Whole Genome Sequencing Reveals Novel Insights about the Biocontrol Potential of Burkholderia ambifaria CF3 on Atractylodes lancea.

Root rot caused by Fusarium spp. is the most destructive disease on Atractylodes lancea, one of the large bulks and most common traditional herbal plants in China. In this study, we isolated a bacterial strain, CF3, from the rhizosphere soil of A. lancea and determined its inhibitory effects on F. oxysporum in both in vitro and in vivo conditions. To deeply explore the biocontrol potential of CF3, we sequenced the whole genome and investigated the key pathways for the biosynthesis of many antibiotic compounds. The results revealed that CF3 is a member of Burkholderia ambifaria, harboring two chromosomes and one plasmid as other strains in this species. Five antibiotic compounds were found that could be synthesized due to the existence of the bio-synthesis pathways in the genome. Furthermore, the synthesis of antibiotic compounds should be confirmed by in vitro experiments and novel compounds should be purified and characterized in further studies.

Biological control and plant growth promotion properties of Streptomyces albidoflavus St-220 isolated from Salvia miltiorrhiza rhizosphere.

Root rot disease caused by Fusarium oxysporum is a devastating disease of Salvia miltiorrhiza and dramatically affected the production and quality of Sa. miltiorrhiza. Besides the agricultural and chemical control, biocontrol agents can be utilized as an additional solution. In the present study, an actinomycete that highly inhibited F. oxysporum was isolated from rhizosphere soil and identified as based on morphological and molecular characteristics. Greenhouse assay proved that the strain had significant biological control effect against Sa. miltiorrhiza root rot disease and growth-promoting properties on Sa. miltiorrhiza seedlings. To elucidate the biocontrol and plant growth-promoting properties of St-220, we employed an analysis combining genome mining and metabolites detection. Our analyses based on genome sequence and bioassays revealed that the inhibitory activity of St-220 against F. oxysporum was associated with the production of enzymes targeting fungal cell wall and metabolites with antifungal activities. Strain St-220 possesses phosphate solubilization activity, nitrogen fixation activity, siderophore and indole-3-acetic acid production activity in vitro, which may promote the growth of Sa. miltiorrhiza seedlings. These results suggest that St. albidoflavus St-220 is a promising biocontrol agent and also a biofertilizer that could be used in the production of Sa. miltiorrhiza.

The complete chloroplast genome sequence of Euphorbia lathyris L. (Euphorbiaceae).

Euphorbia lathyris L. is a well-known bioenergy plant cultivated in many parts of the world. In this study, we sequenced the complete chloroplast (cp) genome sequence of E. lathyris to investigate its phylogenetic relationship in the family Euphorbiaceae. The cp genome was 163,738 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 26,837 bp) separated by a large single-copy region (LSC: 91,783 bp) and a small single-copy region (SSC: 18,281 bp). The GC content of whole cp genome is 35.6%. Annotation showed the presence of 113 unique genes with 79 protein-coding genes, four tRNA genes, and 30 rRNA genes. Phylogenetic analysis indicated that E. lathyris was in the basal position of subgen. Esula, closely related to sect. Esula and sect. Helioscopiae.

Tracing the Geographical Origins of Dendrobe (Dendrobium spp.) by Near-Infrared Spectroscopy Sensor Combined with Porphyrin and Chemometrics.

Dendrobe (Dendrobium spp.) is a traditional medicinal and edible food, which is rich in nutrients and contains biologically active metabolites. The quality and price of dendrobe are related to its geographical origins, and high quality dendrobe is often imitated by low quality dendrobe in the market. In this work, near-infrared (NIR) spectroscopy sensor combined with porphyrin and chemometrics was used to distinguish 360 dendrobe samples from twelve different geographical origins. Partial least squares discriminant analysis (PLSDA) was used to study the sensing performance of traditional NIR and tera-(4-methoxyphenyl)-porphyrin (TMPP)-NIR on the identification of dendrobe origin. In the PLSDA model, the recognition rate of the training and prediction set of the TMPP-NIR could reach 100%, which was higher than the 91.85% and 91.34% of traditional NIR. And the accuracy, sensitivity, and specificity of the TMPP-NIR sensor are all 1.00. The mechanism of TMPP improving the specificity of NIR spectroscopy should be related to the π-π conjugated system and the methoxy groups of TMPP interact with the chemical components of dendrobe. This study reflected that NIR spectrum with TMPP sensor was an effective approach for identifying the geographic origin of dendrobe.

