Metabolic and transcriptomic analyses elucidate a novel insight into the network for biosynthesis of carbohydrate and secondary metabolites in the stems of a medicinal orchid Dendrobium nobile

doi:10.1016/j.pld.2022.10.004

Abstract

Abstract: Dendrobium nobile is an important medicinal and nutraceutical herb. Although the ingredients of D. nobile have been identified as polysaccharides, alkaloids, amino acids, flavonoids and bibenzyls, our understanding of the metabolic pathways that regulate the synthesis of these compounds is limited. Here, we used transcriptomic and metabolic analyses to elucidate the genes and metabolites involved in the biosynthesis of carbohydrate and several secondary metabolites in the stems of D. nobile. A total of 1005 metabolites and 31,745 genes were detected in the stems of D. nobile. The majority of these metabolites and genes were involved in the metabolism of carbohydrates (fructose, mannose, glucose, xylulose and starch), while some were involved in the metabolism of secondary metabolites (alkaloids, β-tyrosine, ferulic acid, 4-hydroxybenzoate and chrysin). Our predicted regulatory network indicated that five genes (AROG, PYK, DXS, ACEE and HMGCR) might play vital roles in the transition from carbohydrate to alkaloid synthesis. Correlation analysis identified that six genes (ALDO, PMM, BGLX, EGLC, XYLB and GLGA) were involved in carbohydrate metabolism, and two genes (ADT and CYP73A) were involved in secondary metabolite biosynthesis. Our analyses also indicated that phosphoenol-pyruvate (PEP) was a crucial bridge that connected carbohydrate to alkaloid biosynthesis. The regulatory network between carbohydrate and secondary metabolite biosynthesis established will provide important insights into the regulation of metabolites and biological systems in Dendrobium species.

Key words: Dendrobium nobile, Transcriptome, Metabolome, Polysaccharides, Alkaloids, Secondary metabolite biosynthesis

Yu-Wen Zhang, Yu-Cen Shi, Shi-Bao Zhang. Metabolic and transcriptomic analyses elucidate a novel insight into the network for biosynthesis of carbohydrate and secondary metabolites in the stems of a medicinal orchid Dendrobium nobile[J]. Plant Diversity, 2023, 45(03): 326-336.

