Search Results (775)

Background/Objectives: Environmental conditions in natural and cultivation-managed habitats strongly influence plant physiology and medicinal quality. However, the molecular mechanisms underlying metabolic differentiation in Anoectochilus roxburghii remain poorly understood. This study aimed to elucidate the metabolic and transcriptional differences between wild and cultivated A. roxburghii and to identify the regulatory mechanisms driving habitat-associated variation in metabolite profiles. Methods: We applied integrated non-targeted metabolomics and transcriptomics to compare metabolic profiles and gene expression in the leaves and stems of 15-month-old wild and cultivated A. roxburghii plants. Gene–metabolite correlation analysis was performed to identify coordinated correlation networks associated with key biosynthetic pathways. Results: Our analyses revealed clear differences in metabolite composition and transcriptional patterns between habitat types, suggesting distinct strategies of metabolic resource allocation. Wild plants showed significant enrichment of amino acids and other primary metabolites, whereas cultivated plants accumulated higher levels of flavonoids. Gene–metabolite correlation analysis indicated that multiple flavonoid metabolites were closely associated with key structural genes, including F3H, C12RT1, and HHT1, forming a tightly connected correlation network. In addition, several transcription factor families, including MYB, bHLH, WRKY, and AP2/ERF, showed strong correlations with genes involved in the flavonoid pathway, suggesting that flavonoid accumulation in cultivated plants may be associated with coordinated transcriptional control. Conclusions: Taken together, these findings suggest that habitat conditions are associated with differences in metabolic networks and resource allocation in A. roxburghii. This work provides new insight into the metabolic plasticity of this medicinal plant and highlights potential factors associated with molecular mechanisms that may contribute to variation in medicinal quality. Full article

The retina is a complex sensory neural tissue composed of six major types of neurons and one type of glial cell. The cell fate specification of retinal cells is tightly governed by intrinsic factors and extrinsic microenvironmental cues. Among the key regulators directing retinal cell fate differentiation is a group of bHLH family transcription factors (TFs). Our previous work demonstrated that the bHLH TF Ngn3 exhibits robust potential to induce retinogenesis in both distantly related fibroblasts in vitro and late retinal progenitor cells (RPCs) in vivo. However, the underlying molecular mechanisms remain largely elusive. In this study, we combined immunohistological examination and RNA-seq and ATAC-seq analyses to investigate the cellular and molecular mechanisms governing Ngn3-driven retinogenesis in late RPCs. Our results revealed that Ngn3 overexpression promotes premature cell cycle exit in late RPCs and remodels their transcriptomic and epigenomic landscape towards a state favoring rod photoreceptor and RGC differentiation. Furthermore, cross-comparison with Ngn3-overexpressing fibroblasts in vitro revealed cell-type-specific mechanisms underlying Ngn3-mediated neuronal fate reprogramming. These findings advance our understanding of Ngn family-mediated retinal cell fate regulation and provide a mechanistic framework for optimizing Ngn3-based retinal regeneration strategies for the treatment of retinal degeneration diseases. Full article

Fruit anthocyanins are primary determinants of color, sensory quality, and nutritional value in grapes; however, their endogenous biosynthesis is governed by complex interactions among genetic, environmental, agronomic, and postharvest factors. This review elaborates recent advances in physiology and molecular biology to clarify the biosynthetic mechanisms in grapes, including the coordinated action of structural enzymes, MYB–bHLH–WD40 regulatory complexes, hormone-mediated signaling pathways, and vacuolar transport processes. Key environmental factors, such as temperature fluctuations, light exposure, water availability, and soil properties, regulate these networks, contributing to significant variation in pigmentation profiles across cultivars and growing regions. Strategic agronomic practices, including canopy management, regulated deficit irrigation, balanced nutrient management, and temperature-mitigation techniques, further influence pigmentation by modifying the microclimate of the fruit zone during development. Based on these mechanistic insights, this review evaluates targeted strategies for enhancing anthocyanin accumulation, highlighting recent progress in genetic improvement through CRISPR/Cas genome editing, transgenic approaches, and marker-assisted selection (MAS), which enable precise modulation of biosynthetic and regulatory genes. Complementary postharvest interventions, such as optimized cold storage, modified-atmosphere packaging, hormonal elicitors, and controlled oxidative technologies, provide additional opportunities to maintain or enhance pigment stability after harvest. Collectively, these advances establish a comprehensive framework linking molecular regulation with practical vineyard, breeding, and postharvest strategies, offering an integrated pathway to improve anthocyanin consistency, berry quality, and the phenolic characteristics of grape-derived products. Full article

