Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism.

Caffeic acid O-methyltransferase from Ligusticum chuanxiong (LcCOMT) showed strict regiospecificity despite a relative degree of preference. Compared with caffeic acid, methyl caffeate was the preferential substrate by its low Km and high Kcat. In this study, we obtained the SAM binary (1.80 Å) and SAH binary (1.95 Å) complex LcCOMT crystal structures, and established the ternary complex structure with methyl caffeate by molecular docking. The active site of LcCOMT included phenolic substrate pocket, SAM/SAH ligand pocket and conserved catalytic residues as well. The regiospecificity of LcCOMT that permitted only 3-hydroxyl group to be methylated arise from the interactions between the active site and the phenyl ring. However, the propanoid tail governed the relative preference of LcCOMT. The ester group in methyl caffeate stabilized the anionic intermediate caused by His268-Asp269 pair, whereas caffeic acid was unable to stabilize the anionic intermediate due to the adjacent carboxylate anion in the propanoid tail. Ser183 residue formed an additional hydrogen bond with SAH and its role was identified by S183A mutation. Ile318 residue might be a potential site for determination of substrate preference, and its mutation led to the change of tertiary conformation. The results supported the selective mechanism of LcCOMT.

Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships.

BACKGROUND: The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. RESULTS: Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. CONCLUSION: The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.

Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification.

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4⁻chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymorpha and L. officinale were well clustered at family Apiaceae. The ycf4-cemA intergenic region in A. polymorpha carried a 418 bp deletion compared with L. officinale. This region was used for the development of a novel indel marker, LYCE, which successfully discriminated between A. polymorpha and L. officinale accessions. Our results provide important taxonomic and phylogenetic information on herbal medicines and facilitate their authentication using the indel marker.

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding.

Metabolic profiling and identification of the genetic varieties and agricultural origin of Cnidium officinale and Ligusticum chuanxiong.

Quality control methods for Cnidium officinale and Ligusticum chuanxiong are lacking because their quality is influenced by multiple factors. Thus, there is a need to develop a multifactorial method for measuring quality that is both standardized and practical. Here, we report a profiling method based on gas chromatography-mass spectrometry (GC-MS) to discriminate among the genetic varieties and agricultural origins of C. officinale and L. chuanxiong. Our metabolome analysis identified 68 metabolites, 13 of which were newly identified in our samples. The S-plot of the OPLS discriminant analysis enabled us to determine significant biomarkers. Using only double-compound biomarkers, the samples were successfully classified into distinct groups defined by genetic variety and cultivation origin. This method will simplify the process of searching for quality control markers that can be used to determine genetic variety and agricultural origin.

Exploratory analysis of chromatographic fingerprints to distinguish rhizoma Chuanxiong and rhizoma Ligustici.

Identification and quality control of products of natural origin, used for preventive and therapeutical goals, is required by regulating authorities, as the World Health Organization. This study focuses on the identification and distinction of the rhizomes from two Chinese herbs, rhizoma Chuanxiong (from Ligusticum chuanxiong Hort.) and rhizoma Ligustici (from Ligusticum jeholense Nakai et Kitag), by chromatographic fingerprints. A second goal is using the fingerprints to assay ferulic acid, as its concentration provides an additional differentiation feature. Several extraction methods were tested, to obtain the highest number of peaks in the fingerprints. The best results were found using 76:19:5 (v/v/v) methanol/water/formic acid as solvent and extracting the pulverized material on a shaking bath for 15 min. Then fingerprint optimization was done. Most information about the herbs, i.e. the highest number of peaks, was observed on a Hypersil ODS column (250 mm × 4.6 mm ID, 5 µm), 1.0% acetic acid in the mobile phase and employing within 50 min linear gradient elution from 5:95 (v/v) to 95:5 (v/v) acetonitrile/water. The final fingerprints were able to distinguish rhizoma Chuanxiong and Ligustici, based on correlation coefficients combined with exploratory data analysis. The distinction was visualized using Principal Component Analysis, Projection Pursuit and Hierarchical Clustering Analysis techniques. Quantification of ferulic acid was possible in the fingerprints of both rhizomes. The time-different intermediate precisions of the fingerprints and of the ferulic acid quantification were shown to be acceptable.

Authentication of the oriental medicinal plant Ligusticum tenuissimum (Nakai) Kitagawa (Korean Go-Bon) by multiplex PCR.

The oriental medicinal plant Ligusticum tenuissimum (Korean name, Go-Bon) is widely used in Korea and China. L. tenuissimum (Go-Bon) has been employed in the treatment of headache and common cold, and as a fever remedy. The internal transcribed spacer (ITS) region was sequenced from thirty-four Go-Bon samples collected from botanical gardens and markets in Korea and China to identify and authenticate L. tenuissimum. Based on the ITS sequences, the thirty-four Go-Bon samples were classified into three groups: L. tenuissimum (Korean Go-Bon), L. jeholense (Chinese Go-Bon), and unknown Chinese Ligusticum species. Three specific primers were designed to identify the three groups of Ligusticum species using multiplex PCR. The established multiplex-PCR was proved to be effective for the differentiation of L. tenuissimum in commercial plant materials.

[Determination and fingerprint analysis of tetramethylpyrazine and ferulic acid in Ligusticum chuanxiong].

OBJECTIVE: To determine the contents of tetramethylpyrazine (TMP) and ferulic acid in Ligusticum chuanxiong from different producing areas and seasons. METHODS: The contents of TMP and ferulic acid were determined by HPLC, and then analyzed by Chromatographic Fingerprints. RESULTS: The contents of TMP and ferulic acid from different seasons were obviously different from each other. It was much higher in "laoxiong" than that in "naixiong". The similarity of fingerprints was high if the samples were collected from the same season, or the same areas, but not different seasons. CONCLUSIONS: The contents of TMP and ferulic acid were different from different producing areas. The evident variety of Ligusticum chuanxiong's fingerprints from different collecting seasons, Laoxiong and Naixiong, was not relevant for clinical use as the same medicine.