References

[1] Ambasht, P.K., Kayastha, A.M., 2002. Plant pyruvate kinase. Biol. Plant. 45 (1), 1-10. https://doi.org/10.1023/A:1015173724712.
[2] Cai, Y.C., Li, S.F., Jiao, G.A., Sheng, Z.H., Wu, Y.W., Shao, G.N., Xie, L.H., Peng, C., Xu, J.F., Tang, S.Q., Wei, X.J., Hu, P.S., 2018. OsPK2 encodes a plastidic pyruvate kinase involved in rice endosperm starch synthesis, compound granule formation and grain filling. Plant Biotechnol. J. 16 (11), 1878-1891. https://doi.org/10.1111/pbi.12923.
[3] Chen, W., Gong, L., Guo, Z.L., Wang, W.S., Zhang, H.Y., Liu, X.Q., Yu, S.B., Xiong, L.Z., Luo, J., 2013. A Novel Integrated method for large-scale detection, identification, and quantification of widely targeted metabolites:application in the study of rice metabolomics. Mol. Plant. 6 (6), 1769-1780. https://doi.org/10.1093/mp/sst080.
[4] de Oliveira, M.V.V., Jin, X., Chen, X., Griffith, D., Batchu, S., Maeda, H.A., 2019. Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana. Plant J. 97 (5), 901-922. https://doi.org/10.1111/tpj.14169.
[5] De Vos, R.C., Moco, S., Lommen, A., Keurentjes, J.J., Bino, R.J., Hall, R.D., 2007. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat. Protoc. 2 (4), 778-791. https://doi.org/10.1038/nprot.2007.95.
[6] Guo, L.H., Qi, J.X., Du, D., Liu, Y., Jiang, X., 2020. Current advances of Dendrobium officinale polysaccharides in dermatology:a literature review. Pharm Biol. 58 (1), 664-673. https://doi.org/10.1080/13880209.2020.1787470.
[7] Guo, X., Li, Y., Li, C.F., Luo, H.M., Wang, L.Z., Qian, J., Luo, X., Xiang, L., Song, J.Y., Sun, C., Xu, H.B., Yao, H., Chen, S.L., 2013. Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers. Gene 527 (1), 131-138. https://doi.org/10.1016/j.gene.2013.05.073.
[8] He, C.M., Zhang, J.X., Liu, X.C., Zeng, S.J., Wu, K.L., Yu, Z.M., Wang, X.J., da Silva, J.A.T., Lin, Z.J., Duan, J., 2015. Identification of genes involved in biosynthesis of mannan polysaccharides in Dendrobium officinale by RNA-seq analysis. Plant Mol. Biol. 88 (33), 219-231. https://doi.org/10.1007/s11103-015-0316-z.
[9] He, L., Su, Q., Bai, L., Li, M.F., Liu, J.R., Liu, X.M., Zhang, C.Y., Jiang, Z.L., He, J., Shi, J.Y., Huang, S., Guo, L., 2020. Recent research progress on natural small molecule bibenzyls and its derivatives in Dendrobium species. Eur. J. Med. Chem. 204, 1-17. https://doi.org/10.1016/j.ejmech.2020.112530.
[10] Holman, J.D., Tabb, D.L., Mallick, P., 2014. Employing proteowizard to convert raw mass spectrometry data. Curr. Protoc. Bioinformatics 46, 1-9. https://doi.org/10.1002/0471250953.bi1324s46.
[11] Jander, G., Kolukisaoglu, U., Stahl, M., Yoon, G.M., 2020. Editorial:physiological aspects of non-proteinogenic amino acids in plants. Front. Plant Sci. 11, 1-3. https://doi.org/10.3389/fpls.2020.519464.
[12] Jiao, C.Y., Song, C., Zheng, S.Y., Zhu, Y.P., Jin, Q., Cai, Y.P., Lin, Y., 2018. Metabolic profiling of Dendrobium officinale in response to precursors and methyl jasmonate. Int. J. Mol. Sci. 19 (3), 728-747. https://doi.org/10.3390/ijms19030728.
[13] Kang, L.Q., Zhou, J.S., Wang, R., Zhang, X.W., Liu, C.C., Liu, Z.H., Yuan, S., 2019. Glucanase-induced stipe wall extension shows distinct differences from chitinase-induced stipe wall extension of Coprinopsis cinerea. Appl. Environ. Microb. 85 (21), 1345-1319. https://doi.org/10.1128/aem.01345-19.
[14] Liu, Y.H., Rainey, P.B., Zhang, X.X., 2015. Molecular mechanisms of xylose utilization by Pseudomonas fluorescens:overlapping genetic responses to xylose, xylulose, ribose and mannitol. Mol. Microbiol. 98 (93), 553-570. https://doi.org/10.1111/mmi.13142.
[15] Livak, K.J., Schmittgen, T.D., 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCT method. Methods 25 (4), 402-408. https://doi.org/10.1006/meth.2001.1262.
[16] Love, M.I., Huber, W., Anders, S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15 (12), 550-571. https://doi.org/10.1186/s13059-014-0550-8.
[17] Mou, Z.M., Zhao, Y., Ye, F., Shi, Y.N., Kennelly, E.J., Chen, S.Y., Zhao, D.K., 2021. Identification, biological activities and biosynthetic pathway of Dendrobium alkaloids. Front. Pharmacol. 12, 1-14. https://doi.org/10.3389/fphar.2021.605994.
[18] Ng, T.B., Liu, J., Wong, J.H., Ye, X., Wing Sze, S.C., Tong, Y., Zhang, K.Y., 2012. Review of research on Dendrobium, a prized folk medicine. Appl. Microbiol. Biot. 93 (5), 1795-1803. https://doi.org/10.1007/s00253-011-3829-7.
[19] Pan, X.H., Li, Y.T., Pan, G.T., Yang, A.G., 2019. Bioinformatics study of 1-deoxy-d-xylulose-5-phosphate synthase (DXS) genes in Solanaceae. Mol. Biol. Rep. 46 (5), 5175-5184. https://doi.org/10.1007/s11033-019-04975-5.
[20] Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T., Salzberg, S.L., 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33 (3), 290-295. https://doi.org/10.1038/nbt.3122.
