Integrated transcriptomics and metabolomics provide insights into the biosynthesis of militarine in the cell suspension culture system of Bletilla striata

Abstract

1. Elicitation modulates militarine biosynthesis in Bletilla striata.

2. Omics reveals key metabolites and genes involved in militarine synthesis.

3. Differential gene expression correlates with militarine content.

4. Insights for enhanced militarine production.

Keywords

Militarine / Elicitor / Suspended calluses / Multiomics / Molecular mechanism

References

[1] Althammer M, Regl C, Herburger K, et al.. Overexpression of UDP-sugar pyrophosphorylase leads to higher sensitivity towards galactose, providing new insights into the mechanisms of galactose toxicity in plants. Plant J, 2022, 109(6): 1416-1426,

[2] Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using diamond. Nat Methods, 2015, 12(1): 59,

[3] Busch T, Petersen M. Identification and biochemical characterisation of tyrosine aminotransferase from anthoceros agrestis unveils the conceivable entry point into rosmarinic acid biosynthesis in hornworts. Planta, 2021, 253(5): 98,

[4] Chen YC. Effects of salicylic acid on the physiological characteristics and theanine metabolism in tea seedlings of 'Tieguanyin'. China Tea, 2023, 45(01): 37-41

[5] Chen QP, Liao WF, Fu CH, et al.. Research progress on hydroxylase in the biosynthesis pathway of paclitaxel. J Biotechnol, 2016, 32(05): 554-564

[6] Chen S, Zhou Y, Chen Y, et al.. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 2018, 34(17): i884-i890,

[7] Chen DD, Bai YN, Zhang R, et al.. Synthesis of Phenyl 3-Phenylpropionate Compounds with NaBH4. Guangdong Chemical Industry, 2020, 47(11): 25-26

[8] Dong X, Huang R. Ferulic acid: An extraordinarily neuroprotective phenolic acid with anti-depressive properties. Phytomedicine, 2022, 105: 154355,

[9] Feduraev P, Skrypnik L, Riabova A, et al.. Phenylalanine and tyrosine as exogenous precursors of wheat (Triticum aestivum L.) secondary metabolism through PAL-associated pathways. Plants (Basel)., 2020, 9(4): 476

[10] Fiallos-Salguero MS, Li J, Li Y, et al.. Identification of AREB/ABF Gene Family involved in the response of ABA under salt and drought Stresses in Jute (Corchorus olitorius L.). Plants (Basel)., 2023, 12(5): 1161

[11] Fisher AK, Freedman BG, Bevan DR, et al.. A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. Comput Struct Biotechnol J, 2014, 11(18): 91-99,

[12] Fugate KK, Finger FL, Lafta AM, et al.. Wounding rapidly alters transcription factor expression, hormonal signaling, and phenolic compound metabolism in harvested sugarbeet roots. Front Plant Sci, 2023, 13: 1070247,

[13] Gao X, Hu Y, Xu Z, et al.. Expression profiling of the phenylalanine ammonia-lyase (PAL) gene family in ginkgo biloba L. Plant Signal Behav, 2023, 18(1): 2271807,

[14] Grabherr M, Haas B, Yassour M, et al.. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol, 2011, 29(7): 644,

[15] Guo J, Ma X, Cai Y, et al.. Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones. New Phytol, 2016, 210(2): 525-534,

[16] Guo L, Tan J, Deng X, et al.. Integrated analysis of metabolome and transcriptome reveals key candidate genes involved in flavonoid biosynthesis in Pinellia ternata under heat stress. J Plant Res, 2023, 136(3): 359-369,

[17] Hansen K, Coussens MJ, Sago J, et al.. Genome editing with CompoZr Custom Zinc Finger Nucleases (ZFNs). J vis Exp, 2012, 64: e3304

[18] Huang Y, Mei G, Fu X, et al.. Ultrasonic waves regulate antioxidant defense and gluconeogenesis to improve germination from naturally aged soybean seeds. Front Plant Sci, 2022, 13: 833858,

[19] Huang YW, Jiang XL, Chen WJ, et al.. Characterization of highly active tyrosine ammonia lyase and its application in biosynthesis of p-coumaric acid. Chin J Biotechnol, 2022, 38(12): 4553-4566

[20] Jaiswal KS, Rathod VK. Process intensification of enzymatic synthesis of flavor esters: A review. Chem Rec, 2022, 22(3): e202100213,

[21] Jia X, Li Q, Xu M, et al.. Advances in militarine: Pharmacology, synthesis, molecular regulation and regulatory mechanisms. Heliyon, 2024, 10(2): e24341,

[22] Ju X, Wang Z, Cai D, et al.. TAT gene polymorphism and its relationship with production traits in Muscovy ducks (Cairina Moschata). Poult Sci, 2023, 102(5): 102551,

[23] Leclerc D, Goujon L, Jaillard S, et al.. Gene editing corrects in vitro a G > A GLB1 transition from a GM1 gangliosidosis patient. CRISPR J, 2023, 6(1): 17-31,

[25] Li L, Hao B, Zhang Y, et al.. Metabolite profiling and distribution of militarine in rats using UPLC-Q-TOF-MS/MS. Mol, 2020, 25(5): 1082,

[26] Li K, Wu F, Chen M, et al.. Identification, biological function profiling and biosynthesis of secondary metabolites in medicinal orchids. Metabolites., 2023, 13(7): 829,

[27] Li Q, Gao L, Yu F, et al.. Evolution and diversification of CaM/CML gene family in green plants. Plant Physiol Biochem, 2023, 202: 107922,

