Transcriptomic Analyses Shed Light on Critical Genes Associated with Bibenzyl Biosynthesis in Dendrobium officinale

Catalytic divergence of O-methyltransferases shapes the chemo-diversity of polymethoxylated bibenzyls in Dendrobium catenatum

Erianin, crepidatin, and chrysotobibenzyl are typical medicinal polymethoxylated bibenzyls (PMBs) that are commercially produced in Dendrobium species. PMBs' chemo-diversity is mediated by the manifold combinations of O-methylation and hydroxylation in a definite order, which remains unsolved. To unequivocally elucidate the methylation mechanism of PMBs, 15 possible intermediates in the biosynthetic pathway of PMBs were chemically synthesized. DcOMT1-5 were highly expressed in tissues where PMBs were biosynthesized, and their expression patterns were well-correlated with the accumulation profiles of PMBs. Moreover, cell-free orthogonal tests based on the synthesized intermediates further confirmed that DcOMT1-5 exhibited distinct substrate preferences and displayed hydroxyl-group regiospecificity during the sequential methylation process. The stepwise methylation of PMBs was discovered from SAM to dihydro-piceatannol (P) in the following order: P → 3-MeP → 4-OH-3-MeP → 4-OH-3,5-diMeP → 3,3'(4'),5-triMeP → 3,4,4',5-tetraMeP (erianin) or 3,3',4,5-tetraMeP (crepidatin) → 3,3',4,4',5-pentaMeP (chrysotobibenzyl). Furthermore, the regioselectivities of DcOMTs were investigated by ligand docking analyses which corresponded precisely with the catalytic activities. In summary, the findings shed light on the sequential catalytic mechanisms of PMB biosynthesis and provide a comprehensive PMB biosynthetic network in D. catenatum. The knowledge gained from this study may also contribute to the development of plant-based medicinal applications and the production of high-value PMBs.

Integrated metabolomic and transcriptomic analyses of Dendrobium chrysotoxum and D. thyrsiflorum reveal the biosynthetic pathway from gigantol to erianin

Erianin is one of the most representative bibenzyls with significant inhibitory activity against a wide range of tumor cells. However, the low erianin level in natural materials has severely inhibited its further development in health care. Our aim was to uncover the erianin biosynthetic pathway to lay the foundation for promoting its production. Firstly, we screened and obtained two Dendrobium species (Dendrobium thyrsiflorum stems with lower erianin content and D. chrysotoxum stems with higher erianin content), belonging to the same Dendrobium section (Chrysotoxae). A systematic analysis of bibenzyl structure and content in two stems revealed that gigantol might be an erianin biosynthetic intermediate, which was verified by introducing deuterium-labeled gigantol. Chemical structure analyses indicated that gigantol was modified by two kinds of enzymes (hydroxylases and O-methyltransferases), leading to erianin synthesis. Up-regulated hydroxylases and O-methyltransferases (OMTs) were screened out and were performed by molecular docking simulation experiments. We propose a rational biosynthetic pathway from gigantol to erianin, as well as relevant enzymes involved in the process. Our findings should significantly contribute to comprehensive resolution of the erianin biosynthetic pathway, promote its large-scale industrial production as well as contribute to biosynthesis studies of other bibenzyls.

Integrated component identification, network pharmacology, and experimental verification revealed mechanism of Dendrobium officinale Kimura et Migo against lung cancer

BACKGROUND

Dendrobium officinale Kimura et Migo (DO), a valuable Chinese herbal medicine, has been reported to exhibit potential effects in the prevention and treatment of lung cancer. However, its material basis and mechanism of action have not been comprehensively analyzed.

PURPOSE

The objective of this study was to preliminarily elucidate the active components and pharmacological mechanisms of DO in treating lung cancer, according to UPLC-Q/TOF-MS, HPAEC-PAD, network pharmacology, molecular docking, and experimental verification.

METHODS

The chemical components of DO were identified via UPLC-Q/TOF-MS, while the monosaccharide composition of Dendrobium officinale polysaccharide (DOP) was determined by HPAEC-PAD. The prospective active constituents of DO as well as their respective targets were predicted in the combined database of Swiss ADME and Swiss Target Prediction. Relevant disease targets for lung cancer were searched in OMIM, TTD, and Genecards databases. Further, the active compounds and potential core targets of DO against lung cancer were found by the C-T-D network and the PPI network, respectively. The core targets were then subjected to enrichment analysis in the Metascape database. The main active compounds were molecularly docked to the core targets and visualized. Finally, the viability of A549 cells and the relative quantity of associated proteins within the major signaling pathway were detected.

