational switching between loop-in and loop-out states, influencing substrate binding, catalysis, and inhibitor recognition. In this study, we identified 5-fluoroorotate (5-FOA) and myricetin as inhibitors of Saccharomyces cerevisiae DHOase and systematically analyzed 97 crystal structures and AlphaFold 3.0 models of DHOases from 16 species representing types I, II, and III. Our results demonstrate that loop conformation is not universally ligand-dependent and varies markedly across DHOase types, with type II enzymes showing the greatest flexibility. Notably, S. cerevisiae DHOase consistently adopted the loop-in state, even with non-substrate ligands, restricting accessibility for docking-based inhibitor screening. Docking experiments with 5-FOA and myricetin confirmed that the loop-in conformation prevented productive active-site docking. These findings highlight the importance of selecting appropriate loop conformations for structure-based drug design and underscore the need to account for loop dynamics in inhibitor screening. Full article

The review is focused on dictyopterenes A, B, C, and D found in marine algae, covering their (a) distribution; (b) methods of isolation and identification; (c) absolute configuration; and (d) biosynthesis considerations. Dictyopterenes A and B are usually present in high amounts in Dictyopteris spp. Dictyopterene A was found to be abundant in D. prolifera, D. undulata, D. latiscula, D. polypodioides, and D. membranacea. Dictyopterene B (hormosirene) was found as the major compound in D. plagiogramma, D. australis, Hormosira banksii, D. potatorum, D. willana, D. antarctica, Xiphophora chondrophylla, X. gladiata, Scytosiphon lomentaria, Colpomenia peregrina, and Haplospora globosa. Dictyopterene C (dictyotene) was a major compound in D. undulata, D. prolifera, D. membranacea, Gomphonema parvulum, Amphora veneta, Phaeodactylum tricornutum, and D. vermicularis. Dictyopterene D (ectocarpene) was present in Ectocarpus siliculosus, Analipus japonicus, D. prolifera, D. undulata, and Sargassum linifolium. The following enantiomers were found: (1S,2R)-dictyopterene A, (1R,2R)-dictyopterene B, (1S,2S)-dictyopterene B, (1S,2R)-dictyopterene B, (R)-dictyopterene C, and (S)-dictyopterene D. In marine algae, C₁₁-hydrocarbons are derived from C₂₀ polyunsaturated fatty acids by the oxidative cleavage via, e.g., 9-hydroperoxyicosa-(5Z,7E,11Z,14Z,17Z)-pentaenoic acid. An alternative biosynthetic pathway for dictyopterene A and B via the proposed intermediates (S)-dictyoprolenols was considered by oxidative cleavage of hydroperoxyicosatetraenoic acid. Full article

Pubertal molting represents a pivotal transition in the life cycle of crustaceans, marking the shift from somatic growth to reproductive development. In mud crabs, mating is known to facilitate this process, yet the molecular mechanisms remain poorly understood. Here, we applied full-length transcriptome sequencing to characterize changes in gene expression and alternative splicing (AS) across post-mating ovarian development. AS analysis revealed extensive transcript diversity, predominantly alternative first exon (AF) and alternative 5′ splice site (A5) events, enriched in genes linked to chromatin remodeling, protein regulation, and metabolism, underscoring AS as a fine-tuning mechanism in ovarian development. Comparative analyses revealed profound molecular reprogramming after mating. In the UM vs. M1 comparison, pathways related to serotonin and catecholamine signaling were enriched, suggesting early neuroendocrine regulation. Serotonin likely promoted, while dopamine inhibited, oocyte maturation, indicating a potential “inhibition–activation” switch. In the UM vs. M3 comparison, pathways associated with oxidative phosphorylation, ATP biosynthesis, and lipid metabolism were upregulated, reflecting heightened energy demands during vitellogenesis. ECM-receptor interaction, HIF-1, and IL-17 signaling pathways further pointed to structural remodeling and tissue regulation. Enhanced antioxidant defenses, including upregulation of SOD2, CAT, GPX4, and GSTO1, highlighted the importance of redox homeostasis. Together, these findings provide the first comprehensive view of transcriptional and splicing dynamics underlying post-mating ovarian maturation in Scylla paramamosain, offering novel insights into the molecular basis of crustacean reproduction. Full article