A Practical Protocol for a Comprehensive Evaluation of Sulfur Fumigation of Trichosanthis Radix Based on Both Non-Targeted and Widely Targeted Metabolomics.

Trichosanthis Radix (TR) is one of the most severely sulfur-fumigated herbs in the market, whose transformation mechanism of chemical compositions and sulfur-fumigation markers of TR have not been clarified. To excavate characteristic sulfur-fumigation markers of TR samples, this study brings up a practical protocol using both ultra-performance liquid chromatography/quadrupole time-of-flight-mass spectrum (UPLC-ESI-QTOF-MS/MS)-based non-targeted metabolomics and ultra-performance liquid chromatography/electrospray ionization/quadrupole multiple-stage linear ion-trap mass spectrum (UPLC-ESI-QTRAP-MS/MS)-based widely targeted metabolomics. The results of study demonstrated that five characteristic markers are sulfur-containing components, which were identified as p-Hydroxybenzyl hydrogen sulfite, cucurbitacin D sulfite I, cucurbitacin D sulfite II, cucurbitacin B sulfite I, and cucurbitacin B sulfite II, respectively. Additionally, cucurbitacin B and D were also filtered and identified as the characteristic sulfur-fumigation markers. Meanwhile, the different sulfur-fumigation extent of TR samples was tested by chemical transformations analysis and sulfur dioxide residues test. Further, 58.16% (139 of 239) of the differential metabolites content significantly reduced in sulfur-fumigated TR samples. Besides, 20 kinds of non-sulfur marker metabolites were tested to evaluate the quality of TR samples before and after sulfur fumigation, predominantly including phenolic acids, amino acids, lipids and nucleotides. Taking TR as an example, this work provides a comprehensive practical protocol for the quality supervision of sulfur-fumigation herbs.

Pharmacodynamic material basis of traditional Chinese medicine based on biomacromolecules: a review.

Biomacromolecules, the first components of bioactive substances in traditional Chinese medicines (TCM) have wide bioactivity-related efficacy but have not yet been fully appreciated compared to small molecule components. The present review brings a novel and systemic point of view to deepen the understanding of the pharmacodynamic material basis of TCM based on biomacromolecules (polysaccharides, proteins and nucleic acids). Biomacromolecules have been, are and will have considerable roles in the efficacy of Chinese medicine, as evidenced by the number of biological activities related to traditional clinical efficacy. The direct and indirect mechanisms of biomacromolecules are further accounted for in a variety of neurotransmitters, hormones, and immune substances to maintain immune function in both sensitive and stable equilibrium. The biological functions of biomacromolecules have been elaborated on in regard to their roles in the process of plant growth and development to the relationship between primary metabolism and secondary metabolism and to the indispensable role of polysaccharides, proteins, and nucleic acids in the quality formation of TCM. Understanding the functional properties and mechanisms of biological macromolecules will help to demystify the drug properties and health benefits of TCM.

CYP76B74 Catalyzes the 3''-Hydroxylation of Geranylhydroquinone in Shikonin Biosynthesis.

Shikonin and its derivatives are the most abundant naphthoquinone pigments formed in species of the medicinally and economically valuable Boraginaceae. A key step in the shikonin biosynthetic pathway, namely the C-3'' hydroxylation of the prenylated phenolic intermediate geranylhydroquinone, is expected to be catalyzed by a cytochrome P450. To identify cytochrome P450 candidates with transcription profiles similar to those of genes known to be involved in shikonin biosynthesis, we carried out coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines and examined the spatial expression of candidate genes in different organs of Arnebia euchroma In biochemical assays using geranylhydroquinone as the substrate, CYP76B74 exhibited geranylhydroquinone 3''-hydroxylase activity and produced 3''-hydroxy-geranylhydroquinone. In CYP76B74 RNA interference A. euchroma hairy roots, shikonin derivative accumulation decreased dramatically, which demonstrated that CYP76B74 is required for shikonin biosynthesis in the plant. Phylogenetic analysis confirmed that CYP76B74 belonged to the CYP76B subfamily and was most likely derived from an ancestral geraniol 10-hydroxylase. In a subcellular localization analysis, a GFP-CYP76B74 fusion localized to endoplasmic reticulum membranes. Our results demonstrate that CYP76B74 catalyzes the key hydroxylation step in shikonin biosynthesis with high efficiency. The characterization of the CYP76B74 described here paves the way for further exploration of the ring closure reactions generating the naphthoquinone skeleton as well as for the alternative metabolism of geranylhydroquinone 3''-hydroxylase to dihydroechinofuran.