[21] Pfister, B., Zeeman, S., 2016. Formation of starch in plant cells. Cell. Mol. Life Sci. 73 (14), 2781-2807. https://doi.org/10.1007/s00018-016-2250-x.
[22] Sato, K., Mase, K., Nakano, Y., Nishikubo, N., Sugita, R., Tsuboi, Y., Kajita, S., Zhou, J.M., Kitano, H., Katayama, Y., 2006. 3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase is regulated for the accumulation of polysaccharide-linked hydroxycinnamoyl esters in rice (Oryza sativa L.) internode cell walls. Plant Cell Rep. 25 (7), 676-688. https://doi.org/10.1007/s00299-006-0124-7.
[23] Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T., 2003. Cytoscape:a software environment for integrated models of biomolecular interaction networks. Genome Res. 13 (11), 2498-2504. https://doi.org/10.1101/gr.1239303.
[24] Shen, C.J., Guo, H., Chen, H.L., Shi, Y.J., Meng, Y.J., Lu, J.J., Feng, S.G., Wang, H.Z., 2017. Identification and analysis of genes associated with the synthesis of bioactive constituents in Dendrobium officinale using RNA-Seq. Sci. Rep. 7 (1), 187-198. https://doi.org/10.1038/s41598-017-00292-8.
[25] Tian, S.K., Wang, D.D., Yang, L., Zhang, Z.X., Liu, Y., 2021. A systematic review of 1-Deoxy-D-xylulose-5-phosphate synthase in terpenoid biosynthesis in plants. Plant Growth Regul. 1-15. https://doi.org/10.1007/s10725-021-00784-8.
[26] Tohge, T., Watanabe, M., Hoefgen, R., Fernie, A., 2013. Shikimate and phenylalanine biosynthesis in the green lineage. Front. Plant Sci. 4 (62), 1-13. https://doi.org/10.3389/fpls.2013.00062.
[27] Wang, Z.C., Zhao, M.L., Cui, H.Q., Li, J., Wang, M.N., 2020. Transcriptomic landscape of medicinal Dendrobium reveals genes associated with the biosynthesis of bioactive components. Front. Plant Sci. 11, 391-401. https://doi.org/10.3389/fpls.2020.00391.
[28] Xu, J., Guan, J., Chen, X.J., Zhao, J., Li, S.P., 2011. Comparison of polysaccharides from different Dendrobium using saccharide mapping. J. Pharmaceut. Biomed. 55 (5), 977-983. https://doi.org/10.1016/j.jpba.2011.03.041.
[29] Yu, C.M., Li, Y.W., Li, B., Liu, X., Hao, L.F., Chen, J., Qian, W.Q., Li, S.M., Wang, G.F., Bai, S.W., Ye, H., Qin, H.J., Shen, Q.H., Chen, L.B., Zhang, A., Wang, D., 2010. Molecular analysis of phosphomannomutase (PMM) genes reveals a unique PMM duplication event in diverse Triticeae species and the main PMM isozymes in bread wheat tissues. BMC Plant Biol. 10, 214-230. https://doi.org/10.1186/1471-2229-10-214.
[30] Yu, C.M., Liu, X.Y., Zhang, Q., He, X.Y., Huai, W., Wang, B.H., Cao, Y.Y., Zhou, R., 2015. Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum. Crop J. 3 (1), 29-36. https://doi.org/10.1016/j.cj.2014.07.003.
[31] Yu, G., Wang, L.G., Han, Y., He, Q.Y., 2012. clusterProfiler:an R package for comparing biological themes among gene clusters. OMICS. 16 (5), 284-287. https://doi.org/10.1089/omi.2011.0118.
[32] Yuan, Y.D., Yu, M.Y., Jia, Z.H., Song, X.E., Liang, Y.Q., Zhang, J.C., 2019a. Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. BMC Genom. 19 (1), 978-984. https://doi.org/10.1186/s12864-018-5305-6.
[33] Yuan, Y.D., Yu, M.Y., Zhang, B., Liu, X., Zhang, J.C., 2019b. Comparative nutritional characteristics of the three major Chinese Dendrobium species with different growth years. PLoS One 14 (9), e0222666. https://doi.org/10.1371/journal.pone.0222666.
[34] Yuan, Y.D., Zhang, J.C., Liu, X., Meng, M.J., Wang, J.P., Lin, J., 2020. Tissue-specific transcriptome for Dendrobium officinale reveals genes involved in flavonoid biosynthesis. Genomics 112 (2), 1781-1794. https://doi.org/10.1016/j.ygeno.2019.10.010.
[35] Yue, H., Zeng, H., Ding, K., 2020. A review of isolation methods, structure features and bioactivities of polysaccharides from Dendrobium species. Chin. J. Nat. Medicines 18 (1), 1-27. https://doi.org/10.1016/S1875-5364(20)30001-7.
[36] Zhang, J.X., He, C.M., Wu, K.L., da Silva, J.A.T., Zeng, S.J., Zhang, X.H., Yu, Z.M., Xia, H.Q., Duan, J., 2016. Transcriptome analysis of Dendrobium officinale and its application to the identification of genes associated with polysaccharide synthesis. Front. Plant Sci. 7, 5-18. https://doi.org/10.3389/fpls.2016.00005.
[37] Zheng, Y.P., Jiang, W., Silva, E.N., Mao, L.Z., Hannaway, D., Lu, H.F., 2012. Optimization of shade condition and harvest time for Dendrobium candidum plants based on leaf gas excachange, alkaloids and polysaccharides contents. Plant Omics 5 (3), 253-260.
[38] Ziveri, J., Tros, F., Guerrera, I.C., Chhuon, C., Audry, M., Dupuis, M., Barel, M., Korniotis, S., Fillatreau, S., Gales, L., Cahoreau, E., Charbit, A., 2017. The metabolic enzyme fructose-1,6-bisphosphate aldolase acts as a transcriptional regulator in pathogenic Francisella. Nat. Commun. 8, 853-868. https://doi.org/10.1038/s41467-017-00889-7.