Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism

Fritillaria steroidal alkaloids and their multi-target therapeutic mechanisms: insights from network pharmacology

Medicinal Fritillaria herbs, known for their rich content of steroidal alkaloids, have emerged as promising candidates in the treatment of chronic diseases due to their diverse pharmacological properties. Leveraging advancements in network pharmacology and molecular docking, this study explores the multi-target mechanisms through which these alkaloids exert therapeutic effects. The integration of bioinformatics, systems biology, and pharmacology in drug discovery has provided insights into the molecular interactions and pathways influenced by Fritillaria steroidal alkaloids. This review synthesizes comprehensive literature from 1985 to 2024, revealing the potential of these compounds in addressing respiratory diseases, inflammation, and cancer. The integration of traditional Chinese medicine (TCM) with modern pharmacological techniques underscores the relevance of these compounds in next-generation drug discovery. While initial findings are promising, further empirical validation is necessary to fully harness the therapeutic potential of Fritillaria steroidal alkaloids.

Cloning and bioinformatics analysis of key gene ShOMT3 of podophyllotoxin biosynthesis pathway in Sinopodophyllum hexandrum

Sinopodophyllum hexandrum (S. hexandrum) is an endangered traditional Chinese medicine as abundant podophyllotoxin with powerful anticancer activity. In this study, the rootstalks of S. hexandrum from different geographical locations in China [S1 (Gansu) and S2 (Shaanxi)] were used as research materials to clone the key gene pluviatolide O-methyltransferase 3 (ShOMT3) in the podophyllotoxin biosynthetic pathway. Subsequently, bioinformatics analysis of the ShOMT3 gene and its encoded protein was subjected to bioinformatics analysis using various analysis software including ProtParam, DeepTMHMM, SubLoc, Signal-P 5.0, and Swiss-model. The results of the analysis revealed that the CDS region of the ShOMT3 gene is 1119 bp long, encoding 372 amino acids. The theoretical molecular weight of the ShOMT3 protein is 41.32784 kD, and the theoretical isoelectric point (pI) is 5.27. The instability coefficient of the protein is 46.05, the aliphatic index is 93.58, and the grand average of hydropathicity (GRAVY) is 0.037, indicating that it is an unstable hydrophobic protein. The protein does not contain transmembrane domains or signal peptides, indicating that it is a non-secreted protein. Secondary structure prediction results suggests that the protein consists of alpha helices, random coils, extended strands, and beta-turns. Tertiary structure prediction results suggests that the protein functions as a monomer. In the phylogenetic tree, the ShOMT3 protein has the highest homology with Podophyllum peltatum (P. peltatum). The successful cloning and bioinformatics analysis of the ShOMT3 gene provide theoretical basis and excellent genetic resources for the molecular regulatory mechanism analysis of the podophyllotoxin biosynthetic pathway and molecular breeding in S. hexandrum.

Transcriptomic analysis reveals effects of fertilization towards growth and quality of Fritillariae thunbergii bulbus

Fritillariae thunbergii Bulbus (FTB) is a traditional Chinese medicine that has been widely cultivated for its expectorant, antitussive, antiasthmatic, antiviral, and anticancer properties. The yield and quality of F. thunbergii are influenced by cultivation conditions, such as the use of fertilizers. However, the optimal type of fertilizers for maximum quality and yield and underlying mechanisms are not clear. We collected F. thunbergii using raw chicken manure (RC), organic fertilizer (OF), and plant ash (PA) as the base fertilizer in Pan'an County, Jinhua City, Zhejiang Province as experimental materials. The combined results of HPLC-ELSD detection and yield statistics showed that the F. thunbergii with OF application was the best, with the content of peimine and peiminine reaching 0.0603% and 0.0502%, respectively. In addition, the yield was 2.70 kg/m2. Transcriptome analysis indicated that up-regulation of the ABA signaling pathway might promote bulb yield. Furthermore, putative key genes responsible for steroidal alkaloid accumulation were identified. These results provided guiding significance for the rational fertilization conditions of F. thunbergii as well as the basis for the exploration of functional genes related to the alkaloid biosynthesis pathway.

