Combinatorial transcriptomics and metabolomics analysis reveals the effects of the harvesting stages on the accumulation of phenylpropanoid metabolites in Lonicera japonica
Zhifang Ran A B # , Weina Ding A # , Hongxia Yu C , Li Zhang D , Lei Fang
A * , Lanping Guo E * and Jie Zhou A *
A School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
B School of Pharmaceutical Sciences, Shandong University of Traditional Chinese Medicine, Jinan 250355, PR China.
C Weihai (Wendeng) Authentic Ginseng Industry Development Co. Ltd., Wendeng 264407, China.
D Shandong Zhongping Pharmaceutical Industry, Linyi 273399, China.
E State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
Handling Editor: David Cahill
Functional Plant Biology 50(10) 808-820 https://doi.org/10.1071/FP23033
Submitted: 12 February 2023 Accepted: 8 August 2023 Published: 23 August 2023
Abstract
The flower buds of Lonicera japonica are widely used for its high medicinal value. It is reported that the accumulation of phenylpropanoids in the buds of L. japonica is affected by the stage at which it is harvested. However, the changes of active components and the underlying mechanisms in flower buds at different harvesting stages have not been reported. Integrative analyses of transcriptomics and metabolomics was used to explore the underlying mechanism of harvesting stages (green bud, GB; and white bud, WB) on the phenylpropanoids metabolites accumulation in L. japonica. The result showed that 3735 differentially expressed genes were identified, and the genes related to glycolysis/gluconeogenesis and phenylalanine biosynthesis pathway were significantly upregulated in GB stage. A total of 510 differential metabolites were identified in GB stage. Among them, 14 phenylpropanoids were changed during the GB and WB, seven of which increased in GB, including caffeic acid, sauchinone, coniferin, secoisolariciresinol diglucoside, scopolin, methyl cinnamate, chlorogenic acid, 7-hydroxycoumarin, while others such as sibiricose A6, coumarin, eleutheroside E decreased. Further correlation analysis showed that the unigenes for CSE, CAD, bg1, ADH, ALDH, DLAT and ENO significantly correlated with the 10 phenylpropanoid. The above results would provide basic data for the selection of harvesting stages in the production of L. japonica.
Keywords: correlation analysis, differentially expressed genes, harvesting stage, Lonicera japonica Thunb., metabolomics, phenylpropanoid metabolites, transcription factors, transcriptomics.
References
Coolen S, Proietti S, Hickman R, Davila Olivas NH, Huang P-P, Van Verk MC, Van Pelt JA, Wittenberg AHJ, De Vos M, Prins M, Van Loon JJA, Aarts MGM, Dicke M, Pieterse CMJ, Van Wees SCM (2016) Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses. The Plant Journal 86, 249-267 PMID:.
| Crossref | Google Scholar | PubMed |
Doerfler H, Lyon D, Nagele T, Sun X, Fragner L, Hadacek F, Egelhofer V, Weckwerth W (2013) Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism. Metabolomics 9, 564-574 PMID:.
| Crossref | Google Scholar | PubMed |
Feng S, Wang Y, Yang S, Xu Y, Chen X (2010) Anthocyanin biosynthesis in pears is regulated by a R2R3-MYB transcription factor PyMYB10. Planta 232, 245-255 PMID:.
| Crossref | Google Scholar | PubMed |
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644 PMID:.
| Crossref | Google Scholar | PubMed |
Guo B, Wei Y, Xu R (2016) Genome-wide analysis of APETALA2/Ethylene-responsive factor (AP2/ERF) gene family in Barley (Hordeum vulgare L.). PLoS ONE 11, e0161322 PMID:.
| Crossref | Google Scholar | PubMed |
Han JM, Kim MH, Choi YY, Lee H, Hong J, Yang WM (2015) Effects of Lonicera japonica Thunb. on type 2 diabetes via PPAR-γ activation in rats. Phytotherapy Research Phytother 29, 1616-1621.
| Crossref | Google Scholar |
Higashi Y, Okazaki Y, Myouga F, Shinozaki K, Saito K (2015) Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana. Scientific Reports 5, 10533 PMID:.
| Crossref | Google Scholar | PubMed |
Jin J, Tian F, Yang D-C, Meng Y-Q, Kong L, Luo J, Gao G (2017) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research 45, D1040-D1045 PMID:.
| Crossref | Google Scholar | PubMed |
Jung S-C, Kim W, Park SC, Jeong J, Park MK, Lim S, Lee Y, Im W-T, Lee JH, Choi G, Kim SC (2014) Two ginseng UDP-glycosyltransferases synthesize ginsenoside Rg3 and Rd. Plant and Cell Physiology 55, 2177-2188 PMID:.
