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High-value active ingredients in medicinal plants have attracted research attention because of their benefits for human health, such as the antimalarial artemisinin, anticardiovascular disease tanshinones, and anticancer Taxol and vinblastine. Here, we review how hormones and environmental factors promote the accumulation of active ingredients, thereby providing a strategy to produce high-value drugs at a low cost. Focusing on major hormone signaling events and environmental factors, we review the transcriptional regulatory network mediating biosynthesis of representative active ingredients. In this network, many transcription factors (TFs) simultaneously control multiple synthase genes; thus, understanding the molecular mechanisms affecting transcriptional regulation of active ingredients will be crucial to developing new breeding possibilities.

Tiegun yam is a typical food and medicine agricultural product, which has the effects of nourishing the kidney and benefitting the lungs. The quality and price of Tiegun yam are affected by its origin, and counterfeiting and adulteration are common. Therefore, it is necessary to establish a method to identify the origin and index component contents of Tiegun yam. Hyperspectral imaging combined with chemometrics was used, for the first time, to explore and implement the identification of origin and index component contents of Tiegun yam. The origin identification models were established by partial least squares-discriminant analysis (PLS-DA), support vector machine (SVM), and random forest (RF) using full wavelength and feature wavelength. Compared with other models, MSC-PLS-DA is the best model, and the accuracy of the training set and prediction set is 100% and 98.40%. Partial least squares regression (PLSR), random forest (RF), and support vector regression (SVR) models were used to predict the contents of starch, polysaccharide, and protein in Tiegun yam powder. The optimal residual predictive deviation (RPD) values of starch, polysaccharide, and protein prediction models selected in this study were 5.21, 3.21, and 2.94, respectively. The characteristic wavelength extracted by the successive projections algorithm (SPA) method can achieve similar results as the full-wavelength model. These results confirmed the application of hyperspectral imaging (HSI) in the identification of the origin and the rapid nondestructive prediction of starch, polysaccharide, and protein contents of Tiegun yam powder. Therefore, the HSI combined with the chemometric method was available for conveniently and accurately determining the origin and index component contents of Tiegun yam, which can expect to be an attractive alternative method for identifying the origin of other food.

The aim of the present study is to use entropy to explore the change of pulse generated by normal pregnant women with gestational. Firstly, the subjects were divided into early (E), middle (M), and late (L) three stages according to gestational age. Then, pulse signals of the Chi position of 90 pregnant women at different gestational ages were collected. Secondly, the four entropies, namely fuzzy entropy (FuEn), approximate entropy (ApEn), sample entropy (SamEn), and permutation entropy (PerEn), were applied to the analysis of the long-term pulse changes of the pregnancy. Finally, the related information about pulse in different stages of pregnancy is given by the analysis of four kinds of entropy. Furthermore, the statistical tests are conducted for further comparison, and the descriptive statistics and the results are presented. In addition, boxplots are employed to show the distribution of four entropies of pregnancy. This work has studied the changes in pulse during pregnancy from quantitative and qualitative aspects. Our results show that entropy improves the diagnostic value of pulse analysis during pregnancy and could be applied to facilitate noninvasive diagnosis of pregnant women’s physiological signals in the future.

A previous 1H-NMR method allowed the quantification of ephedrine alkaloids; however, there were some disadvantages. The cyclized derivatives resulted from the impurities of diethyl ether were identified and benzene was selected as the better extraction solvent. The locations of ephedrine alkaloids were confirmed with 2D NMR. Therefore, a specific 1H-NMR method has been modified for the quantification of ephedrine alkaloids. Accordingly, twenty Ephedrae Herba samples could be classified into three classes: (I) E. sinica-like species; (II) E. intermedia-like species; (III) others (lower alkaloid contents). The results indicated that ephedrine and pseudoephedrine are the major alkaloids in Ephedra plants, but the concentrations vary greatly determined by the plant species and the collection locations.

Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3899 angiosperm plant species were calculated based on a chloroplast data set with 4356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.

Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4-10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology.

With the rapid development and application of artificial intelligence (AI) in medical field, the diagnostic ways of human health and the social medical structures have changed. Based on the concept of holism and the theory of syndrome differentiation and treatment, TCM realizes comprehensive informatization and intelligence with the help of AI technology in data mining, intelligent diagnosis and treatment, intelligent learning, and decision-making. Furthermore, the intelligent research of TCM technology will further promote the improvement in TCM diagnosis and treatment rules and the leaping development of TCM intelligent instruments. In this article, we performed a systematic review of scientific literature about TCM and AI. Moreover, the practical problems of TCM intellectualization, the current situation and demand of TCM, and the influence of AI in the TCM field are discussed by searching for literature using TCM scientific databases, reference lists, expert consultation, and targeted websites. Finally, we look forward to the application prospects of AI and propose a possible future direction of intelligent TCM in the current health-care system in China.

