Integrated chemical and transcriptomic analyses unveils synthetic characteristics of different medicinal root parts of Angelica sinensis

Hypoxia inducible factor-1α related mechanism and TCM intervention in process of early fracture healing

As a common clinical disease, fracture is often accompanied by pain, swelling, bleeding as well as other symptoms and has a high disability rate, even threatening life, seriously endangering patients' physical and psychological health and quality of life. Medical practitioners take many strategies for the treatment of fracture healing, including Traditional Chinese Medicine (TCM). In the early stage of fracture healing, the local fracture is often in a state of hypoxia, accompanied by the expression of hypoxia inducible factor-1α (HIF-1α), which is beneficial to wound healing. Through literature mining, we thought that hypoxia, HIF-1α and downstream factors affected the mechanism of fracture healing, as well as dominated this process. Therefore, we reviewed the local characteristics and related signaling pathways involved in the fracture healing process and summarized the intervention of TCM on these mechanisms, in order to inspirit the new strategy for fracture healing, as well as elaborate on the possible principles of TCM in treating fractures based on the HIF molecular mechanism.

Dynamic metabolites: A bridge between plants and microbes

Plant metabolites have a great influence on soil microbiomes. Although few studies provided insights into plant-microbe interactions, we still know very little about how plants recruit their microbiome. Here, we discuss the dynamic progress that typical metabolites shape microbes by a variety of factors, such as physiographic factors, cultivar factors, phylogeny factors, and environmental stress. Several kinds of metabolites have been reviewed, including plant primary metabolites (PPMs), phytohormones, and plant secondary metabolites (PSMs). The microbes assembled by plant metabolites in return exert beneficial effects on plants, which have been widely applied in agriculture. What's more, we point out existing problems and future research directions, such as unclear mechanisms, few species, simple parts, and ignorance of absolute abundance. This review may inspire readers to study plant-metabolite-microbe interactions in the future.

Changes in marker secondary metabolites revealed the medicinal parts, harvest time, and possible synthetic sites of Rubia cordifolia L

Rubia cordifolia L. is a significant medicinal plant. To investigate the changes of marker metabolites of R. cordifolia, the purpurin, mollugin, carbon, nitrogen contents, and the expression of genes involved in anthraquinones synthesis were examined. The findings indicated that the two secondary metabolites were only detected in stems and roots. Root purpurin content was 5-26 times higher than in stems, and root mollugin content was 92 times higher than in stems in June. These findings suggest that the potential of the roots as a medicinal part. The roots were found to have highest purpurin content in October (2.406 mg g-1), whereas the mollugin content was highest in August (6.193 mg g-1). However, the purpurin content in August was only 0.029 mg g-1 lower than that in October, making August a suitable harvest period for R. cordifolia. The expression 1-deoxy-D-xylulose 5-phosphate synthase (dxs) and 1-deoxy-D-xylulose-5-phosphate reductorisomerase (dxr) genes in roots showed an upward trend. However, the expression level of dxr gene was significantly higher than dxs with the range of 60-518 times higher, indicating the important role of dxr gene. Through correlation and redundancy analyses, it was found that mollugin showed positive correlation with carbon contents and carbon-nitrogen ratio of aerial parts. Additionally, purpurin showed a positive correlation with the expression of both genes. As a result, mollugin is likely to be synthesized in the aerial parts and then stored in the roots, whereas purpurin might be synthesized in the stems and roots. These findings could provide cultivation guidelines for R. cordifolia.

In situ analysis of volatile oil in Angelica sinensis roots by fluorescence imaging combined with mass spectrometry imaging

In this study, the spatial distribution and accumulation dynamics of volatile oil in Angelica sinensis roots was realized by fluorescence imaging combined with mass spectrometry imaging. The laser scanning confocal microscopy was used to determine the optimal excitation wavelength and the fluorescent stability of volatile oil in the sections of Angelica sinensis roots. The results demonstrated that 488 nm was the most suitable excitation wavelength for the identification and quantitative analysis of volatile oil. It was observed that volatile oil accumulated in the oil chamber of the phelloderm and secondary phloem, and the oil canal of the secondary xylem. The results also indicated that there were differences in content during different periods. Furthermore, the MALDI-TOF-MSI technology was used to study the spatial distribution and compare the chemical compositions of different parts of Angelica sinensis roots during the harvest period. A total of 55, 49, 50 and 30 compounds were identified from the head, body, tail of the root and root bark, respectively. The spatial distribution of phthalides, organic acids and other compounds were revealed in Angelica sinensis roots. The method developed in this study could be used for the in situ analysis of volatile oil in Angelica sinensis roots.

