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Suo Y, Li S, Lyu H, Zhao X, Xing J, Chai X, Zhang Q, Fu C, Xu C, Liao J. The biosynthesis of trillin 6'- O-glucoside: A low-abundance yet pharmacologically active polyphyllin from Paris polyphylla. Synth Syst Biotechnol 2025; 10:610-619. [PMID: 40160283 PMCID: PMC11950731 DOI: 10.1016/j.synbio.2025.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2025] [Revised: 02/13/2025] [Accepted: 02/19/2025] [Indexed: 04/02/2025] Open
Abstract
Natural products from medicinal plants serve as an invaluable resource for drug discovery and development. However, low-abundance natural products are often understudied due to the challenges of obtaining sufficient quantities for pharmacological testing in cells or animals. Additionally, their complex stereochemistry and functional groups make chemical synthesis and purification difficult. In this study, we showcased the power of biosynthetic approaches to explore these underexplored compounds, using the low-abundance polyphyllin trillin 6'-O-glucoside from Paris polyphylla as an example. We identified two trillin 6'-O-glucosyltransferases required for its biosynthesis and successfully reconstructed the entire pathway in Nicotiana benthamiana. We demonstrated that trillin 6'-O-glucoside exhibits anti-bacterial activity comparable to major polyphyllins like polyphyllins I, II, and VII. Notably, it also showed much lower hemolytic activity, a common side effect of those major polyphyllins. Together, our study underscores the advantages of employing biosynthetic approaches to explore natural products that exist in low or trace abundances yet possess equally important pharmacological activities.
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Affiliation(s)
| | | | | | - Xin Zhao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiale Xing
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xin Chai
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qian Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chunjin Fu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chengchao Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingjing Liao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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Zhao CX, Yan YF, Zhao LX, Tang X, Chen YG, Song WJ, Long LP, Chen J, Tan CL, Zhang QZ, Pu XL, Shen QQ, Fan YZ, Tao Y, Ye X, Li SH, Liu Y. Characterization of a 4'-O-rhamnosyltransferase and de novo biosynthesis of bioactive steroidal triglycosides from Paris polyphylla. PLANT COMMUNICATIONS 2025; 6:101257. [PMID: 39844466 PMCID: PMC12010398 DOI: 10.1016/j.xplc.2025.101257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 12/28/2024] [Accepted: 01/15/2025] [Indexed: 01/24/2025]
Abstract
Steroidal saponins in Paris polyphylla featuring complicated sugar chains exhibit notable biological activities, but their sugar-chain biosynthesis is still not fully understood. Here, we identified a 4'-O-rhamnosyltransferase (UGT73DY2) from P. polyphylla, which catalyzes the 4'-O-rhamnosylation of polyphyllins V and VI, producing dioscin and pennogenin 3-O-β-chacotrioside, respectively. UGT73DY2 exhibits strict substrate specificity toward steroidal diglycosides and UDP-rhamnose, and a new steroidal triglycoside can be synthesized through enzyme catalysis. A mutation library was generated based on semi-rational design, identifying three mutants, I358T, A342V, and A132T, which displayed approximately two-fold enhanced enzyme activity. Molecular dynamics simulations revealed that shortened distances between the 4'-OH group of the sugar acceptor and either the crucial residue H20 or the donor UDP-Rha contribute to the enhanced enzyme activity. Moreover, subcellular localization analysis of UGT73DY2 and other biosynthetic enzymes indicated that dioscin biosynthesis predominantly occurs in the endoplasmic reticulum of plant cells. By co-expressing 14 biosynthetic genes in Nicotiana benthamiana, optimizing HMGR subcellular localization and cytochrome P450 gene sets, and engineering UGT73DY2, we successfully established a dioscin biosynthesis system with a yield of 3.12 ± 0.11 μg/g dry weight. This study not only clarifies the 4'-O-rhamnosylation process in steroidal saponin biosynthesis but also presents an alternative approach for the production of steroidal saponins in P. polyphylla through synthetic biology and metabolic engineering.