Elucidation of Characteristic Sulfur-Fumigated Markers and Chemical Transformation Mechanism for Quality Control of Achyranthes bidentate Blume Using Metabolome and Sulfur Dioxide Residue Analysis.

Achyranthes bidentata Blume (AB) is a health food and a sulfur-free herbal medicine that is one of the most heavily sulfur-fumigated herbs in the marketplace. In this work, a comprehensive approach using ultra-performance liquid chromatography coupled with quadrupole time-of-flight-MS (UPLC-Q-TOF-MS) and multivariate statistical analysis was developed to identify characteristic sulfur-fumigation markers, elucidate chemical transformation mechanisms and characterize the degree of sulfur-fumigation of AB. Non-fumigated and sulfur-fumigated AB samples were compared by UPLC-Q-TOF-MS/MS analysis. Three triterpene saponins (Betavulgarosides II-IV) and two amides (Feruloyl-4-O-methyldopamine and Moupinamide) were identified as characteristic markers, which were positively correlated with two active AB components, namely oleanic acid and ferulic acid, respectively. Moreover, the extent of the sulfur-fumigation under different weight ratios of sulfur to herbal materials (1:20, 1:40, and 1:80) was analyzed based on chemical transformations and sulfur dioxide residues. Further verification showed that the ratio of 1:40 within 1 h was reasonable and efficient for herb quality preservation and assurance. This study provides a reliable sulfur-fumigation protocol for the quality control of AB and other herbs.

[Geographical origin discriminant of Dendrobium officinale based on stable isotope ratios].

The isotopic ratios of strontium isotope (Sr) and light elements (C/H/O/N) in Dendrobium officinale from different producing areas (Shaoguan, Guangdong; Yulin, Guangxi; Shibing, Guizhou; Wenshan, Yunnan and Zhejiang province) were determined with thermal ionization mass spectrometry (TI-MS) and isotope ratio mass spectrometry (IRMS)．The differences of the stable isotope ratios in D. officinale were obtained by the variance analysis and the correlation analysis, and pattern recognition techniques with principal component analysis (PCA) was used to classify the geographical origins of D. officinale from different producing areas．The isotopic ratios of strontium isotope can be used to identified D. officinale in Zhejiang province, and the isotopic ratios of light elements showed the difference followed with the different producing areas. For δD and δ¹8 O in samples, maybe influenced by the environment effect. A positive correlation was found between δD and δ ¹8O.The principal component analysis was used to discern the samples of D. officinale from different producing areas based on detection technology of stable isotope ratios.These results revealed that it was possible and feasible to classify the geographical origin of D. officinale by the method of determination of isotopes,and provided a new method to identificate origin information of Chinese medicinal materials.

[Sulfur dioxide limit standard and residues in Chinese medicinal materials].