Metabolomics and transcriptomics reveal the mechanism of alkaloid synthesis in Corydalis yanhusuo bulbs

Corydalis yanhusuo W.T. Wang is a traditional herb. Benzylisoquinoline alkaloids (BIAs) are the main pharmacological active ingredients that play an important role in sedation, relieving pain, promoting blood circulation, and inhibiting cancer cells. However, there are few studies on the biosynthetic pathway of benzylisoquinoline alkaloids in Corydalis yanhusuo, especially on some specific components, such as tetrahydropalmatine. We carried out widely targeted metabolome and transcriptomic analyses to construct the biosynthetic pathway of benzylisoquinoline alkaloids and identified candidate genes. In this study, 702 metabolites were detected, including 216 alkaloids. Protoberberine-type and aporphine-type alkaloids are the main chemical components in C. yanhusuo bulbs. Key genes for benzylisoquinoline alkaloids biosynthesis, including 6-OMT, CNMT, NMCH, BBE, SOMT1, CFS, SPS, STOX, MSH, TNMT and P6H, were successfully identified. There was no significant difference in the content of benzylisoquinoline alkaloids and the expression level of genes between the two suborgans (mother-bulb and son-bulb). The expression levels of BIA genes in the expansion stage (MB-A and SB-A) were significantly higher than those in the maturity stage (MB-C and SB-C), and the content of benzylisoquinoline alkaloids was consistent with the pattern of gene regulation. Five complete single genes were likely to encode the functional enzyme of CoOMT, which participated in tetrahydropalmatine biosynthesis in C. yanhusuo bulbs. These studies provide a strong theoretical basis for the subsequent development of metabolic engineering of benzylisoquinoline alkaloids (especially tetrahydropalmatine) of C. yanhusuo.

Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

Lamiophlomis rotata (Benth.) Kudo is a perennial and unique medicinal plant of the Qinghai–Tibet Plateau. It has the effects of diminishing inflammation, activating blood circulation, removing blood stasis, reducing swelling, and relieving pain. However, thus far, reliable reference gene identifications have not been reported in wild L. rotata. In this study, we identified suitable reference genes for the analysis of gene expression related to the medicinal compound synthesis in wild L. rotata subjected to five different-altitude habitats. Based on the RNA-Seq data of wild L. rotata from five different regions, the stability of 15 candidate internal reference genes was analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. TFIIS, EF-1α, and CYP22 were the most suitable internal reference genes in the leaves of L. rotata from different regions, while OBP, TFIIS, and CYP22 were the optimal reference genes in the roots of L. rotata. The reference genes identified here would be very useful for gene expression studies with different tissues in L. rotata from different habitats.

Comparative transcriptome and tissue-specific expression analysis of genes reveal tissue-cultured plants as an alternative source for phenylethanoids and phenylpropanoids in Rhodiola imbricata (Edgew.)

Rhodiola imbricata (Crassulaceae) is a traditional trans-Himalayan endangered medicinal herb with immense therapeutic applications. Over the years, over-exploitation, un-managed harvesting, and lack of captive cultivation procedures persuaded threat to its wild habitat. Plant tissue culture and RNA-Seq-based molecular bioprospection of key regulatory genes aid the understanding of molecular dynamics involved in specialized metabolites (phenylethanoids and phenylpropanoids) biosynthesis and its sustainable production. Hence, comparative transcriptomic analysis was performed using leaf and root tissues from the wild and tissue-cultured plants, revealing tissue-specific production of salidroside and rosavin. The transcriptome profiling resulted in 345 million high-quality reads yielding 92,380 unique transcripts with an N₅₀ of 1260 bp. Tissue-specific gene expression analysis revealed that both phenylethanoids and phenylpropanoids biosynthesis are predominantly associated with the shikimate pathway. In addition to RNA-Seq data, the downstream biosynthesis pathways genes viz., phospho-2-dehydro-3-deoxyheptonate aldolase (DAHPS), 3-dehydroquinate synthase (DHQS), shikimate kinase (SK), chorismate mutase (CM), arogenate dehydrogenase (TYRAAT), aromatic-L-amino-acid decarboxylase (TDC), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4-CL), cinnamoyl-CoA reductase (CCR), and cinnamyl alcohol dehydrogenase (CAD) showed higher expression pattern in wild plant tissues compared to tissue-cultured plants. The transcript fold expression determined by RT-qPCR results followed similar patterns as those observed in RNA-seq and targeted metabolite profiling data. Salidroside and rosavin content in wild plants exhibited 2.40 fold and 1.77 fold increase accumulation compared to the tissue-cultured plant. The present investigation explained the tissue and condition-specific significant differences between the expression of proposed biosynthetic pathway genes and salidroside and rosavin content. Additionally, NAC, bHLH, and ARF were the most abundant transcription factor families found in the transcriptomic analysis of R. imbricata. The generated transcriptome dataset provides a valuable gene(s)/transcription factors hub that can be used for the sustainable production of salidroside and rosavin in R. imbricata under tissue culture conditions.