The first total synthesis of dracaenins A and B is achieved in four steps. The synthesis features the convergent coupling of three readily available fragments with minimized use of protecting groups. The chemical synthesis enables the discovery of their activity in stimulating platelet aggregation, and thus, sheds light on the possible origin of the hemostatic effect of dragon's blood.

Metabolic engineering improvement of plants will play an essential role in future agriculture, but this largely depends on the establishment of genetic transformation.Stephania tetrandraS. Moore is a traditional Chinese medicine used for rheumatalgia that accumulates benzylisoquinoline alkaloids as its main active ingredients. Wild or farmed plants have remained the main source of these essential medicines, resulting in supply pressure due to the scarcity of wild plant resources and the slow growth rate in cultivation. Here, we constructedAgrobacterium rhizogenes(C58C1)-mediated hairy root culture and a co-transformation system inS. tetrandrato obtain a new source of bisbenzylisoquinoline alkaloids production. We show that the biomass of the hairy roots increased by 10-fold, and the content of tetrandrine reached 8.382 ± 0.160 mg/g DW after 50 days of cultivation. In addition, overexpression of (R, S)-norcoclaurine 6-O-methyltransferase (6OMT) gene or treatment of hairy roots with methyl jasmonate (MJ) increased protoberberine alkaloid content. This work provides a method of obtaining hairy roots and a genetic transformation system forS. tetrandra, not only broadening the access toS. tetrandraresources, but also laying a foundation for further elucidation of the biosynthesis of tetrandrine and related alkaloids.

Salvia is a large genus in traditional Chinese medicine with hundreds of species. Tanshinones are a highly representative class of exclusive compounds found in the Salvia genus that exhibit significant biological activity. Tanshinone components have been identified in 16 species of the Salvia genus. The CYP76AH subfamily (P450) is crucial for the synthesis of tanshinone due to its catalytic generation of polyhydroxy structures. 420CYP76AH genes were obtained, clear clustering relationships. In this study 15 CYP76AH genes from 10 Salvia species were cloned and studied from the perspectives of evolution and catalytic efficiency. Structure-function relationship revealed several conserved residues which might be related to the function of CYP76AHs. Amino acids (97I, 116V, and 290T) are conserved in CYP76AH1 group, while amino acids (117G, 208S, 237Y, and 479F) are CYP76AH3 group protein sequence characteristics with unique enzyme function.This research holds significant implications for the classification of the Salvia genus and provide efficient catalytic elements for the synthetic biology production of tanshinones.Keywords: Salvia; CYP76AH; P450; biosynthesis; functional gene

Salvia miltiorrhiza Bunge (Danshen) is a traditional Chinese herb with significant medicinal value. The yield and quality of Danshen are greatly affected by climatic conditions, in particular high temperatures. Heat shock factors (Hsfs) play important regulatory roles in plant response to heat and other environmental stresses. However, little is currently known about the role played by the Hsf gene family in S. miltiorrhiza. Here, we identified 35 SmHsf genes and classified them into three major groups: SmHsfA (n = 22), SmHsfB (n = 11), and SmHsfC (n = 2) using phylogenetic analysis. The gene structure and protein motifs were relatively conserved within subgroups but diverged among the different groups. The expansion of the SmHsf gene family was mainly driven by whole-genome/segmental and dispersed gene duplications. The expression profile of SmHsfs in four distinct organs revealed its members (23/35) are predominantly expressed in the root. The expression of a large number of SmHsfs was regulated by drought, ultraviolet, heat and exogenous hormones. Notably, the SmHsf1 and SmHsf7 genes in SmHsfB2 were the most responsive to heat and are conserved between dicots and monocots. Finally, heterologous expression analysis showed that SmHsf1 and SmHsf7 enhance thermotolerance in yeast. Our results provide a solid foundation for further functional investigation of SmHsfs in Danshen plants as a response to abiotic stresses.