RESULTS

249 ingredients were identified from DO, including 39 flavonoids, 39 bibenzyls, 50 organic acids, 8 phenanthrenes, 27 phenylpropanoids, 17 alkaloids, 17 amino acids and their derivatives, 7 monosaccharides, and 45 others. Here, 50 main active compounds with high degree values were attained through the C-T-D network, mainly consisting of bibenzyls and monosaccharides. Based on the PPI network analysis, 10 core targets were further predicted, including HSP90AA1, SRC, ESR1, CREBBP, MAPK3, AKT1, PIK3R1, PIK3CA, HIF1A, and HDAC1. The results of the enrichment analysis and molecular docking indicated a close association between the therapeutic mechanism of DO and the PI3K-Akt signaling pathway. It was confirmed that the bibenzyl extract and erianin could inhibit the multiplication of A549 cells in vitro. Furthermore, erianin was found to down-regulate the relative expressions of p-AKT and p-PI3K proteins within the PI3K-Akt signaling pathway.

CONCLUSIONS

This study predicted that DO could treat lung cancer through various components, multiple targets, and diverse pathways. Bibenzyls from DO might exert anti-lung cancer activity by inhibiting cancer cell proliferation and modulating the PI3K-Akt signaling pathway. A fundamental reference for further studies and clinical therapy was given by the above data.

Exploring regulatory network of icariin synthesis in Herba Epimedii through integrated omics analysis

Herba Epimedii's leaves are highly valued in traditional Chinese medicine for their substantial concentration of flavonoids, which play a crucial role in manifesting the plant's therapeutic properties. This study investigated the metabolomic, transcriptomic and proteomic profiles of leaves from two Herba Epimedii cultivars, Epipremnum sagittatum (J) and Epipremnum pubescens (R), at three different developmental stages. Metabolite identification and analysis revealed a total of 1,412 and 1,421 metabolites with known structures were found. Flavonoids made up of 33%, including 10 significant accumulated icariin analogues. Transcriptomic analysis unveiled totally 41,644 differentially expressed genes (DEGs) containing five encoded genes participated in icariin biosynthesis pathways. Totally, 9,745 differentially expressed proteins (DEPs) were found, including Cluster-47248.2.p1 (UDP-glucuronosy/UDP-glucosyltransferase), Cluster-30441.2.p1 (O-glucosyltransferase), and Cluster-28344.9.p1 (anthocyanidin 3-O-glucoside 2 "-O-glucosyltransferase-like) through proteomics analysis which are involved to icariin biosynthesis. Protein-protein interaction (PPI) assay exhibited, totally 12 proteins showing a strong relationship of false discovery rate (FDR) <0.05 with these three proteins containing 2 leucine-rich repeat receptor kinase-like protein SRF7, and 5 methyl jasmonate esterase 1. Multi-omics connection networks uncovered 237 DEGs and 72 DEPs exhibited significant associations with the 10 icariin analogues. Overall, our integrated omics approach provides comprehensive insights into the regulatory network underlying icariin synthesis in Herba Epimedii, offering valuable resources for further research and development in medicinal plant cultivation and pharmaceutical applications.

Detection of a bibenzyl core scaffold in 28 common mangrove and associate species of the Indian Sundarbans: potential signature molecule for mangrove salinity stress acclimation

Bibenzyl derivatives comprising two benzene rings are secondary plant metabolites with significant therapeutic value. To date, bibenzyl derivatives in the Plant kingdom have been primarily identified in bryophytes, orchids, and Cannabis sativa. The metabolic cost investment by plant species for the synthesis of these bioactive secondary metabolites is rationalized as a mechanism of plant defense in response to oxidative stress induced by biotic/abiotic factors. Bibenzyl derivatives are synthesized from core phenylpropanoid biosynthetic pathway offshoots in plant species. Mangrove and mangrove associate species thrive under extreme ecological niches such as a hypersaline intertidal environment through unique adaptive and acclimative characteristics, primarily involving osmotic adjustments followed by oxidative stress abatement. Several primary/secondary bioactive metabolites in mangrove species have been identified as components of salinity stress adaptation/acclimation/mitigation; however, the existence of a bibenzyl scaffold in mangrove species functioning in this context remains unknown. We here report the confirmed detection of a core bibenzyl scaffold from extensive gas chromatography-mass spectrometry and gas chromatography-flame ionization detection analyses of 28 mangrove and mangrove associate species from the Indian Sundarbans. We speculate that the common presence of this bibenzyl core molecule in 28 mangrove and associate species may be related to its synthesis via branches of the phenylpropanoid biosynthetic pathway induced under high salinity, which functions to detoxify reactive oxygen species as a protection for the maintenance of plant metabolic processes. This finding reveals a new eco-physiological functional role of bibenzyls in unique mangrove ecosystem.