[28] Li ZG, Wang YX, Xu MW, et al.. Molecular mechanism overview of metabolite biosynthesis in medicinal plants. Plant Physiol Biochem, 2023, 204: 108125,

[29] Liu H, Li L, Wen W, et al.. Full Transcriptome analysis of callus suspension culture system of Bletilla striata. Front Genet, 2020, 11(11): 995,

[30] Liu QQ, Hu XL, Yang YJ, et al.. Growth and metabolites of Chlorella sorokiniana regulated by sodium acetate. Microbiology China, 2021, 48(10): 3580-3587

[31] Liu H, Huang C, Li Q, et al.. Genome-Wide identification of genes related to biosynthesis of phenolic acid derivatives in Bletilla striata at different suspension culture stages. Front Plant Sci, 2022, 13: 875404,

[33] Ma ZH, Nan XT, Li WF, et al.. Comprehensive genomic identification and expression analysis 4CL gene family in apple. Gene., 2023, 858: 147197,

[34] McLarin MA, Leung IKH. Substrate specificity of polyphenol oxidase. Crit Rev Biochem Mol Biol, 2020, 55(3): 274-308,

[35] Mortazavi A, Williams B, McCue K, et al.. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods, 2008, 5(7): 621,

[36] Pan YC, Li L, Xiao SJ, et al.. Research progress on cultivation techniques of Radix Bupleuri. Chinese Patent Medicine, 2018, 40(5): 1142-1149

[37] Patro R, Duggal G, Love MI, et al.. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods, 2017, 14(4): 417,

[38] Pezeshki S, Warmbier I, Busch T, et al.. The first step into phenolic metabolism in the hornwort Anthoceros agrestis: molecular and biochemical characterization of two phenylalanine ammonia-lyase isoforms. Planta, 2022, 256(2): 33,

[39] Rauch S, He E, Srienc M, et al.. Programmable RNA-Guided RNA effector proteins built from human parts. Cell, 2019, 178(1): 122-134.e12,

[40] Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010, 26(1): 139,

[41] Rosengren E, Aman P, Thelin S, et al.. The macrophage migration inhibitory factor MIF is a phenylpyruvate tautomerase. FEBS Lett, 1997, 417(1): 85-88,

[42] Šanjug J, Kuna K, Goldštajn MŠ, et al.. Relationship between COMT Gene Polymorphism, Anxiety, and Pain Perception during Labour. J Clin Med, 2023, 12(19): 6298,

[43] Scheler U, Brandt W, Porzel A, et al.. Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast. Nat Commun, 2016, 7: 12942,

[44] Wang M, Manzoor MA, Wang X, et al.. Comparative genomic analysis of SAUR gene family, cloning and functional characterization of two genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri. Int J Mol Sci, 2022, 23(13): 7054,

[45] Wang M, Feng G, Yang Z, et al.. Genome-Wide characterization of the Aux/IAA gene family in orchardgrass and a functional analysis of DgIAA21 in responding to drought stress. Int J Mol Sci, 2023, 24(22): 16184,

[46] Wang H, Chen W, Xu Z, et al.. Functions of WRKYs in plant growth and development. Trends Plant Sci, 2023, 28(6): 630-645,

[47] Wang H, Zhang H, Liu J, et al.. Transcriptome analysis reveals the mechanism of nitrogen fertilizers in starch synthesis and quality in waxy and non-waxy proso millet. Carbohydr Polym, 2024, 323: 121372,

[48] Xu D, Pan Y, Chen J. Chemical constituents, pharmacologic properties, and clinical applications of Bletilla striata. Front Pharmacol, 2019, 10: 1168,

[49] Xu H, Cui H, Weng S, et al.. Crosstalk of cell death pathways unveils an autophagy-related gene AOC3 as a critical prognostic marker in colorectal cancer. Commun Biol, 2024, 7(1): 296,

[50] Yan X, Fan Y, Wei W, et al.. Production of bioactive ginsenoside compound K in metabolically engineered yeast. Cell Res, 2014, 24(6): 770-773,

[51] Yu HY, Gao RR, Xu ZC, et al.. Identification of SmCYP71AU66 related to tanshinone biosynthesis based on genome and transcriptome of Salvia Miltiorrhiza. World Science and Technology-Modernization of Traditional Chinese Medicine, 2019, 21(5): 859-866

[52] Yue C, Chen Q, Hu J, et al.. Genome-wide identification and characterization of GARP transcription factor gene family members reveal their diverse functions in tea plant (Camellia sinensis). Front Plant Sci, 2022, 13: 947072,

[53] Zeng Z, Zeng X, Guo Y, et al.. Determining the Role of UTP-Glucose-1-Phosphate uridylyltransferase (GalU) in improving the resistance of Lactobacillus acidophilus NCFM to freeze-drying. Foods, 2022, 11(12): 1719,

[54] Zhang JH, Wang Z, Chen HY, et al.. Cloning and functional study of SmCYP81C16 gene related to tanshinone synthesis. World Chinese Medicine, 2020, 15(5): 709-716

[55] Zhang R, Xuan L, Ni L, et al.. ADH Gene cloning and identification of flooding-responsive genes in Taxodium distichum (L.) Rich. Plants (Basel)., 2023, 12(3): 678

[56] Zhang Y, Gao J, Ma L, et al.. Tandemly duplicated CYP82Ds catalyze 14-hydroxylation in triptolide biosynthesis and precursor production in Saccharomyces cerevisiae. Nat Commun, 2023, 14(1): 875,

[57] Zhao S, Wang H, Liu K, et al.. The role of JrPPOs in the browning of walnut explants. BMC Plant Biol, 2021, 21(1): 9,