| Crossref | Google Scholar | PubMed |
Ling L, Song L, Wang Y, Guo C (2017) Genome-wide analysis and expression patterns of the NAC transcription factor family in Medicago truncatula. Physiology and Molecular Biology of Plants 23, 343-356.
| Crossref | Google Scholar |
Liu J, Osbourn A, Ma P (2015) MYB transcription factors as regulators of phenylpropanoid metabolism in plants. Molecular Plant 8, 689-708 PMID:.
| Crossref | Google Scholar | PubMed |
Liu Y, Wang L, Zhang J, Yu B, Wang J, Wang D (2017) The MYB transcription factor StMYBA1 from potato requires light to activate anthocyanin biosynthesis in transgenic tobacco. Journal of Plant Biology 60, 93-101.
| Crossref | Google Scholar |
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25, 402-408 PMID:.
| Crossref | Google Scholar | PubMed |
Lou Q, Liu Y, Qi Y, Jiao S, Tian F, Jiang L, Wang Y (2014) Transcriptome sequencing and metabolite analysis reveals the role of delphinidin metabolism in flower colour in grape hyacinth. Journal of Experimental Botany 65, 3157-3164 PMID:.
| Crossref | Google Scholar | PubMed |
Luo J (2015) Metabolite-based genome-wide association studies in plants. Current Opinion in Plant Biology 24, 31-38 PMID:.
| Crossref | Google Scholar | PubMed |
Lv X, Gao S, Wang S, Zhang X, Yao Y (2021) Analysis of the role of VvCOMT in synthesizing melatonin and ferulic acid in grape. Plant Physiology Communications 57, 1937-1945.
| Google Scholar |
Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21, 3787-3793 PMID:.
| Crossref | Google Scholar | PubMed |
Matsui K, Umemura Y, Ohme-Takagi M (2008) AtMYBL2, a protein with a single MYB domain, acts as a negative regulator of anthocyanin biosynthesis in Arabidopsis. The Plant Journal 55, 954-967.
| Crossref | Google Scholar |
Mehrtens F, Kranz H, Bednarek P, Weisshaar B (2005) The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiology 138, 1083-1096.
| Crossref | Google Scholar |
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-628 PMID:.
| Crossref | Google Scholar | PubMed |
Nakashima K, Tran L-SP, Van Nguyen D, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. The Plant Journal 51, 617-630.
| Crossref | Google Scholar |
Ortmann S, Pferschy WEM, Zhao YM, Miao J, Bauer R (2012) Lonicera japonica Thunb. – anti-inflammatory activity of various extracts from herb, stems and leaves. Planta Medica 78, PI121.
| Crossref | Google Scholar |
Park H-S, Park K-I, Lee D-H, Kang S-R, Nagappan A, Kim J-A, Kim EH, Lee WS, Shin SC, Hah Y-S, Kim G-S (2012) Polyphenolic extract isolated from Korean Lonicera japonica Thunb. induce G2/M cell cycle arrest and apoptosis in HepG2 cells: involvements of PI3K/Akt and MAPKs. Food and Chemical Toxicology 50, 2407-2416 PMID:.
| Crossref | Google Scholar | PubMed |
Park KI, Park H, Nagappan A, Hong GE, Yumnam S, Lee HJ, Kim EH, Lee WS, Shin SC, Kim JA, Lee SJ, Ma JY, Min T, Heo JD, Kim GS (2017) Polyphenolic compounds from Korean Lonicera japonica Thunb. induces apoptosis via AKT and caspase cascade activation in A549 cells. Oncology Letters 13, 2521-2530 PMID:.
| Crossref | Google Scholar | PubMed |
Paupiere MJ, Muller F, Li H, Rieu I, Tikunov YM, Visser RGF, Bovy AG (2017) Untargeted metabolomic analysis of tomato pollen development and heat stress response. Plant Reproduction 30, 81-94 PMID:.
| Google Scholar | PubMed |
Pu X, Li Z, Tian Y, Gao R, Hao L, Hu Y, He C, Sun W, Xu M, Peters RJ, Van de Peer Y, Xu Z, Song J (2020) The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. New Phytologist 227, 930-943.
| Crossref | Google Scholar |
Shah ST, Pang C, Fan S, Song M, Arain S, Yu S (2013) Isolation and expression profiling of GhNAC transcription factor genes in cotton (Gossypium hirsutum L.) during leaf senescence and in response to stresses. Gene 531, 220-234 PMID:.