Wound-Induced Temporal Reprogramming of Gene Expression during Agarwood Formation in Aquilaria sinensis

Agarwood is a resinous heartwood of Aquilaria sinensis that is formed in response to mechanical wounding. However, the transcriptional response of A. sinensis to mechanical wounding during the agarwood formation process is still unclear. Here, three five-year-old A. sinensis trees were mechanically damaged by a chisel, and time-series transcriptomic analysis of xylem tissues in the treated area (TA) was performed at 15 (TA1), 70 (TA2) and 180 days after treatment (TA3). Samples from untreated areas at the corresponding time points (UA1, UA2, UA3, respectively) were collected as controls. A total of 1862 (TA1 vs. UA1), 961 (TA2 vs. UA2), 1370 (TA3 vs. UA3), 3305 (TA2 vs. TA1), 2625 (TA3 vs. TA1), 2899 (TA3 vs. TA2), 782 (UA2 vs. UA1), 4443 (UA3 vs. UA1) and 4031 (UA3 vs. UA2) genes were differentially expressed (DEGs). Functional enrichment analysis showed that DEGs were significantly enriched for secondary metabolic processes, signal transduction and transcriptional regulation processes. Most of the genes involved in lignin biosynthesis were more abundant in the TA groups, which included phenylalanine ammonia-lyase, 4-coumarate CoA ligase, cinnamate 4-hydroxylase, caffeoyl-CoA O-methyltransferase and cinnamoyl-CoA reductase. DEGs involved in sesquiterpene biosynthesis were also identified. Hydroxymethylglutaryl-CoA synthase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase, phosphomevalonate kinase and terpene synthase genes were significantly increased in the TA groups, promoting sesquiterpene biosynthesis in the wounded xylem tissues. The TF-gene transcriptomic networks suggested that MYB DNA-binding, NAM, WRKY, HLH and AP2 TFs co-expressed with genes related to lignin and sesquiterpene synthesis, indicating their critical regulatory roles in the biosynthesis of these compounds. Overall, our study reveals a dynamic transcriptional response of A. sinensis to mechanical wounding, provides a resource for identifying candidate genes for molecular breeding of agarwood quality, and sheds light on the molecular mechanisms of agarwood formation in A. sinensis.

An UPLC-Q-TOF/MS-Based Analysis of the Differential Composition of Dendrobium officinale in Different Regions

Dendrobium officinale (D. officinale) is a valuable traditional Chinese herbal medicine with high commercial value. In Chinese Pharmacopoeia (Ch.P., 2020 edition), the quality of D. officinale is mainly evaluated by its polysaccharide content. However, varying growth and production conditions, such as cultivation environment, origin, harvesting process, or processing methods, resulting in highly variable yields, quality, and composition. The aim of this study was to investigate whether the content of secondary metabolites in D. officinale from different origins is consistent with the polysaccharide content. The results showed that the polysaccharide content and pass rate were ranked as GX > AH > GZ > YN. Based on the nontargeted metabolomics approach, we searched for differential components in 22 different regions of D. officinale, including amides, bibenzyls, disaccharide, flavonoids, organic nitrogenous compounds, and phenolic glycosides. The overall expression was opposite to the polysaccharide, and the most expressed was YN, followed by GZ, AH, and GX. These results indicated that the current quality standard for evaluating the quality of D. officinale by polysaccharide content alone is imperfect, and small molecule compounds need to be included as quality markers.

Bioactivities and Mechanism of Actions of Dendrobium officinale: A Comprehensive Review

Dendrobium officinale has a long history of being consumed as a functional food and medicinal herb for preventing and managing diseases. The phytochemical studies revealed that Dendrobium officinale contained abundant bioactive compounds, such as bibenzyls, polysaccharides, flavonoids, and alkaloids. The experimental studies showed that Dendrobium officinale and its bioactive compounds exerted multiple biological properties like antioxidant, anti-inflammatory, and immune-regulatory activities and showed various health benefits like anticancer, antidiabetes, cardiovascular protective, gastrointestinal modulatory, hepatoprotective, lung protective, and neuroprotective effects. In this review, we summarize the phytochemical studies, bioactivities, and the mechanism of actions of Dendrobium officinale, and the safety and current challenges are also discussed, which might provide new perspectives for its development of drug and functional food as well as clinical applications.