The traditional sulfur fumigation processing method has been widely used in the initial processing and storage of traditional Chinese medicinal materials due to its economy, efficiency, convenience, high operability and effect on mold and insect prevention. However, excessive sulfur fumigation of traditional Chinese medicinal materials would lead to the changes in chemical compositions, and even endanger human health. This study showed that traditional Chinese medicinal materials were sulfur fumigated directly after being harvested for quick drying, or fumigated after being weted in the storage process for preventing mold and insects. We found that the sulfur dioxide limits for traditional Chinese medicinal materials were stricter than those for foods. Based on the existing limit standards, we obtained the data of sulfur dioxide residues for 35 types of traditional Chinese medicinal materials in a total of 862 batches. According to the limit standard in the Chinese Pharmacopoeia (150， 400 mg·kg⁻¹), the average over-standard rate of sulfur dioxide was as high as 52.43%, but it was reduced to 29.47% if calculated based on the limit for vegetable additive standard (500 mg·kg⁻¹). Sulfur fumigation issue shall be considered correctly: sulfur dioxide is a type of low toxic substance and less dangerous than aflatoxin and other highly toxic substances, and a small amount of residue would not increase the toxicity of traditional Chinese medicinal materials. However, sulfur fumigation might change the content of chemical substances and affect the quality of traditional Chinese medicinal materials. Furthermore, the exposure hazards of toxic substances are comprehensively correlated with exposure cycle, exposure frequency, and application method. In conclusion, it is suggested to strengthen the studies on the limit standard of traditional Chinese medicinal materials, formulate practical and feasible limit standard for sulfur dioxide residues in traditional Chinese medicinal materials that are consistent with the medication characteristics of traditional Chinese medicinal materials and can guarantee people's demand for safe medication.

[Quantitative analysis and stability of p-hydroxybenzyl hydrogen sulfite in sulfur-fumigated Gastrodiae Rhizoma].

Studies on the characteristic chemical markers of sulfur fumigation have become an effective auxiliary way for quality control of traditional Chinese medicine. This study established a quantitative analysis method for the determination of p-hydroxybenzyl hydrogen sulfite (p-HS) in Gastrodiae Rhizoma (GR) based on UPLC-MS/MS. Then, 37 batches of GR were screened, and the results showed that 27 batches of them were sulfur-fumigated. Especially, the GR samples in Yunnan producing areas were sulfur-fumigated more seriously. Based on the stability of p-HS after different storage time and heat treatment methods, it was found that the content of p-HS was stable and reliable in the storage period of 8 months and under normal heat treatment (50, 60, 70, 80 °C) conditions. In conclusion, this study shows a high sensitivity, good selectivity and good stability of p-HS, which can provide reference for the quality control and sulfur fumigation screening of GR.

[Changes of chemical compositions and sulfur dioxide residues of Gastrodiae Rhizoma with different storage times].

To study the effect of different storage time on the chemical compositions and sulfur dioxide residues of sulfur-fumigated Gastrodiae Rhizoma (GR), and provide scientific basis for solving the quality and safety issues of sulfur-fumigated traditional Chinese medicinal materials. GR, sulfur-fumigated GR and its medicinal slices were stored under the same conditions, and then 8 active ingredients and sulfur dioxide residues were measured respectively. The results showed that the content of gastrodins in sulfur-fumigated GR and its medicinal slices was significantly lower than that in the non-fumigated GR. Moreover, the content of sulfur dioxide residue in sulfur-fumigated GR was significantly higher than that in its medicinal slices. That is to say, sulfur fumigation degree had significantly higher effect on GR quality as compared with its medicinal slices. During the whole storage time (8 months), the content of the eight chemical components in GR was not changed greatly in general. However, after the storage for 4 months, the content of 8 components and sulfur dioxide residues in all of GR samples were significantly changed. In particular, the content of sulfur dioxide residue in GR medicinal materials decreased up to 50% or more.

[Quality changes in Gastrodia Rhizoma of different origins and forms before and after sulfur fumigation].

As Gastrodiae Rhizoma (GR) is one of the herbs more seriously affected by sulfur fumigation, so its quality has been always of a great concern. In this paper, GR samples collected from eight main producing areas and in three forms were fumigated with sulfur and quantitatively and qualitatively analyzed based on UPLC-Q-TOF-MS/MS. The results showed that the contents of gastrodin, parishin, parishin B and parishin C were decreased, while the content of parishin E was increased after sulfur fumigation treatment. Besides, a new sulfur marker named p-hydroxybenzyl hydrogen sulfite was produced in sulfur-fumigated GR samples. As compared with producing origins, forms had a greater impact on the quality of GR, especially in Hongtianma and Wutianma. Besides, the contents of gastrodins and parishins in Hongtianma from Jilin were lowest as compared with those in other producing areas. This might be correlated with planting patterns and environmental factors. In conclusion, sulfur fumigation has a more obvious impact on the quality of GR than origins and forms, which is attributed to the generation of new sulfur fumigated markers.

