Search Results (978)

Soil salinity is a major environmental constraint limiting plant productivity and modulating secondary metabolism. Triterpenoid saponins play crucial roles in plant stress adaptation, yet their biosynthetic regulation in Cyclocarya paliurus under salt stress remains poorly understood. This research integrated transcriptomic and metabolomic analyses to investigate triterpenoid saponin metabolism in C. paliurus leaves at four NaCl concentrations and two sampling times. Salt stress altered ion homeostasis, suppressed growth, and induced distinct triterpenoid saponins accumulation patterns, with cyclocaric acid B and oleanolic acid showing significant increases. Weighted gene co-expression network analysis identified two modules significantly correlated with triterpenoid saponin accumulation and highlighted transcription factors including WRKY18, bHLH121, ERF4, and ERF1 as regulators of key biosynthetic genes (DXS, SQS, and HMGR). Molecular docking further validated these regulatory interactions, demonstrating that bHLH35, MYC2, ERF113, and MED26B form stable complexes with target gene promoters through extensive hydrogen-bond networks. These findings elucidate the regulatory framework of triterpenoid saponin metabolism under salinity and provide a foundation for molecular breeding and cultivation of C. paliurus in saline regions. Full article

Trichomes are specialized epidermal structures that play pivotal roles in plant defense against biotic and abiotic stresses. Inositol polyphosphate kinase 2 (IPK2) is a key enzyme in inositol phosphate metabolism with diverse functions in eukaryotic cellular processes. However, its involvement in trichome development remains uncharacterized. Here, we systematically analyzed the function of a rice inositol polyphosphate kinase gene (OsIPK2) in trichome development using transgenic rice lines and heterologously expressing Arabidopsis lines. Scanning electron microscopy (SEM) analysis revealed that OsIPK2 acts as an organ-specific modulator of trichome development in rice. Its overexpression repressed macrohair initiation and microhair elongation in leaves, while promoting trichome development on the glumes. Metabolomic profiling revealed that OsIPK2 overexpression reprogrammed cuticular wax metabolism in transgenic rice leaves, shifting fatty acid flux toward long-chain wax precursors and increasing soluble carbohydrate levels. Transcriptomic and qPCR analysis confirmed that OsIPK2 modulated the expression of genes involved in cuticular wax biosynthesis, auxin homeostasis, and the core trichome regulatory cascade in rice. Conversely, heterologous overexpression of OsIPK2 in Arabidopsis strongly suppressed trichome initiation and branching, resulting in drastically reduced trichome density and fewer trichome branches. These phenotypes were associated with the downregulation of the MYB-bHLH-WD40 (MBW) transcriptional complex and its downstream target genes. Collectively, our findings suggest that OsIPK2 modulated trichome development through organ- and species-specific mechanisms. In rice, it coordinated wax metabolism and the OsSPL10-OsSCR1/2-OsWOX3B-OsHL6 cascade to affect organ-specific trichome formation. In Arabidopsis, it inhibited trichome development by repressing the MBW complex. These results uncover a novel role of OsIPK2 in plant epidermal cell fate specification and advance our understanding of the molecular mechanisms underlying organ- and species-specific regulation of trichome development. Full article

Purple-leaf tea plants are of considerable interest because they show elevated anthocyanin contents. However, the underlying biosynthetic mechanisms of this are incompletely understood. We use metabolomic profiling to analyze anthocyanin accumulation patterns across different purple-leaf plant (‘Nanhan Ziya’) tissues and report that the second and third leaves have significantly higher anthocyanin levels than other tissue types. By integrating transcriptomic sequencing data, we systematically characterize the expression profiles of key genes involved in the anthocyanin biosynthesis pathway. Correlation analysis reveals that the expression levels of anthocyanin synthase (ANS) highly, significantly, and positively correlate with anthocyanin content, with a stronger association than other genes in the pathway. This suggests that ANS may function as a critical rate-limiting enzyme in anthocyanin synthesis in purple-leaf tea plants. Weighted gene co-expression network analysis revealed several transcription factors (e.g., MYB14, NAC35, bHLH90) strongly associated with anthocyanin accumulation. We elucidate the central regulatory role of ANS at the transcriptional level, construct a preliminary interaction network with key transcription factors for it, and provide theoretical foundations for further deciphering the anthocyanin biosynthesis mechanism and for breeding tea varieties with enhanced anthocyanin traits. Full article