Coix lachryma-jobi L. is an excellent plant resource that has a concomitant function for medicine, foodstuff and forage in China. At present, the commonly used cultivar for both medicine and foodstuff is Xiaobaike, and the cultivar for foraging is Daheishan. However, differences in the internal composition of plants lead to the expression of different phenotypic traits. In order to comprehensively elucidate the differences in nutrient composition changes in Coix seeds, a non-targeted metabolomics method based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) was used to analyze the metabolic changes in Coix seeds at different developmental stages. An edible Coix relative (Xiaobaike) and a feeding Coix relative (Daheishan) were selected as the research subjects. In the metabolome analysis of Coix seed, 314 metabolites were identified and detected, among which organic acids, carbohydrates, lipids, nucleotides and flavonoids were the main components. As an important standard for evaluating the quality of Coix seed, seven lipids were detected, among which fatty acids included not only even-chain fatty acids, but also odd-chain fatty acids, which was the first time detecting a variety of odd-chain fatty acids in Coix seed. The analysis of the compound contents in edible and feeding-type Coix lachryma-jobi L. and the lipid content at the mature stage showed that, among them, arachidic acid, behenic acid, heptadecanoic acid, heneicosanoic acid and pristanic acid may be the key compounds affecting the lipid content. In addition, in the whole process of semen coicis maturation, edible and feeding Coix show similar trends, and changes in the third period show clear compounds in the opposite situation, suggesting that edible and feeding Coix not only guarantee the relative stability of species but also provide raw materials for genetic breeding. This study provides valuable information on the formation of the edible and medicinal qualities of Coix.

Pregnancy pulse diagnosis is an important part of traditional Chinese medicine. In this literature, we propose a hybrid deep learning framework by combining the network advantages of one-dimensional convolutional neural network(1DCNN), gated recurrent unit(GRU) and attention mechanism(ATT), which realized automatic identification and classification of pregnancy period through wrist pulse data. First, the wrist pulse signals of 120 healthy pregnant women in different stages of pregnancy were collected. Second, a hybrid networks for classification in three stages of pregnancy pulse was designed, which is comprised of six 1DCNN blocks and GRU module and attention module. Specifically, the proposed 1DCNN layer are adopted to extract local features from the input wrist pulse data and GRU unit was utilized for overall pulse sequence learning. In addition, the attention mechanism assigned different weights to feature parts according to pulse trends to focus and highlight effective features. Finally, the designed network was used to realize the discrimination of pregnancy pulse. On our local research dataset evaluation, the accuracy of pulse classification of this network for the three stages achieves encouraging results of 93.7%, 93.6%, and 94%, respectively. Furthermore, the model reaches 90.4%, 90.7%, 90.6% and 98% in terms of average precision, sensitivity and F1 score and AUC, respectively. The experiment shows that the designed network has a good reference value for the auxiliary diagnosis of TCM pregnancy pulse diagnosis, which is conducive to promoting the development of modernization of TCM.

The coronavirus disease 2019 (COVID-19) pandemic is an ongoing global health concern, and effective antiviral reagents are urgently needed. Traditional Chinese medicine theory-driven natural drug research and development (TCMT-NDRD) is a feasible method to address this issue as the traditional Chinese medicine formulae have been shown effective in the treatment of COVID-19. Huashi Baidu decoction (Q-14) is a clinically approved formula for COVID-19 therapy with antiviral and anti-inflammatory effects. Here, an integrative pharmacological strategy was applied to identify the antiviral and anti-inflammatory bioactive compounds from Q-14. Overall, a total of 343 chemical compounds were initially characterized, and 60 prototype compounds in Q-14 were subsequently traced in plasma using ultrahigh-performance liquid chromatography with quadrupole time-of-flight mass spectrometry. Among the 60 compounds, six compounds (magnolol, glycyrrhisoflavone, licoisoflavone A, emodin, echinatin, and quercetin) were identified showing a dose-dependent inhibition effect on the SARS-CoV-2 infection, including two inhibitors (echinatin and quercetin) of the main protease (M pro ), as well as two inhibitors (glycyrrhisoflavone and licoisoflavone A) of the RNA-dependent RNA polymerase (RdRp). Meanwhile, three anti-inflammatory components, including licochalcone B, echinatin, and glycyrrhisoflavone, were identified in a SARS-CoV-2-infected inflammatory cell model. In addition, glycyrrhisoflavone and licoisoflavone A also displayed strong inhibitory activities against cAMP-specific 3′,5′-cyclic phosphodiesterase 4 (PDE4). Crystal structures of PDE4 in complex with glycyrrhisoflavone or licoisoflavone A were determined at resolutions of 1.54 Å and 1.65 Å, respectively, and both compounds bind in the active site of PDE4 with similar interactions. These findings will greatly stimulate the study of TCMT-NDRD against COVID-19.