Genome-wide identification and characterization of active ingredients related β-Glucosidases in Dendrobium catenatum

BACKGROUND

Dendrobium catenatum/D. officinale (here after D. catenatum), a well-known economically important traditional medicinal herb, produces a variety of bioactive metabolites including polysaccharides, alkaloids, and flavonoids with excellent pharmacological and clinical values. Although many genes associated with the biosynthesis of medicinal components have been cloned and characterized, the biosynthetic pathway, especially the downstream and regulatory pathway of major medicinal components in the herb, is far from clear. β-glucosidases (BGLUs) comprise a diverse group of enzymes that widely exist in plants and play essential functions in cell wall modification, defense response, phytohormone signaling, secondary metabolism, herbivore resistance, and scent release by hydrolyzing β-D-glycosidic bond from a carbohydrate moiety. The recent release of the chromosome-level reference genome of D. catenatum enables the characterization of gene families. Although the genome-wide analysis of the BGLU gene family has been successfully conducted in various plants, no systematic analysis is available for the D. catenatum. We previously isolated DcBGLU2 in the BGLU family as a key regulator for polysaccharide biosynthesis in D. catenatum. Yet, the exact number of DcBGLUs in the D. catenatum genome and their possible roles in bioactive compound production deserve more attention.

RESULTS

To investigate the role of BGLUs in active metabolites production, 22 BGLUs (DcBGLU1-22) of the glycoside hydrolase family 1 (GH1) were identified from D. catenatum genome. Protein prediction showed that most of the DcBGLUs were acidic and phylogenetic analysis classified the family into four distinct clusters. The sequence alignments revealed several conserved motifs among the DcBGLU proteins and analyses of the putative signal peptides and N-glycosylation site revealed that the majority of DcBGLU members dually targeted to the vacuole and/or chloroplast. Organ-specific expression profiles and specific responses to MeJA and MF23 were also determined. Furthermore, four DcBGLUs were selected to test their involvement in metabolism regulation. Overexpression of DcBGLU2, 6, 8, and 13 significantly increased contents of flavonoid, reducing-polysaccharide, alkaloid and soluble-polysaccharide, respectively.

CONCLUSION

The genome-wide systematic analysis identified candidate DcBGLU genes with possible roles in medicinal metabolites production and laid a theoretical foundation for further functional characterization and molecular breeding of D. catenatum.

The Transcriptome Profiling of Flavonoids and Bibenzyls Reveals Medicinal Importance of Rare Orchid Arundina graminifolia

Orchids are very important flowering plants that spend long juvenile phases before flowering. Along with aesthetic importance, they are rich sources of medicinal components. However, their long reproductive cycle is the major hurdle to study the medicinal efficacy. Arundina graminifolia is a rare orchid that grows fast, unlike other orchids, and this characteristic makes it an ideal plant to study the medicinal enrichment of orchids. Therefore, this study presents the identification of important medicinal components in various parts of A. graminifolia. Transcriptome analysis was performed for five stages (FD1-FD5) of flower development and four tissue types (mature flower, silique, root, and leaf) to ascertain genetic regulators of flavonoids and bibenzyls. Most of the genes showed the highest expression in roots as compared with other tissues. Weighted gene coexpression network analysis (WGCNA) was performed to identify the coexpression modules and the candidate genes involving biosynthesis pathways of these chemicals. MEyellow module contained the highly coexpressed genes. Moreover, the concentrations of phenylpropanoid, bibenzyls, and flavone were ascertained through high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Phenylpropanoid and bibenzyl were comparatively high in the leaf, while flavone showed a high concentration in the stem. The selected candidate genes [bibenzyl biosynthesis (BIBSY212), CYP84A1, CYP73A4, 4CLL7, UGT88B1, UGT73C3, anthocyanin synthase (ANS), phenylalanine ammonia-lyase (PAL), flavanone synthase FLS, and CHS8] were validated through quantitative real-time PCR (qRT-PCR). Most of these genes showed high expression in leaf and root as compared with other tissue. Therefore, the presence of bibenzyls and flavonoids in different parts of A. graminifolia and their molecular regulators can provide a quick source to decipher the medicinal efficacy of orchids.