[Secondary metabolic responses to treatment of 2-aminoindan-2-phosphonic acid in cell lines from Arnebia euchroma].

The accumulation of rosmarinic acid, acetylshikonin, deoxyshikonin, ß, ß'-dimethylacrylshikonin and isovalerylshikonin was investigated in cell suspension cultures of Arnebia euchroma (Royle) Johnst under the influence of 2-aminoindan-2-phosphonic acid (AIP), an inhibitor of phenylalanine ammonia lyase (PAL), and of the effector methyl jasmonate (MeJA). The results showed that methyl jasmonate promoted the accumulation of rosmarinic acid and shikonin derivatives. Conversely, 2-aminoindan-2-phosphonic acid suppressed the formation of rosmarinic acid, which indicated that AIP, indeed, was able to inhibit the phenylpropanoid pathway in A. euchroma. Meanwhile, the content of total shinkonins and other four kinds of shikonin derivatives, though varied in degrees, was also inhibited. And the inhibition was dose-dependent and time-dependent. Acetylshikonin responsed most rapidly to the treatment of AIP, the content reduced after 24 h of treatment and decreased to only half of those untreated control 48 h after teratment. ß, ß'-Dimethylacrylshikonin, difffer from acetylshikonin, responded much slowly to the treatment, inhibition could only be observed 96 h later. These suggest that phenylpropanoid pathway plays an important role in the shikoninsbiosynthesis, and this study provides a reference for the further research in metabolic regulation of producing shikonins by cell culture technology and biosynthesis pathways of shikonin derivatives. Still, shikonins biosynthesis pathways is complicated, the exact dose- and time-effect relationship of AIP and interaction between AIP and other effectors like MeJA need further research.

Production of 3-geranyl-4-hydroxybenzoate acid in yeast, an important intermediate of shikonin biosynthesis pathway.

Shikonin and its derivatives are the main active components in the medicinal plant Arnebia euchroma and possess extensive pharmaceutical properties. In this study, we developed an optimized yeast system to obtain high-level production of 3-geranyl-4-hydroxybenzoate acid (GBA), an important intermediate involved in shikonin biosynthesis pathway. For host selection, recombinant expression of p-hydroxybenzoate:geranyltransferase (PGT) derived from A. euchroma was performed in Saccharomyces cerevisiae WAT11U strain and high yield monoterpene strain. In shake flask culture with 1 mM p-hydroxybenzoate acid (PHBA), they could yield GBA at 0.1567 and 20.8624 mg L-1, respectively. Additionally, AePGT6 showed higher enzymatic activity than its homologs. Moreover, by combining improvement in the homologous mevalonate pathway with reconstruction in the heterologous shikimic pathway, a de novo GBA synthesis pathway was constructed in StHP6tHC with co-overexpressed SctHMG1, optimized EcUbiC and AePGT6. A high titer of 179.29 mg L-1 GBA was achieved in StHP6tHC under shake flask fermentation with 1 mM PHBA. These results suggest that yeast could be engineered systematically to enable an efficient monoterpene-quinone or naphthoquinone production.

A practical protocol for comprehensive evaluation of sulfur-fumigation of Gastrodia Rhizoma using metabolome and health risk assessment analysis.

Gastrodia Rhizoma is one of the most heavily sulfur-fumigated edible and medical herbs in the marketplace. We developed a practical protocol using an ultra-performance liquid chromatography coupled with quadrupole time-of-flight-MSE (UPLC/QTOF-MSE)-based metabolome and health risk assessment model to identify characteristic sulfur-fumigated markers, dissect chemical transformation mechanisms, and control the quality of sulfur-fumigated Gastrodia Rhizoma. Two sulfur-containing p-hydroxybenzyl products, one sulfur-containing disaccharide, one glycolipid, and two phospholipids were selected and identified as markers based on multivariate statistical analysis. In particular, the sulfur-containing markers p-hydroxybenzyl hydrogen sulfite and trace p-mercaptobenzyl hydrogen sulfate were positively correlated with the active major phenolics. Moreover, a practical index the time of the minimum content was useful for evaluating the extent of the sulfur-fumigation under different weight ratios of the sulfur to herbal materials (1:20, 1:40, and 1:80). Ultimately, the 1:40 ratio within 1h of sulfur-fumigation was considered as safe and efficient for herb quality preservation under the maximum residue limit of 750mg/kg. This study shows that the practical protocol-based discriminated markers and practical limits can be applied to quality assurance of sulfur-fumigation and non-fumigation Gastrodia Rhizoma and other edible or medical materials.