Background: Information on the autopolyploid of Gossypium herbaceum remains limited until now. Previously, the autotetraploid of G. herbaceum was successfully generated via colchicine-induced chromosome doubling from the diploid cultivar ‘Hongxing’ in our lab. Methods: To investigate the drought stress response mechanism of this tetraploid, the autotetraploid S4 was used as the experimental material. The plants were subjected to drought stress during the flowering stage, followed by measurements of physiological and biochemical indicators and transcriptomic sequencing analysis. Results: Under drought stress, MDA content increased, and cell membranes sustained oxidative damage. Photosynthetic parameters, such as net photosynthetic rate (Pn), were significantly suppressed, while the activity of osmotic regulators and key antioxidant enzymes increased significantly. After rehydration, all of the above physiological indicators showed varying degrees of recovery. Transcriptome analysis revealed that, when comparing the treatment group with the control group, a total of 5530 differentially expressed genes (DEGs) were identified, with 2714 up-regulated and 2816 down-regulated. Furthermore, this study investigated the drought resistance mechanism involving the interaction between the MAPK signaling pathway and other metabolic pathways in the autotetraploid. Nine drought-resistant genes, including MAPK3, bHLH47, GaRbohD, RIBA1, PIP1-3, RCA1, RbohD, CYP707A and HSP70, were selected and analyzed using real-time quantitative PCR; the results were generally consistent with the transcriptomic data. Conclusions: These findings substantially enhance our understanding of the molecular mechanisms underlying drought responses in autotetraploids. This novel autotetraploid genotype expands the available cotton germplasm resources and is expected to hold significant value for research on polyploidy evolution. Full article

Aspergillus flavus is a globally distributed filamentous fungus of major agricultural and medical importance, capable of producing carcinogenic aflatoxins and forming two specialized developmental structures, conidia and sclerotia. While the molecular framework governing conidiation has been well characterized in Aspergillus nidulans, the corresponding mechanisms in A. flavus remain somewhat unelucidated. In this study, we identified and functionally characterized AfldrnA, a gene encoding a basic helix–loop–helix (bHLH) transcription factor. Targeted deletion of AfldrnA resulted in an aconidial phenotype accompanied by a significant increase in sclerotia formation, whereas complementation with the intact AfldrnA gene restored conidiation and reduced sclerotia development. Phenotypic assays revealed that the ΔAfldrnA mutant exhibited normal vegetative growth, unchanged antifungal susceptibility, and unaffected aflatoxin B₁ production, indicating that AfldrnA primarily regulates developmental rather than metabolic differentiation. Additionally, observed differences between standard and dark incubation conditions suggest that AfldrnA may be involved in environmentally responsive regulation of fungal development. Overall, this study identifies AfldrnA as a pivotal transcriptional regulator essential for coordinating conidiation and sclerotia formation in A. flavus, providing new insights into the genetic and environmental regulation of fungal developmental programs. Full article

Background/Objectives: Ludisia discolor, an endangered medicinal orchid, is a vital source of bioactive flavonoids which requires in vitro tissue culture for propagation and metabolite production. While light quality influences metabolic processes, the mechanisms connecting light conditions, phytohormone signaling, and flavonoid biosynthesis remain unclear. This study investigates how specific light qualities trigger secondary metabolism to improve tissue culture and conservation strategies. Methods: L. discolor was cultivated under strictly regulated LED environments (blue, red, yellow, and green). An integrated multi-omics approach, combining transcriptomic sequencing and targeted metabolomic profiling, was employed to analyze leaves, correlating plant hormone changes with flavonoid metabolite levels. Results: LED light qualities significantly altered flavonoid and phytohormone profiles, yielding 80 unique flavonoids. Blue and red light effectively promoted flavonoid accumulation, whereas yellow light suppressed it. Transcriptomics, validated by qRT-PCR, revealed distinct expression patterns in key structural genes (e.g., 4CL, PAL, CYP73A, FLS, CCoAOMT, C12RT1). Ten transcription factors (including MYB93, bZIP36, bHLH4, and bZIP44) with hormone-responsive cis-elements were co-expressed with 16 structural genes. Notably, blue light induced reactive oxygen species (ROS) signaling, activating phytohormone production (IAA, GA, ABA). These hormones subsequently stimulated transcription factors, increasing the biosynthesis of compounds like neohesperidin and hesperetin. Conclusions: We propose a novel regulatory model where light-induced ROS and phytohormone cascades activate specific transcription factors, enhancing structural gene expression in the flavonoid pathway. These findings elucidate the molecular mechanisms of light-driven secondary metabolism, providing valuable insights for the sustainable agriculture and ex situ conservation of endangered medicinal orchids. Full article

Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, a key acyltransferase in the phenylpropanoid pathway and a canonical member of the BAHD acyltransferase family (BAHD), catalyzes the formation of pivotal intermediates in the biosynthesis of secondary metabolites such as lignin, chlorogenic acid, and flavonoids. These compounds serve indispensable protective functions in terrestrial plants, underpinning their adaptive responses to abiotic stresses such as drought, ultraviolet (UV) radiation, and oxidative damage. Although the role of HCT/HQT in the core phenylpropanoid pathway has been extensively characterized, its precise functional contributions to the flavonoid biosynthetic branch—particularly with respect to substrate selectivity, kinetic regulation, and metabolic channeling—remain incompletely understood. This review systematically analyzes the structural features, spatial conformation, catalytic mechanism, and substrate promiscuity of HCT/HQT to clarify its molecular determinants of activity and specificity. Furthermore, it highlights regulatory factors influencing HCT/HQT gene expression, such as transcription factors (MYB, bHLH, WRKY), phytohormones (GA₃, Eth, MeJA, 6-BA, MT), and abiotic/biotic stressors (temperature, blue light, nitric oxide, nano-selenium). Collectively, these insights illuminate how plants dynamically fine-tune phenylpropanoid metabolism in coordination with developmental programs and environmental challenges. This work provides a foundation for further research on HCT/HQT and supports efforts to develop improved crop varieties through targeted regulation of this central metabolic node. Full article

Caladium bicolor is an important ornamental foliage plant; however, its tropical origin makes it highly sensitive to environmental stresses such as drought and low temperature, which limits its cultivation and industrial development. Basic helix–loop–helix (bHLH) transcription factors play key roles in plant responses to abiotic stresses, but their functions in C. bicolor remain largely unknown. Here, a bHLH transcription factor gene, CbbHLH35, was cloned from C. bicolor, and its sequence characteristics, subcellular localization, expression patterns, and potential roles in stress responses were analyzed. The results showed that CbbHLH35 contains a conserved bHLH domain and is localized in the nucleus. qRT-PCR analysis revealed that CbbHLH35 is expressed in different tissues, with the highest expression in tubers, and is significantly induced by methyl jasmonate (MeJA), abscisic acid (ABA), drought, and low-temperature treatments. Transgenic C. bicolor plants overexpressing CbbHLH35 were generated and subjected to drought and cold stress. Compared with control plants, the overexpression lines showed higher chlorophyll content and POD activity but lower electrolyte leakage and MDA content, indicating enhanced drought and cold tolerance. These results suggest that CbbHLH35 plays a positive role in regulating drought and cold tolerance in C. bicolor and represents a promising candidate gene for the molecular breeding of stress-resistant cultivars. Full article

Drought severely limits maize production. Basic helix-loop-helix (bHLH) transcription factors act as key regulators of plant drought responses; however, the precise regulatory networks they coordinate in maize remain largely unclear. Here, we functionally characterized ZmbHLH81, a drought- and abscisic acid (ABA)-responsive bHLH transcription factor in maize. Subcellular localization confirmed that ZmbHLH81 is a nuclear protein. Overexpression of ZmbHLH81 in Arabidopsis enhanced drought tolerance, whereas CRISPR/Cas9-mediated targeted mutagenesis in maize significantly increased plant sensitivity to drought stress. Physiologically, these mutant lines exhibited accelerated water loss, delayed stomatal closure, compromised antioxidant enzyme activities and elevated malondialdehyde (MDA) accumulation under drought stress. DAP-seq analysis demonstrated that ZmbHLH81 specifically recognizes the conserved G-box motif (CACGTG). Furthermore, integrating DAP-seq and transcriptomic data successfully identified the key downstream targets governed by ZmbHLH81. Molecular assays confirmed that ZmbHLH81 directly targets and transactivates the core ABA signaling kinase gene ZmSnRK2.9 and stress-responsive transcription factor genes ZmNAC20 and ZmHDZ4. Taken together, ZmbHLH81 positively regulates maize drought tolerance by directly activating a specific regulatory module that orchestrates ABA-mediated stomatal closure and reactive oxygen species (ROS) scavenging, providing a promising genetic target for breeding climate-resilient crops. Full article