Pre-harvest sprouting (PHS) reduces the quality and quantity of crop seeds. PHS can be imposed through the embryo or husk pathway of cereal crops. Most reported PHS seeds are imposed via the embryo pathway. Here, we generated transgenic rice plants overexpressing rice melatonin 2-hydroxylase (OsM2H), which catalyzes the hydroxylation of melatonin to 2-hydroxymelatonin (2-OHM). OsM2H overexpression (M2H-OE) showed PHS under paddy conditions. Germination assays revealed that intact seeds harvested at 26 and 36 days after heading (DAH) showed PHS, whereas dehusked seeds did not, indicating husk-imposed PHS. Overproduction of 2-OHM was observed in M2H-OE seeds compared to wild-type control. In addition, M2H-OE lines produced more hydrogen peroxide than the wild-type. 2-OHM-induced reactive oxygen species resulted in the induction of OsGA3ox2, a gibberellin (GA) biosynthesis gene, and repression of OsGA2ox3, a GA degradation gene, in caryopses at 2 DAH, but in the induction of the ABA degradation gene OsABA8ox3 in intact seeds at 26 DAH. In addition, M2H-OE seedlings were longer and showed increased levels of hydrogen peroxide and OsGA3ox2 expression versus the wild-type. This is the first report showing that 2-OHM can induce PHS via the husk pathway in rice seeds through the induction of GA biosynthetic and ABA degradation genes. Full article

Schisandra chinensis (Turcz.) Baill. (S. chinensis) is a widely used medicinal plant whose therapeutic efficacy is closely linked to its lignan content. While previous studies have focused on soil fertility and cultivar variation, the interplay among soil nutrients, rhizosphere microbiota, and lignan accumulation remains poorly understood. This study investigated S. chinensis grown across 20 cultivation sites to elucidate the relationships among soil nutrient profiles, fruit lignan composition, and rhizosphere microbial communities. Six major lignans were quantified using HPLC, soil nutrients were analyzed via standard chemical assays, and rhizosphere bacterial communities were profiled using 16S rRNA sequencing. Multivariate analyses revealed significant variation in soil properties and lignan content across sites. Notably, available phosphorus, organic matter, and total nitrogen showed strong correlations with specific lignan compounds. From the top 50 taxa ranked by relative abundance at the genus level, 18 bacterial genera associated with lignan components were identified. Among them, Mycobacterium, Arthrobacter, Haliangium, Bacillus, Sphingomonas, Rhodanobacter, Ellin6067, Bradyrhizobium, Pseudolabrys, Chujaibacter, Gemmatimonas, Bryobacter, MND1, Candidatus Sollbacter, Gaiella, Paenibacillus, RB41, and Candidatus_Udaeobacter were significantly associated with lignan levels, suggesting potential microbial involvement in lignan biosynthesis. These findings provide insights into the ecological factors shaping the medicinal quality of S. chinensis and offer a foundation for targeted cultivation and breeding strategies. Full article

ASYMMETRIC LEAVES1 (AS1) and AS2 play essential roles in regulating leaf development in plants. However, their functional roles in soybean remain poorly understood. Here, we identified two members of the soybean AS1 gene family, GmAS1a and GmAS1c, which exhibit high expression levels in stem and leaf tissues. Using the CRISPR/Cas9 system, we targeted four GmAS1 and three GmAS2 genes, generating mutant lines with distinct leaf development phenotypes, including wrinkling (refers to fine lines and creases on the leaf surface, like aged skin texture), curling (describes the inward or outward rolling of leaf edges, deviating from the typical flat shape), and narrow. We found that functional redundancy exists among the four GmAS1 genes in soybean. GmAS1 and GmAS2 cooperatively regulate leaf curling, leaf crinkling phenotypes, and leaf width in soybean, with functional redundancy also observed between these two genes. Transcriptome sequencing analysis of w3 mutant (as1b as1c as1d as2a as2b as2c) identified 1801 differentially expressed genes (DEGs), including 192 transcription factors (TFs). Gene ontology enrichment analysis revealed significant enrichment of DEGs in pathways associated with plant hormone biosynthesis and signal transduction. A detailed examination of the DEGs showed several genes involved in the development of leaf lateral organs, such as KNOX (SHOOT MERISTEMLESS (STM), KNAT1, KNAT2, and KNAT6), LOB (LBD25, LBD30), and ARP5, were down-regulated in w3/WT (wild-type) comparison. CRISPR/Cas9-mediated targeted mutagenesis of the GmAS1/2 genes significantly impairs leaf development and polarity establishment in soybean, providing valuable germplasm resources and a theoretical framework for future studies on leaf morphogenesis. Full article