The chromosome-level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis

Coumarins are natural products with important medicinal values, and include simple coumarins, furanocoumarins and pyranocoumarins. Female ginseng (Angelica sinensis) is a renowned herb with abundant coumarins, originated in China and known for the treatment of female ailments for thousands of years. The molecular basis of simple coumarin biosynthesis in A. sinensis and the evolutionary history of the genes involved in furanocoumarin biosynthesis are largely unknown. Here, we generated the first chromosome-scale genome of A. sinensis. It has a genome size of 2.37 Gb, which was generated by combining PacBio and Hi-C sequencing technologies. The genome was predicted to contain 43 202 protein-coding genes dispersed mainly on 11 pseudochromosomes. We not only provided evidence for whole-genome duplication (WGD) specifically occurring in the Apioideae subfamily, but also demonstrated the vital role of tandem duplication for phenylpropanoid biosynthesis in A. sinensis. Combined analyses of transcriptomic and metabolomic data revealed key genes and candidate transcription factors regulating simple coumarin biosynthesis. Furthermore, phylogenomic synteny network analyses suggested prenyltransferase genes involved in furanocoumarin biosynthesis evolved independently in the Moraceae, Fabaceae, Rutaceae and Apiaceae after ζ and ε WGD. Our work sheds light on coumarin biosynthesis, and provides a benchmark for accelerating genetic research and molecular breeding in A. sinensis.

Spatial Genomic Resource Reveals Molecular Insights into Key Bioactive-Metabolite Biosynthesis in Endangered Angelica glauca Edgew

Angelica glauca Edgew, which is an endangered medicinal and aromatic herb, is a rich source of numerous industrially important bioactive metabolites, including terpenoids, phenolics, and phthalides. Nevertheless, genomic interventions for the sustainable utilization and restoration of its genetic resources are greatly offset due to the scarcity of the genomic resources and key regulators of the underlying specialized metabolism. To unravel the global atlas of the specialized metabolism, the first spatial transcriptome sequencing of the leaf, stem, and root generated 109 million high-quality paired-end reads, assembled de novo into 81,162 unigenes, which exhibit a 61.53% significant homology with the six public protein databases. The organ-specific clustering grouped 1136 differentially expressed unigenes into four subclusters differentially enriched in the leaf, stem, and root tissues. The prediction of the transcriptional-interactome network by integrating enriched gene ontology (GO) and the KEGG metabolic pathways identified the key regulatory unigenes that correspond to terpenoid, flavonoid, and carotenoid biosynthesis in the leaf tissue, followed by the stem and root tissues. Furthermore, the stem and root-specific significant enrichments of phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and caffeic acid 3-O-methyltransferase (COMT) indicate that phenylalanine mediated the ferulic acid biosynthesis in the stem and root. However, the root-specific expressions of NADPH-dependent alkenal/one oxidoreductase (NADPH-AOR), S-adenosyl-L-methionine-dependent methyltransferases (SDMs), polyketide cyclase (PKC), and CYP72A15 suggest the “root” as the primary site of phthalide biosynthesis. Additionally, the GC-MS and UPLC analyses corresponded to the organ-specific gene expressions, with higher contents of limonene and phthalide compounds in the roots, while there was a higher accumulation of ferulic acid in the stem, followed by in the root and leaf tissues. The first comprehensive genomic resource with an array of candidate genes of the key metabolic pathways can be potentially utilized for the targeted upscaling of aromatic and pharmaceutically important bioactive metabolites. This will also expedite genomic-assisted conservation and breeding strategies for the revival of the endangered A. glauca.

Storax Inhibits Caveolae-Mediated Transcytosis at Blood-Brain Barrier After Ischemic Stroke in Rats

Background and Purpose: Blood-brain barrier (BBB) disruption following ischemic stroke (IS) contributes to hemorrhagic transformation, brain edema, increased neural dysfunction, secondary injury, and mortality. The prevailing view attributes the destruction of tight junction proteins (TJs) to the resulting BBB damage following IS. However, recent studies define a stepwise impairment of the transcellular barrier followed by the paracellular barrier which accounts for the BBB leakage in IS. The increased endothelial transcytosis that has been proven to be caveolae-mediated, preceding and independent of TJs disintegration. Emerging experimental investigations suggested Storax attenuates BBB damage after stroke. This study aimed to test our hypothesis that Storax inhibits caveolae-mediated transcytosis at BBB after ischemic stroke in rats.

Methods: Male Wistar rats (250–300 g) were subjected to transient middle cerebral artery occlusion (t-MCAO). Brain water content and the cerebral infarction size were assessed by brain tissue drying-wet method and 2,3,5-triphenyltetrazolium chloride (TTC) staining. BBB permeability was detected by the leakage of Evans blue and Albumin-Alexa594. The ultrastructure of BBB was examined by transmission electron microscopy (TEM). Cav-1 and Mfsd2a were quantified by western blotting and immunofluorescence staining, AQP4, PDGFR-β, ZO-1 and Occludin were quantified by western blotting.