Sulfated peptides, such as PSK, PSY, CIF, and RGF, are crucial regulators of plant growth, development, and stress responses, with their activity dependent on post-translational tyrosine sulfation by tyrosylprotein sulfotransferase (TPST). This study explores the evolutionary history and the interaction mechanisms between TPST and sulfated peptides in plants. Systematic analyses of multi-species genomes show that TPST can be traced back to the chlorophyte lineage, whereas PSK, a sulfated peptide, appears to have emerged in gymnosperms. TPST is evolutionarily conserved, typically present in low copy numbers across plant lineages, while its peptide substrates have expanded in angiosperms. In Liriodendron chinense, TPST-sulfated peptide gene promoters are enriched with cis-regulatory elements linked to abscisic acid, gibberellin responsiveness, and anaerobic induction. Synteny analyses revealed collinearity between sulfated peptide genes in L. chinense, Magnolia biondii, Arabidopsis thaliana, and Populus trichocarpa, but not with Oryza sativa. Molecular docking identified key TPST-PSK interaction sites in the sulfotransferase domain, with several critical residues facilitating binding. Transcriptomic and co-expression network analyses revealed that LcTPST was expressed at lower levels than its peptide precursor genes, while LcPSK2 remained highly expressed after the torpedo stage of somatic embryogenesis. Stress conditions significantly increased PSK-associated module connectivity, enriched in transcription factors such as WRKY, bHLH, bZIP, and MADS. This study provides insights into the evolutionary, structural, and regulatory aspects of the TPST-sulfated peptide system in plants. Full article

(1) Background: The bHLH (basic helix-loop-helix) transcription factor family is one of the most abundant in plants and is involved in plant growth, development, and abiotic stress responses. Notably, the functions of most bHLH family members remain poorly characterized. (2) Results: CmbHLH112, a nuclear-localized bHLH transcription factor from chrysanthemum, exhibits transcriptional activation activity. Overexpression of CmbHLH112 in Arabidopsis significantly promotes flowering and enhances drought resistance. qRT-PCR analysis revealed that CmbHLH112 regulates flowering time by affecting the expression of key flowering genes, including FT, SOC1, LFY, and FLC. Under drought stress, CmbHLH112 overexpression plants showed reduced ROS accumulation compared with wild-type plants, accompanied by elevated activities of key antioxidant enzymes and increased proline content. Moreover, transgenic plants exhibited lower MDA concentrations and reduced water loss rates under drought conditions, further indicating enhanced stress resilience. Overexpression of CmbHLH112 also upregulates ABA levels under drought stress, while simultaneously promoting the expression of genes involved in ABA biosynthesis and ABA signaling pathways. (3) Conclusions: Our results demonstrate that heterologous overexpression of CmbHLH112 in Arabidopsis enhances drought tolerance and promotes flowering. Thus, CmbHLH112 is proposed to play a dual role in modulating flowering time and drought tolerance, at least partly by regulating ABA biosynthesis. Full article

Hypecoum erectum L. is a medicinal plant known for its high content of isoquinoline alkaloids (IQAs), a class of compounds with diverse pharmacological activities. To elucidate the biosynthetic mechanisms and tissue-specific accumulation of IQAs, we integrated HPLC-MS/MS-based metabolomic analysis with RNA sequencing (RNA-seq) transcriptomic profiling across the roots, stems, and leaves of H. erectum. Metabolomic analysis identified twenty-six IQAs as differentially accumulated metabolites (DAMs) among the three tissues, while transcriptomic analysis revealed twenty-two categories of differentially expressed genes (DEGs) involved in IQA biosynthesis. KEGG pathway enrichment analysis demonstrated that nine DAMs and twenty categories of DEGs were co-enriched in the IQA biosynthetic pathway of Hypecoum erectum. Notably, seven key DAMs—Stylopine, Protopine, Magnoflorine, Corydaline, Tetrahydropalmatine, Sanguinarine, and Palmatine—preferentially accumulated in the root, concomitant with the elevated expression of eleven root-specific DEGs, including GOT1, CYP719A14, SMT, CYP719A1_2_3_13, PSOMT1, E2.1.1.116, CYP80B1, E2.1.1.128, NCS, ASP5, and BBE1. Gene–metabolite correlation network analysis further identified nine DAMs and fifteen DEGs closely associated with IQA biosynthesis, highlighting key enzymatic regulators of alkaloid accumulation. Additionally, several transcription factor (TF) families, including bHLH, NAC, and ERF families, were predicted to participate in the transcriptional regulation of IQA-related genes. Collectively, these findings demonstrate that roots are the primary site of IQA biosynthesis in H. erectum and provide a molecular framework for understanding the regulation and utilization of its medicinally active components. Full article