Ilex rotunda Thunb. is a prestigious ornamental tree renowned for its vibrant red fruits, yet the molecular mechanisms governing its fruit color variation remain poorly understood. The discovery of a rare yellow-fruited natural bud sport cultivar, ‘Peace Time’, provides an ideal model to investigate these processes compared to the wild-type red fruit. In this study, we integrated physiological evaluations, untargeted metabolomics, and de novo transcriptomics across multiple fruit developmental stages to elucidate the basis of this color transition. Our results demonstrated that the yellow phenotype is characterized by high lightness and yellowness values, driven by the profound suppression of anthocyanin biosynthesis. Biochemical and transcriptomic profiling revealed that DFR (dihydroflavonol 4-reductase), a critical “gatekeeper” gene, experiences severe transcriptional silencing in the yellow-fruited cultivar. This enzymatic bottleneck triggers a “passive substrate overflow,” redirecting shared precursors toward the parallel flavonol branch, resulting in the substantial accumulation of specific flavonols, including rutin and isoquercitrin. Furthermore, correlation network analysis highlighted a putative dual regulatory module associated with this metabolic reprogramming: the down-regulation of the putative activator bHLH30 coupled with the robust up-regulation of the putative repressor bHLH51, together likely contributing to the silencing of DFR transcription. These findings provide a comprehensive “dual-module” and “passive overflow” framework for fruit coloration in I. rotunda, highlighting a remarkable metabolic plasticity that reshapes this cultivar’s phytochemical profile and offers vital insights for future ornamental breeding. Full article

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

Objectives: Hemophagocytic lymphohistiocytosis (HLH) is a rare but life-threatening hyperinflammatory syndrome increasingly reported with immune checkpoint inhibitors (ICIs). However, comparative real-world data across different ICI classes and treatment strategies are limited. This study aimed to characterize HLH reporting patterns associated with ICIs and to compare disproportionality signals among PD-1 inhibitors, PD-L1 inhibitors, and combination regimens using the U.S. Food and Drug Administration Adverse Event Reporting System (FAERS). Methods: A retrospective pharmacovigilance analysis was performed using FAERS reports submitted between 2013 and 2025. HLH-related cases were identified using core Medical Dictionary for Regulatory Activities (MedDRA) Preferred Terms. Reporting odds ratios (RORs) with 95% confidence intervals (Cis) were calculated to assess disproportionality across ICI treatment strategies, with ICI monotherapy as the reference. Restricted analyses compared PD-1 inhibitors, PD-L1 inhibitors, and ICI plus CTLA-4 inhibitor therapy. Results: A total of 733 HLH-related reports associated with ICIs were identified. The median age was 65 years (range 1–92), and 54.9% of patients were male. Lung cancer (34.4%) and melanoma (16.0%) were the most frequently reported malignancies. ICI monotherapy accounted for 34.7% of cases, while combination regimens included ICI plus chemotherapy (31.6%), ICI plus targeted therapy (17.8%), and ICI plus CTLA-4 inhibitors (15.9%). All cases were classified as serious adverse events; hospitalization occurred in 69.2% and death in 25.1%. Compared with monotherapy, combination regimens showed higher reporting odds of HLH, with the strongest signal for ICI plus targeted therapy (ROR 2.17, 95% CI 1.72–2.73). PD-1 inhibitors demonstrated higher reporting odds than PD-L1 inhibitors (ROR 1.86, 95% CI 1.41–2.46). Conclusions: This large real-world pharmacovigilance analysis demonstrates differential HLH reporting patterns across ICI classes and treatment strategies. Higher reporting odds with combination regimens and PD-1 inhibitors highlight the need for heightened clinical vigilance, particularly in combination treatment settings. Full article