Two new stilbenoid diglycosides from the stems of Dendrobium 'Sonia'

Two undescribed stilbenoid diglycosides, dendrosonside A and dendrosonside B (1 and 2), were isolated from the stems of Dendrobium 'Sonia'. Their structures were elucidated based on 1 D/2D NMR and HRESIMS. The glycosyls contained in the two isolates were determined as D-glucose by acid hydrolysis and GC-MS analyses. In addition, 1 and 2 were further tested for the inhibition of nitric oxide production.

Biomass and Active Compounds Accumulation of the Medicinal Orchid Pleione bulbocodioides in Response to Light Intensity and Irrigation Frequency

Pseudobulbs of Pleione species are widely used as traditional medicine in Asian countries, but the mechanism of active compound accumulation remains unclear. In the present study, we investigated the accumulation of biomass and three active compounds (dactylorhin A, militarine and batatasin III) of Pleione bulbocodioides in response to different light intensities and irrigation frequencies. We found that single high light (65 % of full sunlight) or drought stress (14-day irrigation interval) increased active compounds accumulation but the combined effect of these two treatments decreased the total content of these three active compounds. This decrease was due to the plants under combined stress having a significantly lower photosynthetic rate, leaf area and longevity, leading to a dramatic decrease in pseudobulb biomass. Among all treatments, the highest total content of active compounds was observed in plants subjected to the high light level with a high water level (3-day irrigation interval), and plants under medium light intensity (30 % of full sunlight) also had considerable content of active compounds accumulation. To balance the quality and quantity of Pleione pseudobulbs during artificial cultivation, 30∼65 % of full sunlight with the avoidance of drought stress is recommended. Our results suggest the accumulation of the three active compounds is significantly influenced by light intensity and irrigation frequency, which may contribute to the artificial cultivation and quality control of medicinal Pleione.

A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach

Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.

Improving large-scale biomass and total alkaloid production of Dendrobium nobile Lindl. using a temporary immersion bioreactor system and MeJA elicitation

BACKGROUND

Dendrobium nobile Lindl. is an important pharmacopeial plant with medicinal and ornamental value. This study sought to provide a technical means for the large-scale production of total alkaloid in D. nobile. Seedlings were cultured in vitro using a temporary immersion bioreactor system (TIBS). The four tested immersion frequencies (min/h; 5/2, 5/4, 5/6, and 5/8) influenced the production of biomass and total alkaloid content. In addition, to compare the effects of different concentrations of the phytohormone methyl jasmonate (MeJA) and treatment time on biomass and total alkaloid accumulation, MeJA was added to the TIBS medium after 50 days. Finally, total alkaloid production in semi-solid system (SSS), TIBS, and TIBS combined with the MeJA system (TIBS-MeJA) were compared.

RESULTS

The best immersion frequency was found to be 5/6 (5 min every 6 h), which ensured appropriate levels of biomass and total alkaloid content in plantlets. The alkaloid content and production level of seedlings were the highest after treatment with 10 μM MeJA separately for 20 and 30 days using TIBS. The maximum content (7.41 mg/g DW) and production level (361.24 mg/L) of total alkaloid on use of TIBS-MeJA were 2.32- and 4.69-fold, respectively, higher in terms of content, and 2.07- and 10.49-fold, respectively, higher in terms of production level than those on using of TIBS (3.20 mg/g DW, 174.34 mg/L) and SSS (1.58 mg/g DW, 34.44 mg/L).

CONCLUSIONS

Our results show TIBS-MeJA is suitable for large-scale production of total alkaloid in in vitro seedlings. Therefore, this study provides a technical means for the large-scale production of total alkaloid in D. nobile.

Research Advances in Multi-Omics on the Traditional Chinese Herb Dendrobium officinale

Dendrobium officinale Kimura et Migo is an important epiphytic plant, belonging to the Orchidaceae family. There are various bioactive components in D. officinale plants, mainly including polysaccharides, alkaloids, and phenolic compounds. These compounds have been demonstrated to possess multiple functions, such as anti-oxidation, immune regulation, and anti-cancer. Due to serious shortages of wild resources, deterioration of cultivated germplasm and the unstable quality of D. officinale, the study has been focused on the biosynthetic pathway and regulation mechanisms of bioactive compounds. In recent years, with rapid developments in detection technologies and analysis tools, omics research including genomics, transcriptomics, proteomics and metabolomics have all been widely applied in various medicinal plants, including D. officinale. Many important advances have been achieved in D. officinale research, such as chromosome-level reference genome assembly and the identification of key genes involved in the biosynthesis of active components. In this review, we summarize the latest research advances in D. officinale based on multiple omics studies. At the same time, we discuss limitations of the current research. Finally, we put forward prospective topics in need of further study on D. officinale.