Vascular complications of diabetes pose a severe threat to human health. Prevention and treatment protocols based on a single vascular complication are no longer suitable for the long-term management of patients with diabetes. Diabetic panvascular disease (DPD) is a clinical syndrome in which vessels of various sizes, including macrovessels and microvessels in the cardiac, cerebral, renal, ophthalmic, and peripheral systems of patients with diabetes, develop atherosclerosis as a common pathology. Pathological manifestations of DPDs usually manifest macrovascular atherosclerosis, as well as microvascular endothelial function impairment, basement membrane thickening, and microthrombosis. Cardiac, cerebral, and peripheral microangiopathy coexist with microangiopathy, while renal and retinal are predominantly microangiopathic. The following associations exist between DPDs: numerous similar molecular mechanisms, and risk-predictive relationships between diseases. Aggressive glycemic control combined with early comprehensive vascular intervention is the key to prevention and treatment. In addition to the widely recommended metformin, glucagon-like peptide-1 agonist, and sodium-glucose cotransporter-2 inhibitors, for the latest molecular mechanisms, aldose reductase inhibitors, peroxisome proliferator-activated receptor-γ agonizts, glucokinases agonizts, mitochondrial energy modulators, etc. are under active development. DPDs are proposed for patients to obtain more systematic clinical care requires a comprehensive diabetes care center focusing on panvascular diseases. This would leverage the advantages of a cross-disciplinary approach to achieve better integration of the pathogenesis and therapeutic evidence. Such a strategy would confer more clinical benefits to patients and promote the comprehensive development of DPD as a discipline.

Artemisia annua, Artemisia argyi, Artemisia absinthium, Artemisia leucophylla and Artemisia lavandulaefolia are five herbal species of Artemisia usually misidentified, adulterated or substituted in commerce. Using light microscopy, scanning electron microscopy and microscopic quantitative analysis, the transverse sections, morphological, powder and quantitative microscopic features of glandular trichome density and area were observed for correct authentication. The results indicated that microscopic characteristics such as the distribution of fiber bundles in the vascular bundle of the main vein, the shape of xylem, the density and type of non-glandular trichomes, the morphology of T-shaped non-glandular trichomes, the type of calcium oxalate crystals, and the number and size of glandular trichomes can be used to authenticate the five Artemisia crude herbs. Differences in the morphology and density of glandular and non-glandular trichomes are key features for the identification of five Artemisia species. Therefore, our study provides a more comprehensive microscopic identification diagram and additional microscopic evidence for the five Artemisia species. HIGHLIGHTS: This study provides a more comprehensive microscopic identification diagram and statistical information on the glandular trichome density and area for accurate authentication of five Artemisia herbs using light microscopy, scanning electron microscopy and microscopic quantitative analysis.

The influence of preparation material residues in wastewater and soil on plants has been paid more and more attention by researchers. Secondary metabolites play an important role in the application of plants. It was found that nanomaterials can increase the content of plant secondary metabolites in addition to their role in pharmaceutical preparations. For example, 800 mg/kg copper oxide nanoparticles (NPs) increased the content of p-coumaric acid in cucumber by 225 times. Nanoparticles can cause oxidative stress in plants, increase signal molecule, and upregulate the synthase gene expression, increasing the content of secondary metabolites. The increase of components such as polyphenols and total flavonoids may be related to oxidative stress. This paper reviews the application and mechanism of metal nanomaterials (Ag-NP, ZnO-NP, CeO

This paper mainly focused on the asymmetric synthesis of natural product PTOX by biosynthesis and total synthesis, and pharmacological activities of its derivatives.

Erigeron breviscapus is an important medicinal plant with high medicinal and economic value. It is currently the best natural biological drug for the treatment of obliterative cerebrovascular disease and the sequela of cerebral hemorrhage. Therefore, to solve the contradiction between supply and demand, the study of genetic transformation of E. breviscapus is essential for targeted breeding. However, establishing an efficient genetic transformation system is a lengthy process. In this study, we established a rapid and efficient optimized protocol for genetic transformation of E. breviscapus using the hybrid orthogonal method. The effect of different concentrations of selection pressure (Hygromycin B) on callus induction and the optimal pre-culture time of 7 days were demonstrated. The optimal transformation conditions were as follows: precipitant agents MgCl2 + PEG, target tissue distance 9 cm, helium pressure 650 psi, bombardment once, plasmid DNA concentration 1.0 μg·μL−1, and chamber vacuum pressure 27 mmHg. Integration of the desired genes was verified by amplifying 1.02 kb of htp gene from the T0 transgenic line. Genetic transformation of E. breviscapus was carried out by particle bombardment under the optimized conditions, and a stable transformation efficiency of 36.7% was achieved. This method will also contribute to improving the genetic transformation rate of other medicinal plants.

