Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb

Kumar, Pankaj; Ashrita,; Acharya, Vishal; Warghat, Ashish R.

doi:10.1016/j.phytochem.2020.112631

Cited by 26 publications

(20 citation statements)

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“…In this study, six genes predicted to be involved in DMAPP/IPP synthesis via the MVA pathway were found to be highly expressed in BFC, while another set of genes predicted to be involved in the MEP pathway was expressed higher in F. thunbergii. Thus, we inferred that the MVA pathway is the primary route responsible for DMAPP/IPP synthesis in BFC, which is consistent with the results from another recent study [17]. On the other hand, the enzymes in the MEP pathway are more likely to control how DMAPP/ IPP is synthesized in BFT.…”

Section: Discussionsupporting

confidence: 92%

“…In this study, we identified a couple of candidate transcription factors, belonging to AP2/ERF, MYB, C2H2, and bHLH families, that were highly expressed in BFC. These transcription factors have been shown to directly or indirectly regulate the biosynthesis of alkaloids in Fritillaria roylei Hook [17,18,47,48].…”

Section: Discussionmentioning

confidence: 99%

“…For example, Zhao et al performed transcriptome analysis to map the gene expression profile of in vitro regenerated BFC [16]. Kumar et al identified the essential genes and regulatory transcription factors (TFs) of imperialine biosynthesis in Fritillaria roylei Hook using comparative de novo transcriptome analysis [17]. The molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in F. roylei Hook was investigated by transcriptome analysis [18].…”

Section: Introductionmentioning

confidence: 99%

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Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Liao

et al. 2022

BMC Genomics

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Background Bulbus Fritillariae Cirrhosae (BFC) is an endangered high-altitude medicine and food homology plant with anti-tumor, anti-asthmatic, and antitussive activities as it contains a variety of active ingredients, especially steroidal alkaloids. Bulbus Fritillariae Thunbergia (BFT) is another species of Fritillaria that grows at lower altitude areas. Production of plant-derived active ingredients through a synthetic biology strategy is one of the current hot topics in biological research, which requires a complete understanding of the related molecular pathways. Our knowledge of the steroidal alkaloid biosynthesis in Fritillaria species is still very limited. Results To promote our understanding of these pathways, we performed non-target metabolomics and transcriptome analysis of BFC and BFT. Metabolomics analysis identified 1288 metabolites in BFC and BFT in total. Steroidal alkaloids, including the proposed active ingredients of Fritillaria species peimine, peimisine, peiminine, etc., were the most abundant alkaloids detected. Our metabolomics data also showed that the contents of the majority of the steroidal alkaloids in BFC were higher than in BFT. Further, our comparative transcriptome analyses between BFC and BFT identified differentially expressed gene sets among these species, which are potentially involved in the alkaloids biosynthesis of BFC. Conclusion These findings promote our understanding of the mechanism of steroidal alkaloids biosynthesis in Fritillaria species.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Liao

et al. 2022

BMC Genomics

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“… 19 – 21 . Chinese medicinal practitioners have employed this plant to implicate its medicinal and therapeutic potency 22 . It's a bitter tonic and gastrointestinal stimulant that relieves fevers and urinary tract infections and is a medicine for 80 diseases 23 .…”

Section: Introductionmentioning

confidence: 99%

Metabolite fingerprinting of phytoconstituents from Fritillaria cirrhosa D. Don and molecular docking analysis of bioactive peonidin with microbial drug target proteins