Biphenyl Phytoalexin in Sorbus pohuashanensis Suspension Cell Induced by Yeast Extract.

Biphenyls are unique phytoalexins de novo synthesized in plants in response to pathogen attack. These compounds are found in Maloideae, a subfamily of the Rosaceae. The anti-microbial activities of biphenyls have been reported in a number of studies and they appear to represent an important defense strategy against pathogens common in the Maloideae, such as species in Malus, Pyrus, Sorbus, and Chaenomeles. Here, cell suspension cultures of Sorbus pohuashanensis were established to study biphenyl phytoalexins formation after yeast extract (YE) treatment. An ultra-performance liquid chromatography (UPLC) method coupled with quadrupole time of flight mass spectrometry (Q-TOF-MS) LC-MS/MS was applied to determine the time course of these biphenyl biomarkers accumulation in YE-treated S. pohuashanensis suspension cells. The results of quantitative analyses show the content of Noraucuparin, 2'-Hydroxyaucuparin, and their glycosides initially increased, then decreased over time. The Noraucuparin content reached its highest (225.76 µg·g(-1)) at 18 h after treatment, 6 hours earlier than that of Noraucuparin 5-O-ß-d-glucopyranoside. The content of 2'-Hydroxyaucuparin reached its highest (422.75 µg·g(-1)) at 30 h after treatment, also earlier than that of its glycoside. The understanding of phytoalexin metabolism in this study may provide a basis for improving Maloideae resistance to pathogens.

[Mitogen-activated protein kinase genes of Artemisia annua and their expression analysis under Cadmium stress].

In order to study Artemisia annua under cadmium stress, whether there are corresponding MAPK genes involved in transduction of the cadmium signal. 17 AaMAPK genes, named AaMAPK1-AaMAPK17 repectively, were finally obtained by using Trinity method for de novo assembly of transcripts from SRA database and BLAST search against AtMAPK genes and determing conserved domain using a series of bioinformatics tools. There exist 16 MAPK genes contained T[D/E]Y conserved domains among the obtained genes. The expressions of these genes were analyzed by Real-time PCR under cadmium stress. The results showed that the expressions level of AaMAPK3 and AaMAPK10 were down-regulated and MAPK7, MAPK9 and MAPK12 were up-regulated. These indicated that there exist corresponding MAPK genes involved in transduction of the cadmium signal.

[Transcriptome-based gene mining and bioinformatics analysis of p-hydroxybenzoate geranyltransferase genes in Arnebia euchroma].

The p-hydroxybenzoate geranyltransferases(PGT) play an important role in the biosynthesis pathways of shikonin derivatives. Six PGTs were obtained from transcriptome datebase of Arnebia euchroma by using bioinformatics methods and the proteins＇physiochemical properties they encoded were predicted. The result of protein domain prediction showed all of the six protein sequences contained the conserved domain of Ubia prenyltransferase family and possessed the motif NDxxDxxxD for prenyldiphosphate binding and a GX(K/Y)STAL sequence for putative aromatic ring binding. The phylogenetic tree showed that PGT and p-hydroxybenzoate polyprenyltransferase(PPT) belonged to two different clades. The results of gene expression analyses showed that the expression levels in the red shikonin-proficient line and the overground part of A. euchroma that could produce shikonin derivatives was much higher than the white shikonin-deficient line and the underground part, which suggested a positive correlation between the expression levels of PGT genes and shikonin production. This study aims to lay a foudation for further understanding of the function and enzymatic properties of PGT and provide a basis for the biosynthesis pathways and metabolic regulation of shikonin derivatives.