Fallopia multiflora (Thunb.) Harald, a vine belonging to the Polygonaceae family, is used in traditional medicine. The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging. This study describes the assembly of the F. multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data (with a contig N50 of 1.97 megabases), 1.44 gigabases of which was assigned to 11 pseudochromosomes. Comparative genomics confirmed that F. multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation. Combining genomics, transcriptomics, and metabolomics data to map a network of associated genes and metabolites, we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F. multiflora. These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes. Moreover, the reference genome of F. multiflora is a useful addition to the genomes of the Polygonaceae family.

Although there are differences in the appearance of Mountain-Cultivated Ginseng (MCG) and Garden-Cultivated Ginseng (GCG), it is very difficult to distinguish them when the samples are processed to slices or powder. Moreover, there is significant price difference between them, which leads to the widespread adulteration or falsification in the market. Thus, the authentication of MCG and GCG is crucial for the effectiveness, safety, and quality stability of ginseng. In the present study, a headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS) coupled with chemometrics approach was developed to characterize the volatile component profiles in MCG and GCG with 5-,10-,15-growth years, and subsequently to discover differentiating chemical markers. As a result, we characterized, for the first time, 46 volatile components from all the samples by using the NIST database and the Wiley library. The base peak intensity chromatograms were subjected to multivariate statistical analysis to comprehensively compare the chemical differences among the above samples. MCG5-,10-,15-years and GCG5-,10-,15-years samples were mainly divided into two groups by unsupervised principal component analysis (PCA), and 5 potential cultivation-dependent markers were discovered based on orthogonal partial least squares-discriminant analysis (OPLS-DA). Moreover, MCG5-,10-,15-years samples were divided into three blocks, and 12 potential growth-year-dependent markers enabled differentiation. Similarly, GCG5-,10-,15-years samples were also separated into three groups, and six potential growth-year-dependent markers were determined. The proposed approach could be applied to directly distinguish MCG and GCG with different growth years and to identify the differentiation chemo-markers, which is an important criterion for evaluating the effectiveness, safety, and quality stability of ginseng.

Triptolide is a valuable multipotent antitumor diterpenoid in Tripterygium wilfordii, and its C-14 hydroxyl group is often selected for modification to enhance both the bioavailability and antitumor efficacy. However, the mechanism for 14-hydroxylation formation remains unknown. Here, we discover 133 kb of tandem duplicated CYP82Ds encoding 11 genes on chromosome 12 and characterize CYP82D274 and CYP82D263 as 14-hydroxylases that catalyze the metabolic grid in triptolide biosynthesis. The two CYP82Ds catalyze the aromatization of miltiradiene, which has been repeatedly reported to be a spontaneous process. In vivo assays and evaluations of the kinetic parameters of CYP82Ds indicate the most significant affinity to dehydroabietic acid among multiple intermediates. The precursor 14-hydroxy-dehydroabietic acid is successfully produced by engineered Saccharomyces cerevisiae. Our study provides genetic elements for further elucidation of the downstream biosynthetic pathways and heterologous production of triptolide and of the currently intractable biosynthesis of other 14-hydroxyl labdane-type secondary metabolites.

The rapid and accurate authentication of traditional Chinese medicines (TCMs) has always been a key scientific and technical problem in the field of pharmaceutical analysis. Herein, a novel heating online extraction electrospray ionization mass spectrometry (H-oEESI-MS) was developed for the rapid and direct analysis of extremely complex substances without the requirement for any sample pretreatment or pre-separation steps. The overall molecular profile and fragment structure features of various herbal medicines could be completely captured within 10–15 s, with minimal sample ( 0.87, R(2)Y > 0.91, and Q(2) > 0.72), which further verified the feasibility and reliability of this comprehensive strategy for the rapid authentication of different TCMs based on H-oEESI-MS. In summary, this rapid authentication strategy realized the ultra-high-throughput, low-cost, and standardized detection of various complex TCMs for the first time, thereby demonstrating wide applicability and value for the development of quality standards for TCMs.