Phosphorus (P) limitation is a major selective pressure in plant evolution and a persistent constraint on modern crop production. However, how domestication has reshaped P adaptation strategies remains poorly understood. Here, we compared wild (Solanum pimpinellifolium) and cultivated (Solanum lycopersicum) tomatoes under contrasting P conditions using integrated physiological, ionomic, and transcriptomic analyses. Our findings reveal distinct P strategies between the examined genotypes. Cultivated tomatoes achieved higher biomass under sufficient P supply but were highly sensitive to P deficiency, responding through acquisition-driven phenotypic plasticity characterized by extensive root remodeling and enhanced external P mobilization. In contrast, wild accessions maintained growth and higher P use efficiency under low P by relying on an optimized internal P management strategy, including efficient P uptake, preferential allocation to photosynthetically active tissues, and effective remobilization from older leaves. Consistently, ionomic profiling revealed that wild tomatoes preserved coordinated macro- and micronutrient homeostasis under P stress. Tissue-specific transcriptomic analyses further uncovered pronounced divergence in P-responsive regulation, with cultivated tomatoes showing predominantly root-centered responses, whereas wild accessions exhibited strong activation in old source leaves. This tissue-specific specialization was accompanied by a putative regulatory divergence, with HD-ZIP transcription factors enriched in cultivated tomatoes and G2-like and bHLH factors central in wild accessions. Together, our results indicate that modern cultivars exhibit a stronger reliance on external P acquisition and greater growth sensitivity under sustained P limitation compared to wild accessions, which showed relatively more stable internal P allocation patterns, highlighting wild germplasm as a resource for improving crop P efficiency. Full article

Salinity is a major limiting factor for alfalfa production. This study analyzed the differential regulatory mechanisms of ZT1 and ZT2 under salt stress (100 and 200 mM) through physiological and biochemical responses, the photosynthetic system, and transcriptome and metabolome. The results show that ZT1 is more tolerant than ZT2. Under salt stress, root vitality (30.95–66.28%), shoot dry weight (13.23–53.01%), and chlorophyll a (20.00–50.00%) decreased significantly. However, Na⁺/K⁺ (0.93–3.62 times), MDA (0.19–2.52 times), and superoxide dismutase (28.94–79.56%) increased significantly. From a physiological perspective, ZT1 and ZT2 can endow plants with salt tolerance by regulating the Na⁺/K⁺ balance, inducing osmotic agents, enhancing antioxidant activity, and regulating the photosynthetic system. In omics analysis, there were significant differences in their regulation of the biosynthetic pathways of phenylpropanin and flavonoids. ZT1’s salt tolerance is strengthened by the positive regulation of transcription factors (GRAS) and genes (CHS, POD, CAD, F3H, and PAL), together with the accumulation of (-)-epicatechin, eriodictyol, and butein. In contrast, ZT2 responded positively to salt stress via the regulation of TFs (GRAS, TRAF, and bHLH) and genes (POD, C4H, CHS, and F3′5′H), as well as the accumulation of caffeic acid. The research results will provide new insights into alfalfa cultivation and new variety breeding in saline–alkali land. Full article

R2R3-MYB and bHLH transcription factors (TFs) are key regulators of floral secondary metabolism and epidermal development in flowering plants. Orchids exhibit remarkable floral diversity, which is critical for pollination success and ornamental value, yet the evolutionary and functional diversification of these TF families within the genus remains largely unexplored. Here, we conducted a comprehensive pan-genome dissection of R2R3-MYB and bHLH TF families across 18 Dendrobium species, integrating orthologs assignment, phylogenetics, duplication profiling, cis-regulatory annotation, and tissue-specific expression analysis. We identified 3074 R2R3-MYB and 2282 bHLH genes, classified into 69 and 61 orthologous gene groups (OGGs), respectively. Core OGGs accounted for two-thirds of both families, indicating strong evolutionary conservation, whereas variable OGGs reflected lineage-specific diversification. Phylogenetic analyses resolved R2R3-MYBs into 24 canonical subfamilies and revealed conserved heterogeneous expansion patterns in bHLH subfamilies. Promoter architectures of R2R3-MYB genes were enriched in hormone-, stress-, and light-responsive elements, whereas bHLH promoters were dominated by development-related motifs. Tissue-specific expression profiling in Dendrobium ‘Chao Praya Smile’ showed that floral bud-enriched genes were associated with flavonoid/anthocyanin biosynthesis, whereas root-enriched genes were linked to stress and hormone responses. Integration of pan-genomics and transcriptomics highlighted evolutionary trajectory and functional divergence between core and variable gene sets within Dendrobium. Our study establishes a comprehensive, genus-wide framework for understanding the evolutionary and functional characteristics of MYB–bHLH regulatory networks in Dendrobium. These findings provide valuable genetic resources and key candidate targets for functional characterization and molecular breeding, with important implications for genetic improvement of reproductive traits, floral quality, stress resistance, and ornamental and agronomic value in orchids. Full article