Results: Storax treatment of 0.1 g/kg had no significant effects on brain lesions. Storax treatment of 0.2, 0.4, and 0.8 g/kg led to a significant decrease in infarction size, and the Storax 0.4, 0.8 g/kg groups displayed a significant reduction in brain water content. Storax treatment of 0.8 g/kg showed mild toxic reactions. Thus, 0.4 g/kg Storax was selected as the optimal dose for subsequent studies. Storax significantly inhibited the fluorescent albumin intensity in the brain parenchyma and the number of caveolae in ECs, alongside attenuating the ultrastructural disruption of BBB at 6 h after stroke. Meanwhile, Storax significantly increased the expression of Mfsd2a and PDGFR-β, and decrease the expression of Cav-1 and AQP4, corresponding to the significantly decreased Cav-1 positive cells and increased Mfsd2a positive cells. However, Storax has no significant effects on Evan blue leakage or the expression ZO-1, Occludin.

Conclusion: Our experimental findings demonstrate Storax treatment inhibits caveolae-mediated transcytosis at BBB in the focal stroke model of rats. We also speculate that regulation of Cav-1, Mfsd2a, AQP4, and PDGFR-β expressions might be associated with its beneficial pharmacological effect, but remain to define and elucidate in future investigation.

Herb Formula (GCis) Prevents Pulmonary Infection Secondary to Intracerebral Hemorrhage by Enhancing Peripheral Immunity and Intestinal Mucosal Immune Barrier

Lung infection is a common complication induced by stroke and seriously affects the prognosis and life quality of patients. However, effective therapeutic strategies are still lacking. In the present study, the herb formula GCis was confirmed to prevent pulmonary infection induced by intracerebral hemorrhage (ICH). The animal model of lung infection induced by ICH, GCis (Ginseng Radix et Rhizoma, Aconiti Lateralis Radix Praeparata, and Cistanches Herba) was orally administrated every day for 7 days. Lung microbial biomass and pathological results showed that the GCis formula pretreatment significantly reduced lung bacterial biomass and alleviated pathological abnormalities. These results indicated that the GCis formula has a clear pharmacological effect on preventing lung infection induced by ICH. Immunosuppression induced by ICH seemed to be the main mechanism of lung infection. Our results showed that the spleen and thymus indexes, WBC, and LY% contents were significantly increased in the GCis formula group. Moreover, bone marrow cells were further analyzed by transcriptome sequencing, and GO and KEGG enrichment analysis results showed that immune function was the main pathway enriched by differential genes after GCis formula intervention. More importantly, our results showed that GCis pretreatment had no significant effect on the mRNA expression of IL-1β, IL-6, and TNF-α in the brain. These results indicated that the GCis formula could enhance immunity after ICH. The intestinal barrier function was further investigated in the present study, considering the origin of the source of infection. Our results showed that the mRNA expressions of intestinal ZO-1, SIgA, and MUC2 were significantly increased, villi structure was intact, inflammatory cell infiltration was reduced, and goblet cell number was increased after GCis formula treatment. These results suggest that the GCis formula can enhance the intestinal mucosal immune barrier. This study provides a herb formula (GCis) that could enhance peripheral immunity and intestinal mucosal immune barrier to prevent pulmonary infection induced by ICH. It would be beneficial in the prevention of severe clinical infections.

Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization

Angelica sinensis is a low-temperature and long-day perennial herb that has been widely used for cardio-cerebrovascular diseases in recent years. In commercial cultivation, up to 40% of flowering decreases the officinal yield of roots and accumulation of bioactive compounds. Although the regulatory mechanism of flowering genes during the photoperiod has been revealed, the networks during vernalization have not been mapped. Here, transcriptomics profiles of A. sinensis with uncompleted (T1), completed (T2) and avoided vernalization (T3) were performed using RNA-seq, and genes expression was validated with qRT-PCR. A total of 61,241 isoforms were annotated on KEGG, KOG, Nr and Swiss-Prot databases; 4212 and 5301 differentially expressed genes (DEGs) were observed; and 151 and 155 genes involved in flowering were dug out at T2 vs. T1 and T3 vs. T1, respectively. According to functional annotation, 104 co-expressed genes were classified into six categories: FLC expression (22; e.g., VILs, FCA and FLK), sucrose metabolism (12; e.g., TPSs, SUS3 and SPSs), hormone response (18; e.g., GID1B, RAP2s and IAAs), circadian clock (2; i.e., ELF3 and COR27), downstream floral integrators and meristem identity (15; e.g., SOC1, AGL65 and SPLs) and cold response (35; e.g., PYLs, ERFs and CORs). The expression levels of candidate genes were almost consistent with FPKM values and changes in sugar and hormone contents. Based on their functions, four pathways that regulate flowering during vernalization were mapped, including the vernalization pathway, the autonomic pathway, the age pathway and the GA (hormone) pathway. This transcriptomic analysis provides new insights into the gene-regulatory networks of flowering in A. sinensis.

Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization

Angelica sinensis is a “low-temperature and long-day” perennial plant that produces bioactive compounds such as phthalides, organic acids, and polysaccharides for various types of clinical agents, including those with cardio-cerebrovascular, hepatoprotective, and immunomodulatory effects. To date, the regulatory mechanism of flowering under the photoperiod has been revealed, while the regulatory network of flowering genes during vernalization, especially in the role of lncRNAs, has yet to be identified. Here, lncRNAs associated with flowering were identified based on the full-length transcriptomic analysis of A. sinensis at vernalization and freezing temperatures, and the coexpressed mRNAs of lncRNAs were validated by qRT-PCR. We obtained a total of 2327 lncRNAs after assessing the protein-coding potential of coexpressed mRNAs, with 607 lncRNAs aligned against the TAIR database of model plant Arabidopsis, 345 lncRNAs identified, and 272 lncRNAs characterized on the SwissProt database. Based on the biological functions of coexpressed mRNAs, the 272 lncRNAs were divided into six categories: (1) chromatin, DNA/RNA and protein modification; (2) flowering; (3) stress response; (4) metabolism; (5) bio-signaling; and (6) energy and transport. The differential expression levels of representatively coexpressed mRNAs were almost consistent with the flowering of A. sinensis. It can be concluded that the flowering of A. sinensis is positively or negatively regulated by lncRNAs, which provides new insights into the regulation mechanism of the flowering of A. sinensis.

Cool Temperature Enhances Growth, Ferulic Acid and Flavonoid Biosynthesis While Inhibiting Polysaccharide Biosynthesis in Angelica sinensis

Angelica sinensis, a perennial herb that produces ferulic acid and phthalides for the treatment of cardio-cerebrovascular diseases, prefers growing at an altitude of 1800-3000 m. Geographical models have predicted that high altitude, cool temperature and sunshade play determining roles in geo-authentic formation. Although the roles of altitude and light in yield and quality have been investigated, the role of temperature in regulating growth, metabolites biosynthesis and gene expression is still unclear. In this study, growth characteristics, metabolites contents and related genes expression were investigated by exposing A. sinensis to cooler (15 °C) and normal temperatures (22 °C). The results showed that plant biomass, the contents of ferulic acid and flavonoids and the expression levels of genes related to the biosynthesis of ferulic acid (PAL1, 4CLL4, 4CLL9, C3H, HCT, CCOAMT and CCR) and flavonoids (CHS and CHI) were enhanced at 15 °C compared to 22 °C. The contents of ligustilide and volatile oils exhibited slight increases, while polysaccharide contents decreased in response to cooler temperature. Based on gene expression levels, ferulic acid biosynthesis probably depends on the CCOAMT pathway and not the COMT pathway. It can be concluded that cool temperature enhances plant growth, ferulic acid and flavonoid accumulation but inhibits polysaccharide biosynthesis in A. sinensis. These findings authenticate that cool temperature plays a determining role in the formation of geo-authentic and also provide a strong foundation for regulating metabolites production of A. sinensis.

Bolting reduces ferulic acid and flavonoid biosynthesis and induces root lignification in Angelica sinensis

Angelica sinensis is a perennial herbaceous species that produces the bioactive metabolites ferulic acid and alkylphthalides widely applied in the treatment of cardio-cerebrovascular diseases. While the effects of bolting on plant biomass and metabolites accumulation have been partly investigated, the mechanism of bolting reducing metabolites biosynthesis is still limited. In this study, the root biomass, accumulations of ferulic acid, flavonoids and lignin, antioxidant capacity, and related genes expression at four different bolting stages were investigated. The results showed that there was a 2.2-, 2.4- and 2.9-fold decrease of the root biomass, ferulic acid and flavonoids contents, while a 2.9-fold increase of lignin content on a per plant basis during the bolting stages. The antioxidant capacity also exhibited significant decrease with growth and development. The differential expression levels of the 20 genes, which are involved in biosynthesis of ferulic acid (e.g. AsPAL1, As4CLs and AsHCT), flavonoids (e.g. AsCHS, AsCHI and AsI3'H) and lignin (e.g. AsCAD1 and AsLACs), were consistent with changes in the above metabolites accumulation. The findings will provide useful references for improving the production of bioactive metabolites in A. sinensis.