Benzylisoquinoline alkaloids (BIAs) are a type of secondary metabolite with clinical application value. (S)-stylopine is a special BIA which contains methylenedioxy bridge structures. CYP719As could catalyze the methylenedioxy bridge-formation on the A or D rings of protoberberine alkaloids, while displaying significant substrate regiospecificity. To explore the substrate preference of CYP719As, we cloned and identified five CyCYP719A candidates from Corydalis yanhusuo. Two CyCYP719As (CyCYP719A39 and CyCYP719A42) with high catalytic efficiency for the methylenedioxy bridge-formation on the D or A rings were characterized, respectively. The residues (Leu 294 for CyCYP719A42 and Asp 289 for CyCYP719A39) were identified as the key to controlling the regioselectivity of CYP719As affecting the methylenedioxy bridge-formation on the A or D rings by homology modeling and mutation analysis. Furthermore, for de novo production of BIAs, CyCYP719A39, CyCYP719A42, and their mutants were introduced into the (S)-scoulerine-producing yeast to produce 32 mg/L (S)-stylopine. These results lay a foundation for understanding the structure-function relationship of CYP719A-mediated methylenedioxy bridge-formation and provide yeast strains for the BIAs production by synthetic biology.

Semen coicis is not only a traditional Chinese medicine (TCM), but also a typical food in China, with significant medical and healthcare value. Because semen coicis is rich in starch and oil, it can be easily contaminated with Aspergillus flavus and its aflatoxins (AFs). Preventing and controlling the contamination of semen coicis with Aspergillus flavus and its aflatoxins is vital to ensuring its safety as a drug and as a food. In this study, the endosphere bacteria Pseudomonas palleroniana strain B-BH16-1 produced volatiles that strongly inhibited the mycelial growth and spore formation activity of A. flavus. Gas chromatography–mass spectrometry profiling revealed three volatiles emitted from B-BH16-1, of which 1-undecene was the most abundant. We obtained authentic reference standards for these three volatiles; these significantly reduced mycelial growth and sporulation in Aspergillus, with dimethyl disulfide showing the most robust inhibitory activity. Strain B-BH16-1 was able to completely inhibit the biosynthesis of aflatoxins in semen coicis samples during storage by emitting volatile bioactive components. The microscope revealed severely damaged mycelia and a complete lack of sporulation. This newly identified plant endophyte bacterium was able to strongly inhibit the sporulation and growth of Aspergillus and the synthesis of associated mycotoxins, thus not only providing valuable information regarding an efficient potential strategy for the prevention of A. flavus contamination in TCM and food, but potentially also serving as a reference in the control of toxic fungi.

SummaryShikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such asLithospermum erythrorhizonandArnebia euchroma. Phytochemical researches utilizingL. erythrorhizonandA. euchromacultured cells both indicate the existence of a competing route branching out from the shikonin biosynthetic pathway toward benzo/hydroquinones. A previous study has shown that the branch point is a putative alcohol dehydrogenase converting (Z)-3’’-hydroxygeranylhydroquinone [(Z)-3’’-OH-GHQ] to an aldehyde intermediate (E)-3’’-oxo-GHQ. However, the enzyme involved in the branch reaction is not characterized at the molecular level yet. In this study, we clone a candidate gene belonging to the cinnamyl alcohol dehydrogenase (CAD) family,AeHGO, through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines ofA. euchroma. In biochemical assays, purified AeHGO protein reversibly oxidizes (Z)-3’’-OH-GHQ to produce (E)-3’’-oxo-GHQ followed by reversibly reducing (E)-3’’-oxo-GHQ to (E)-3’’-OH-GHQ, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters show that the reaction with (Z)-3’’-OH-GHQ is about twice as efficient as with (E)-3’’-OH-GHQ, which leads to the predominance of (E)-3’’-OH-GHQ and (E)-3’’-oxo-GHQ in the equilibrium mixture. According to a previous report, (E)-3’’-oxo-GHQ can be converted to deoxyshikonofuran, a hydroquinone metabolite produced by boraginaceous plants. Considering there is a competition for accumulation between shikonin derivatives and benzo/hydroquinones in bothL. erythrorhizonandA. euchromacultured cells, AeHGO is supposed to play an important role in the metabolic regulation of shikonin biosynthetic pathway.

CYP76AH1 is the key enzyme in the biosynthesis pathway of tanshinones in Salvia miltiorrhiza, which are famous natural products with activities against various heart diseases and others. CYP76AH1 is a membrane-associated typical plant class II cytochrome P450 enzyme and its catalytic mechanism has not to be clearly elucidated. Structural determination of eukaryotic P450 enzymes is extremely challenging. Recently, we solved the crystal structures of CYP76AH1 and CYP76AH1 in complex with its natural substrate miltiradiene. The structure of CYP76AH1 complexed with miltiradiene is the first plant cytochrome P450 structure in complex with natural substrate. The studies revealed a unique array pattern of amino acid residues, which may play an important role in orienting and stabilizing the substrate for catalysis. This work would provide structural insights into CYP76AH1 and related P450s and the basis to efficiently improve tanshinone production by synthetic biology techniques.