Bhat

Mir

Sheikh

et al. 2022

Sci Rep

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Fritillaria cirrhosa D. Don (Liliaceae), a valuable and critically endangered medicinal herb of northwest India, including Jammu and Kashmir, grows in temperate to alpine regions of the Himalaya. It is known as the traditional herb for cardiovascular diseases, respiratory diseases, and metabolic disorders. The plant bulbs are precious and are used to cure many other health complications. The current study analysed the phytoconstituents by liquid chromatography-mass spectrometry (LC–MS) of different crude extracts (methanolic, petroleum ether, and ethyl acetate) of F. cirrhosa. The LC–MS analysis from the bulbs of F. cirrhosa yielded 88 bioactive compounds, with the vast majority having therapeutic applications. Further, determination of minimum inhibitory concentrations (MICs) by broth microdilution method of F. cirrhosa against tested bacterial and fungal pathogens showed remarkable results with MICs ranging between 6.25–200 µg/mL and 50–400 µg/mL, respectively. Subsequently, these 88 identified phytocompounds were tested for their bioactivity through ADMET prediction by SwissADME and in silico molecular docking studies. Results revealed that Peonidin might have maximum antibacterial and antifungal activity against various microbial protein drug targets among the phytochemical compounds identified. Furthermore, the highest binding affinity complex was subjected to molecular dynamic simulation (MDS) analysis using Desmond Schrodinger v3.8. The root-mean-square deviation (RMSD) graphs obtained through the molecular dynamic simulations indicated the true bonding interactions, further validated using the root-mean-square fluctuation (RMSF) graphs which provided a better understanding of the amino acids present in the proteins responsible for the molecular motions and fluctuations. To our best knowledge, this is the first description of the phytochemical constituents of the bulbs of F.cirrhosa analyzed through LC–MS, which show pharmacological significance. The in silico molecular docking and molecular dynamics study of peonidin was also performed to confirm its broad-spectrum activities based on the binding interactions with the antibacterial and antifungal target proteins. The present study results will create a way for the invention of herbal medicines for several ailments by using F. cirrhosa plants, which may lead to the development of novel drugs.

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“…With its outstanding advantages of high throughput, high accuracy, high sensitivity, and relatively low cost, next‐generation sequencing has become an attractive choice for non‐model organisms without genomic sequences (Ozsolak & Milos, 2011; Wang et al, 2009). Recently, a number of transcriptome analyses of Fritillaria species have been reported, namely F. cirrhosa , Fritillaria imperialis , Fritillaria hupehensis , and Fritillaria roylei (Chao et al, 2011; Eshaghi et al, 2019; Guo et al, 2021; Kumar et al, 2021; Sharma et al, 2021; Zhao et al, 2018). By contrast, there is no reference genome or transcriptome available for F. anhuiensis , which severely limits the development and utilization of this medicinal herb.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals candidate genes related to steroid alkaloid biosynthesis in Fritillaria anhuiensis

Shan

Shi

et al. 2022

Physiologia Plantarum

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Fritillaria anhuiensis (F. anhuiensis), a traditional medicinal herb of the Liliaceae family, has various pharmacological effects, including anti‐tussive, anti‐asthmatic, and expectorant activities. Peimine, a steroidal alkaloid, is a major active constituent of F. anhuiensis. Although steroidal alkaloids of F. anhuiensis have been explored chemically and pharmacologically, the molecular basis of their biosynthesis remains unknown due to a lack of genomic and transcriptomic information. In this study, peimine was detected in bulbs, stems, and leaves of F. anhuiensis, with the highest content in the bulbs. We analyzed the transcriptomes of the bulbs, stems, and leaves of F. anhuiensis using an Illumina HiSeq 4000 platform. A total of 92,829 unigenes with a mean length of 804 base pairs (bp) and an N50 value of 1354 bp were assembled from a total of 30.56 Gb high‐quality reads. Based on the Kyoto Encyclopedia of Genes and Genomes annotation, 83 unigenes were found to be related to the steroid biosynthesis pathway, while 155 unigenes were related to the terpenoid backbone biosynthesis pathway. Numerous transcription factors are involved in the regulation of alkaloid biosynthesis. A putative steroidal alkaloid biosynthesis pathway in F. anhuiensis was constructed, providing a novel understanding of peimine biosynthesis. We performed extensive bioinformatics and phylogenetic analyses to investigate the functional characteristics and evolutionary history of cycloartenol synthase. This study is the first to report transcriptome data from F. anhuiensis and extends our knowledge of the molecular mechanisms of steroid alkaloid biosynthesis.

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Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb

Cited by 26 publications

References 50 publications

Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Metabolite fingerprinting of phytoconstituents from Fritillaria cirrhosa D. Don and molecular docking analysis of bioactive peonidin with microbial drug target proteins

Transcriptome analysis reveals candidate genes related to steroid alkaloid biosynthesis in Fritillaria anhuiensis

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