| Crossref | Google Scholar | PubMed |
Shang X, Pan H, Li M, Miao X, Ding H (2011) Lonicera japonica Thunb.: ethnopharmacology, phytochemistry and pharmacology of an important traditional Chinese medicine. Journal of Ethnopharmacology 138, 1-21 PMID:.
| Crossref | Google Scholar | PubMed |
Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EMK, Chen S (2010) De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 11, 262.
| Crossref | Google Scholar |
Sun L-J, Li D-Y, Zhang H-J, Song F-M (2012) Functions of NAC transcription factors in biotic and abiotic stress responses in plants. Genetics 34, 993-1002.
| Crossref | Google Scholar |
Vanholme R, Cesarino I, Rataj K, Xiao Y, Sundin L, Goeminne G, Kim H, Cross J, Morreel K, Araujo P, Welsh L, Haustraete J, McClellan C, Vanholme B, Ralph J, Simpson GG, Halpin C, Boerjan W (2013) Caffeoyl shikimate esterase (CSE) is an enzyme in the lignin biosynthetic pathway in Arabidopsis. Science 341, 1103-1106.
| Crossref | Google Scholar |
Varet H, Brillet-Gueguen L, Coppee J-Y, Dillies M-A (2016) SARTools: a DESeq2- and EdgeR-Based R pipeline for comprehensive differential analysis of RNA-Seq data. PLoS ONE 11, e0157022 PMID:.
| Crossref | Google Scholar | PubMed |
Vogt T (2010) Phenylpropanoid biosynthesis. Molecular Plant 3, 2-20 PMID:.
| Crossref | Google Scholar | PubMed |
Vom Endt D, Kijne JW, Memelink J (2002) Transcription factors controlling plant secondary metabolism: what regulates the regulators? Phytochemistry 61, 107-114.
| Crossref | Google Scholar |
Wang J, Li J, Li J, Liu S, Wu X, Li J, Gao W (2016) Transcriptome profiling shows gene regulation patterns in ginsenoside pathway in response to methyl jasmonate in Panax Quinquefolium adventitious root. Scientific Reports 6, 37263 PMID:.
| Crossref | Google Scholar | PubMed |
Wang T, Yang B, Guan Q, Chen X, Zhong Z, Huang W, Zhu W, Tian J (2019a) Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors. BMC Plant Biology 19, 198 PMID:.
| Crossref | Google Scholar | PubMed |
Wang X, Chao N, Zhang M, Jiang X, Gai Y (2019b) Functional characteristics of caffeoyl shikimate esterase in Larix kaempferi and monolignol biosynthesis in gymnosperms. International Journal of Molecular Sciences 20, 6071 PMID:.
| Crossref | Google Scholar | PubMed |
Xiong J, Li S, Wang W, Hong Y, Tang K, Luo Q (2013) Screening and identification of the antibacterial bioactive compounds from Lonicera japonica Thunb. leaves. Food Chemistry 138, 327-333 PMID:.
| Crossref | Google Scholar | PubMed |
Xue Q, Fan H, Yao F, Cao X, Liu M, Sun J, Liu Y (2020) Transcriptomics and targeted metabolomics profilings for elucidation of pigmentation in Lonicera japonica flowers at different developmental stages. Industrial Crops and Products 145, 111981.
| Crossref | Google Scholar |
Yang B, He S, Liu Y, Liu B, Ju Y, Kang D, Sun X, Fang Y (2020) Transcriptomics integrated with metabolomics reveals the effect of regulated deficit irrigation on anthocyanin biosynthesis in Cabernet Sauvignon grape berries. Food Chemistry 314, 126170 PMID:.
| Crossref | Google Scholar | PubMed |
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11, R14 PMID:.
| Crossref | Google Scholar | PubMed |
Zhang T, Liu H, Bai X, Liu P, Yang Y, Huang J, Zhou L, Min X (2020) Fractionation and antioxidant activities of the water-soluble polysaccharides from Lonicera japonica Thunb. International Journal of Biological Macromolecules 151, 1058-1066.
| Crossref | Google Scholar |
Zhao J, Li H, Yin Y, An W, Qin X, Wang Y, Li Y, Fan Y, Cao Y (2020) Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. Scientific Reports 10, 4354 PMID:.
| Crossref | Google Scholar | PubMed |
Zheng S, Hao Y, Fan S, Cai J, Chen W, Li X, Zhu X (2021) Metabolomic and transcriptomic profiling provide novel insights into fruit ripening and ripening disorder caused by 1-MCP treatments in Papaya. International Journal of Molecular Sciences 22, 916 PMID:.
| Crossref | Google Scholar | PubMed |
