Putative genes in alkaloid biosynthesis identified in Dendrobium officinale by correlating the contents of major bioactive metabolites with genes expression between Protocorm-like bodies and leaves

Abstract

Background Dendrobium officinale, an endangered Chinese herb, possesses extensive therapeutic effects and contains bioactive ingredients such as major polysaccharides, alkaloids, and minimal flavonoids. We first obtained the protocorm-like bodies (PLBs) of this plant through tissue culture in order to determine the distribution of the main secondary metabolites in each organelle and the PLBs. We then analyzed the correlation between gene expression level from comparative transcriptome sequencing and metabolite content in different organs to identify putative genes encoding enzymes involved in the biosynthesis of polysaccharides, alkaloids, and flavonoids. Results We used seeds as explants for protocorm induction and PLB propagation of D. officinale. The optimal medium formula for PLB propagation was 1/2 MS + α-NAA 0.5 mg·L− 1 + 6-BA 1.0 mg·L− 1 + 2, 4-D 1.5–2.0 mg·L− 1 + potato juice 100 g·L− 1. Stems, PLBs and leaves of D. officinale had the highest content of polysaccharides, alkaloids and flavonoids, respectively. Naringenin was only produced in stem; however, PLBs with high alkaloid content can replace other organs producing alkaloids. The hot water extraction method outperformed the ultrasound-assisted extraction method for extracting polysaccharides from D. officinale. A comparative transcriptome analysis of PLBs and leaves of D. officinale revealed differential expression of genes encoding enzymes involved in polysaccharide, alkaloid and flavonoid biosynthetic pathways. Putative genes encoding enzymes involved in these biosynthetic pathways were identified. Notably, we identified genes encoding the alkaloid biosynthesis enzymes strictosidine β-D-Glucosidase, geissoschizine synthase and vinorine synthase in D. officinale. Conclusions The identification of candidate genes encoding enzymes involved in metabolite biosynthesis will help to explore and protect this endangered species and facilitate further analysis of the molecular mechanism of secondary metabolite biosynthesis in D. officinale.

Integration of Transcriptome and Metabolome Provides New Insights to Flavonoids Biosynthesis in Dendrobium huoshanense

“… Yuan et al (2020) found that genes controlling flavonoid biosynthesis, such as LAR , DFR , and F3H , were significantly upregulated in D. officinale leaves as compared to roots and stems. In D. officinale , Wang Z. et al (2021) found that the expression of genes encoding enzymes involved in flavonoid biosynthesis was different between protocorm-like bodies and leaves. The expression of genes involved in flavonoid biosynthesis in D. catenatum from different geographical locations differed, with most of them being highly expressed in the Zhejiang samples ( Lei et al, 2018 ).…”

Comparative Proteome and Phosphoproteome Analyses Reveal Different Molecular Mechanism Between Stone Planting Under the Forest and Greenhouse Planting of Dendrobium huoshanense

“…RT-qPCR analysis was performed using a SuperReal PreMix Plus SyBr Green PCR kit [Tiangen Biotech (Beijing) Co., Ltd., Beijing, China] on a Cobas z480 Real-Time PCR System, following the method previously described ( Wang et al, 2021 ). Candidate primers were designed using Primer 5.0 ( Supplementary Table 1 ).…”

Research Advances in Multi-Omics on the Traditional Chinese Herb Dendrobium officinale

“…Int. 2020:6512895. doi: 10.1155/2020/6512895 Shan, T., Zhou, L., Li, B., Chen, X., Guo, S., Wang, A., et al (2021). The plant growth-promoting fungus MF23 (Mycena sp.)…”

“…Although there are different types of alkaloids accumulated in D. officinale ( Jiao et al, 2018 ), the main classes of alkaloids are terpenoid indole alkaloids (TIAs; Guo et al, 2013 ; Niu et al, 2021 ). Alkaloids are present in multiple tissues, including protocorm-like bodies (PLB), flower, root, leaf and stem, and the content in PLBs was the highest ( Wang et al, 2021 ). There were 25 genes that participated in the shikimate, mevalonate (MVA) and methylerythritol phosphate (MEP) and strictosidine pathways, and other genes were potentially related to the alkaloid synthesis, such as cytochrome P450s, aminotransferases, methyltransferases, multidrug resistance protein (MDR), transporters and transcription factors ( Guo et al, 2013 ; Figure 1 ).…”

“…Further expression analysis confirmed that the genes responsible for 1-deoxy-D-xylulose-5-phosphate synthase (DXS), 5-enolpyruvylshikimate-3-phosphate synthase, shikimate dehydrogenase, mevalonate kinase (MVK), and aminotransferases were mainly expressed in leaves, which could be the main reason for higher alkaloid content in leaves ( Shen et al, 2017 ). Recently, 41 genes showing significant differences in expression levels were detected between PLBs and leaves, including genes in the strictosidine biosynthesis ( Wang et al, 2021 ). The candidate genes encoding strictosidine β-D-Glucosidase, geissoschizine synthase and vinorine synthase in the alkaloid biosynthesis enzymes were first identified, which facilitates the analysis of its metabolite biosynthesis in future studies.…”