Light-dependent protochlorophyllide oxidoreductase (LPOR, E.C.1.3.1.33) plays a crucial role in the biosynthesis of chlorophyll in plants. Therefore, inactivating LPOR can hinder the production of chlorophyll to achieve the effect of weed control. In this research, utilizing an active substructure splicing method, 20 new 1,2,4-oxadiazole compounds targeting LPOR were synthesized. Among them, compounds 5j, 5k and 5q exhibited superior inhibitory efficacy in greenhouse herbicidal trials. In vitro enzyme activity assays indicated that 5q significantly inhibited Arabidopsis thaliana LPOR (AtLPOR), with an IC₅₀ value of 17.63 μM. Furthermore, compound 5q exhibited superior crop safety and holds potential application prospects for weed management in cotton. Molecular docking and dynamic simulations were employed to elucidate the binding mode and molecular mechanism of 5q with AtLPOR. These experimental and theoretical results indicate that 5q is a promising candidate for the development of novel herbicides targeting LPOR. Full article

The MADS-box transcription factors play essential roles in various processes of plant growth and development. Here, we identified 107 MADS-box genes in Osmanthus fragrans Lour. genome (OfMADS), encoding proteins ranging from 61 to 608 amino acids. Phylogenetic analysis classified these genes into five subfamilies: MIKC*, MIKCC, Mα, Mβ, and Mγ, with conserved motif architectures within subfamilies. Tandem and whole-genome duplications were identified as key drivers of OfMADS expansion. Cis-regulatory element analysis revealed enrichment for hormone response and developmental regulatory motifs, implicating roles in growth and flowering processes. Transcriptome dynamics across six floral developmental stages (bolting to petal shedding) uncovered 78 differentially expressed OfMADS genes, including 16 exhibiting flower-specific expressions. Integrated metabolome profiling demonstrated robust correlations between critical OfMADS regulators and scent metabolites. This nexus suggests a potential role of these OfMADS in regulating specialized metabolite biosynthesis pathways. Our multi-omics study provides insights into the regulatory hierarchy of OfMADS in coordinating floral morphogenesis and the accumulation of economically significant metabolites in O. fragrans. These findings establish a foundation for subsequent functional validation and molecular breeding of horticultural traits. Full article

Brassinosteroids (BRs) are essential regulators of plant development and stress responses, but the distinct contributions of BR biosynthesis and signaling to hormonal crosstalk remain poorly defined. Here, we investigated the effects of the BR biosynthesis inhibitor brassinazole (BRZ) and the BR-insensitive mutant bri1-6 on endogenous phytohormone profiles in Arabidopsis thaliana. Using multivariate analysis and targeted hormone quantification, we show that BRZ treatment and BRI1 disruption alter hormone balance through partially overlapping but mechanistically distinct pathways. Principal component analysis (PCA) and hierarchical clustering revealed that BRZ and the bri1-6 mutation do not phenocopy each other and that BRZ still alters hormone profiles even in the bri1-6 mutant, suggesting potential BRI1-independent effects. Both BRZ treatment and the bri1-6 mutation tend to influence cytokinins and auxin conjugates divergently. On the contrary, their effects on stress-related hormones converge: BRZ decreases salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in the WT leaves; similarly, bri1-6 mutants show reduced SA, JA, and ABA. These results indicate that BR biosynthesis and BRI1-mediated perception may contribute independently to hormonal reprogramming, with BRZ eliciting additional effects, possibly via metabolic feedback, compensatory signaling, or off-target action. Hormone correlation analyses revealed conserved co-regulation clusters that reflect underlying regulatory modules. Altogether, our findings provide evidence for a partial uncoupling of BR levels and BR signaling and illustrate how BR pathways intersect with broader hormone networks to coordinate growth and stress responses. Full article

Aroma volatiles constitute the primary molecular basis of fruit flavor quality, governing sensory attributes and marketability. Based on their chemical states, aroma compounds are categorized into bound and free forms. Bound aroma compounds predominantly exist as non-volatile glycosides, which can be hydrolyzed enzymatically or through acid treatment to release volatile free aroma compounds, thereby enhancing fruit fragrance. Although the dynamic interconversion between free and bound aroma compounds is pivotal for fruit flavor development, the governing mechanisms, including the principal controlling factors, regulatory networks, and external influences, are still under investigation. This review primarily synthesizes recent advances regarding the structural diversity, analysis, biosynthesis, and regulation of bound aroma compounds. Additionally, it examines how key regulatory networks and environmental factors modulate the synthesis and transformation of these compounds. The integrated overview provides new insights for future regulation of aroma metabolism in fruits. Full article