Triterpenes are among the most diverse plant natural products, and their diversity is closely related to various triterpene skeletons catalyzed by different 2,3-oxidosqualene cyclases (OSCs). Celastrol, a friedelane-type triterpene with significant bioactivities, is specifically distributed in higher plants, such as Celastraceae species. Friedelin is an important precursor for the biosynthesis of celastrol, and it is synthesized through the cyclization of 2,3-oxidosqualene, with the highest number of rearrangements being catalyzed by friedelane-type triterpene cyclases. However, the molecular mechanisms underlying the catalysis of friedelin production by friedelane-type triterpene cyclases have not yet been fully elucidated. In this study, transcriptome data of four celastrol-producing plants from Celastraceae were used to identify a total of 21 putative OSCs. Through functional characterization, the friedelane-type triterpene cyclases were separately verified in the four plants. Analysis of the selection pressure showed that purifying selection acted on these OSCs, and the friedelane-type triterpene cyclases may undergo weaker selective restriction during evolution. Molecular docking and site-directed mutagenesis revealed that changes in some amino acids that are unique to friedelane-type triterpene cyclases may lead to variations in catalytic specificity or efficiency, thereby affecting the synthesis of friedelin. Our research explored the functional diversity of triterpene synthases from a multispecies perspective. It also provides some references for further research on the relative mechanisms of friedelin biosynthesis.

Benzylisoquinoline alkaloids (BIAs) are compounds naturally found in plants and can have significant value in clinical settings. Metabolic engineering and synthetic biology are both promising approaches for the heterologous acquisition of benzylisoquinoline alkaloids. (S)–N-methylcoclaurine 3′-hydroxylase (NMCH), a member of the CYP80 family of CYP450, is the penultimate catalytic enzyme that forms the central branch-point intermediate (S)-reticuline and plays a key role in the biosynthesis of BIAs. In this study, an NMCH gene was cloned from Corydalis yanhusuo, while in vitro reactions demonstrated that CyNMCH can catalyze (S)–N-methylcoclaurine to produce (S)-3′-hydroxy-N-methylcoclaurine. The Km and Kcat of CyNMCH were estimated and compared with those identified in Eschscholzia californica and Coptis japonica. This newly discovered CyNMCH will provide alternative genetic resources for the synthetic biological production of benzylisoquinoline alkaloids and provides a foundation to help analyze the biosynthetic pathway of BIAs biosynthesis in C. yanhusuo.

Salvia miltiorrhiza Bunge (Danshen in Chinese) is vulnerable to Fusarium wilt, which severely affects the quality of the crude drug. Mycorrhizal colonization enhances resistance to fungal pathogens in many plant species. In this study, pre-inoculation of S. miltiorrhiza with the arbuscular mycorrhizal fungi (AMF) Glomus versiforme significantly alleviated Fusarium wilt caused by Fusarium oxysporum. Mycorrhizal colonization protected S. miltiorrhiza from pathogen infection, thereby preventing a loss of biomass and photosynthesis. There were greater defense responses induced by pathogen infection in AMF pre-inoculated plants than those in non-treated plants. AMF pre-inoculation resulted in systemic responses upon pathogen inoculation, including significant increases in the protein content and activities of phenylalanine ammonia-lyase (PAL), chitinase, and β-1,3-glucanase in S. miltiorrhiza roots. In addition, mycorrhizal pre-inoculation caused upregulation of defense-related genes, and jasmonic acid (JA) and salicylic acid (SA) signaling pathway genes after pathogen infection. The above findings indicate that mycorrhizal colonization enhances S. miltiorrhiza resistance against F. oxysporum infection by enhancing photosynthesis, root structure, and inducing the expression of defense enzymes and defense-related genes on the other hand.