Soil compaction is a major constraint on global agriculture productivity. It disrupts soil structure, reduces soil porosity and fertility, and increases mechanical impedance, thereby restricting root growth and crop yield. Recent studies on rice (Oryza sativa) reveal that the phytohormone ethylene serves as a primary signal and functions as a hub in orchestrating root response to soil compaction. Mechanical impedance promotes ethylene biosynthesis and compacted soil impedes ethylene diffusion, resulting in ethylene accumulation in root tissues and triggering a complex hormonal crosstalk network to orchestrate root system architectural modification to facilitate plant adaptation to compacted soil. This review summarizes the recent advances on rice root adaptation response to compacted soil and emphasizes the regulatory network triggered by ethylene, which will improve our understanding of the role of ethylene in root growth and development and provide a pathway for breeders to optimize crop performance under specific agronomic conditions. Full article

The Nile tilapia (Oreochromis niloticus), a key aquaculture species, displays marked sexual growth dimorphism, with males growing faster than females. This process is governed by intricate interactions between antagonistic regulators, including transcription factors, growth factors, and steroid hormones, operating through sex-specific developmental pathways. While circular RNAs (circRNAs) are known to modulate gene expression by sponging microRNAs (miRNAs), their role in teleost sex differentiation remains poorly understood. To address this gap, we profiled circRNA expression in tilapia gonads by constructing six circRNA libraries from testes and ovaries of 180 days after hatching (dah) fish, followed by high-throughput sequencing. We identified 6564 gonadal circRNAs distributed across all 22 linkage groups, including 226 differentially expressed circRNAs (DECs; 108 testis-biased, 118 ovary-biased). Functional enrichment analysis linked their host genes to critical pathways such as cAMP signaling, cell adhesion molecules, and—notably—sexual differentiation processes (e.g., estrogen signaling, oocyte meiosis, and steroid hormone biosynthesis). Furthermore, we deciphered competing endogenous RNA (ceRNA) networks, uncovering circRNA–miRNA–mRNA interactions targeting germ cell determinants, sex-specific transcription factors, and steroidogenic enzymes. This study provides the first systematic exploration of circRNA involvement in tilapia sex differentiation and gonadal differentiation, offering novel insights into the post-transcriptional regulation of sexual dimorphism. Our findings advance the understanding of circRNA biology in fish and establish a framework for future studies on aquaculture species with similar reproductive strategies. Full article

Cold stress significantly impairs plant growth and development, making the study of cold resistance mechanisms a critical research focus. Oreorchis patens (Lindl.) exhibits strong cold hardiness, yet its molecular and physiological adaptations to cold stress remain unclear. This study utilized microscopy, physiological assays, and RNA sequencing to comprehensively investigate O. patens’s responses to cold stress. The results reveal that cold stress altered leaf anatomy, leading to irregular mesophyll cells, deformed chloroplasts, and variable epidermal thickness. Physiologically, SOD and POD activities peaked at 5 °C/−10 °C, while CAT activity declined; osmotic regulators (soluble sugars, proline) increased with decreasing temperatures. Compared to the reference plants (e.g., Erigeron canadensis, Allium fistulosum), O. patens exhibited lower SOD and POD but markedly higher CAT activities, alongside reduced MDA, soluble sugars, proline, and proteins, underscoring its distinctive tolerance strategy. Low temperature stress (≤10 °C/5 °C) significantly decreased the SPAD index; the net photosynthetic rate (Pn) initially increased and then approached zero within the temperature range from 30 °C/25 °C to 25 °C/20 °C; transpiration rate (Tr) and stomatal conductance (Gs) changed synchronously, accompanied by an increase in intercellular CO₂ concentration (Ci). RNA sequencing identified 1139 cold-responsive differentially expressed genes, which were primarily enriched in flavonoid/lignin biosynthesis, jasmonic acid synthesis, and ROS scavenging pathways. qRT-PCR analysis revealed the role of secondary metabolites in O. patens response to cold stress. This study was the first to discuss the physiological, biochemical, and molecular regulatory mechanisms of O. patens resistance to cold stress, which provides foundational insights into its overwintering mechanisms and informs breeding strategies for cold-hardy horticultural crops in northern China. Full article