The genus Coptis belongs to the Ranunculaceae family, containing 15 recognized species highly diverse in morphology. It is a conspicuous taxon with special evolutionary position, distribution pattern and medicinal value, which makes it to be of great research and conservation significance. In order to better understand the evolutionary dynamics of Coptis and promote more practical conservation measures, we performed plastome sequencing and used the sequencing data in combination with worldwide occurrence data of Coptis to estimate genetic diversity and divergence times, rebuild biogeographic history and predict its potential suitable distribution area. The average nucleotide diversity of Coptis was 0.0067 and the hotspot regions with the highest hypermutation levels were located in the ycf1 gene. Coptis is most likely to have originated in North America and Japanese archipelago and has a typical Eastern Asian and North American disjunct distribution pattern, while the species diversity center is located in Mid-West China and Japan. The crown age of the genus is estimated at around 8.49 Mya. The most suitable climatic conditions for Coptis were as follows: precipitation of driest quarter > 25.5 mm, annual precipitation > 844.9 mm and annual mean temperature -3.1 to 19 °C. The global and China suitable area shows an upward trend in the future when emission of greenhouse gases is well controlled, but the area, especially in China, decreases significantly without greenhouse gas policy interventions. The results of this study provide a comprehensive insight into the Coptis evolutionary dynamics and will facilitate future conservation efforts.

Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies of medicinal plants have been performed to identify molecular markers of species and functional genes controlling key biological traits, as well as to understand biosynthetic pathways of bioactive metabolites and the regulatory mechanisms of environmental responses. Omics technologies have been widely applied to medicinal plants, including as taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics and mutagenomics. However, because of the complex biological regulation network, single omics usually fail to explain the specific biological phenomena. In recent years, reports of integrated multi-omics studies of medicinal plants have increased. Until now, there have few assessments of recent developments and upcoming trends in omics studies of medicinal plants. We highlight recent developments in omics research of medicinal plants, summarise the typical bioinformatics resources available for analysing omics datasets, and discuss related future directions and challenges. This information facilitates further studies of medicinal plants, refinement of current approaches and leads to new ideas.

There is mounting evidence demonstrating that oral dysbiosis causes periodontal disease and promotes the development of cardiovascular disease. The advancement of omics techniques has driven the optimization of oral microbiota species analysis and has provided a deeper understanding of oral pathogenic bacteria. A bi-directional relationship exists between the oral microbiota and the host, and oral-gut microbiota transfer is known to alter the composition of the gut microbiota and may cause local metabolic disorders. Furthermore, cardiovascular health can also be highly affected by oral microbiota functions and metabolites, including short-chain fatty acids (SCFAs), nitric oxide (NO), hydrogen sulfide (H2S), and some lipid metabolites. Studies have found that trimethylamine oxide (TMAO) may have adverse effects on cardiovascular health, whereas SCFAs, NO, and H2S have cardioprotective effects. SCFAs and H2S exert varying oral and cardiovascular effects, however reports on this specific topic remain controversial. Previous evidences are accustomed to summarizing the functions of oral microbiota in the context of periodontitis. The direct relationship between oral microbiota and cardiovascular diseases is insufficient. By systematically summarizing the methods associated with oral microbiota transplantation (OMT), this review facilitates an investigation into the causal links between oral microbiota and cardiovascular disease. The concomitant development of omics, bioinformatics, bacterial culture techniques, and microbiota transplantation techniques is required to gain a deeper understanding of the relationship between oral microbiota and cardiovascular disease occurrence.

Nonalcoholic steatohepatitis (NASH), as the aggressive form of nonalcoholic fatty liver disease (NAFLD), rapidly becomes the leading cause of end-stage liver disease or liver transplantation. Nowadays, there has no approved drug for NASH treatment. Diosgenin possesses multiple beneficial effects towards inhibition of lipid accumulation, cholesterol metabolism, fibrotic progression and inflammatory response. However, there has been no report concerning its effects on NASH so far. Using methionine and choline-deficient (MCD) feeding mice, we evaluated the anti-NASH effects of diosgenin. 16 S rDNA was used to investigate gut microbiota composition. Transcriptome sequencing, LC/MS and GC/MS analysis were used to evaluate bile acids (BAs) metabolism and their related pathway. Compared with the MCD group, diosgenin treatment improved the hepatic dysfunction, especially decreased the serum and hepatic TC, TG, ALT, AST and TBA to nearly 50%. Content of BAs, especially CA and TCA, were decreased from 59.30 and 26.00-39.71 and 11.48 ng/mg in liver and from 0.96 and 2.1-0.47 and 1.13 μg/mL in serum, and increased from 7.01 and 11.08-3.278 and 5.11 ng/mg in feces, respectively. Antibiotic and fecal microbiota transplantation (FMT) treatment further confirmed the therapeutic effect of diosgenin on gut microbiota, especially Clostridia (LDA score of 4.94), which regulated BAs metabolism through the hepatic FXR-SHP and intestinal FXR-FGF15 pathways. These data indicate that diosgenin prevents NASH by altering Clostridia and BAs metabolism. Our results shed light on the mechanisms of diosgenin in treating NASH, which pave way for the design of novel clinical therapeutic strategies.