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Affiliation(s)
- Chen-Xiao Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Yuan-Feng Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Li-Xiao Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Xue Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Yue-Gui Chen
- State Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China
| | - Wen-Jun Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Li-Ping Long
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Jing Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Chun-Lin Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Qiao-Zhuo Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Xiu-Lan Pu
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Qin-Qin Shen
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Yu-Zhou Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Yang Tao
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Xiao Ye
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Sheng-Hong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China; State Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P.R. China.
| | - Yan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China.
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Hua X, Kou C, Wang F, Zhang J, Yuan J, Xue Z. Steroidal compounds in Paris polyphylla:structure, biological activities, and biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2025; 84:102695. [PMID: 39970503 DOI: 10.1016/j.pbi.2025.102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 01/02/2025] [Accepted: 01/28/2025] [Indexed: 02/21/2025]
Abstract
Steroidal compounds are chemical constituents found in the traditional medicinal plant Paris polyphylla, known for their significant pharmacological activities. Due to their complex structures, the biosynthetic pathways of these compounds have garnered considerable attention. In recent years, substantial progress has been made in elucidating the biosynthetic pathways of steroidal compounds from P. polyphylla, with several complete biosynthetic routes being fully characterized. The de novo synthesis of diosgenin has been successfully achieved in both Saccharomyces cerevisiae and Nicotiana benthamiana using various metabolic engineering techniques. Herein, we summarize the latest research progress regarding the structural classification, biological activities, and biosynthesis studies of steroidal compounds from P. polyphylla.
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Affiliation(s)
- Xin Hua
- Beijing Life Science Academy, Beijing, 102209, China; Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China
| | - Chengxi Kou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China
| | - Fengge Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China
| | | | - Jifeng Yuan
- School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, China.
| | - Zheyong Xue
- Beijing Life Science Academy, Beijing, 102209, China; Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, China; State Key Laboratory of Rice Biology and Breeding, Northern Center of China National Rice Research Institute, China National Rice Research Institute, Hangzhou 310006, China.
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Shirke HA, Darshetkar AM, Naikawadi VB, Kavi Kishor PB, Nikam TD, Barvkar VT. Genomics of sterols biosynthesis in plants: Current status and future prospects. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 353:112426. [PMID: 39956365 DOI: 10.1016/j.plantsci.2025.112426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 02/01/2025] [Accepted: 02/07/2025] [Indexed: 02/18/2025]
Abstract
Sterols produced by bacteria and all eukaryotic organisms are essential for membrane functionality and stability. They play a vital role in growth, development and in abiotic stress tolerance. They are involved in diverse responses to biotic and abiotic stresses that lead to providing resistance against multiple diseases. Additionally, sterols serve as defensive compounds against herbivorous insects and animals. Phytosterols derived from plants, improve human nutrition and health and cure different ailments. The biosynthetic pathways for sterols and triterpenes exhibit similarities until the synthesis of 2,3-oxidosqualene. The complexity of sterol pathways increases during the advanced stages of polycyclic structure synthesis, and remain poorly comprehended in plants. This review explores the various omics techniques used to unveil the functions of genes associated with the phytosterol pathways. The study investigates the biosynthetic gene clusters to clarify the structural arrangements of genes linked to metabolic pathways. Both the upstream and downstream genes associated with these pathways, as well as their evolutionary connections and interrelations within the pathways were brought to the forefront. Moreover, developing strategies to unravel the biosynthesis completely and their multi-layered regulation are crucial to comprehend the global roles that sterols play in plant growth, development, stress tolerance and in imparting defence against pathogens.
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Affiliation(s)
- Harshad A Shirke
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India.
| | | | - Vikas B Naikawadi
- Department of Botany, Chandmal Tarachand Bora College, Shirur, Pune 412210, India.
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
| | - Tukaram D Nikam
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India.
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India.
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Wang J, Wang Z, Wang H, Pai M, Li T, Zhang H, Ye B, Tang L, Fu R, Zhang Y. UDP-glucosyltransferases from UGT73 family catalyze 3-O-glucosylation of isosteroidal and steroidal alkaloids in Fritillaria unibracteata var. wabuensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70042. [PMID: 40026195 DOI: 10.1111/tpj.70042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 12/30/2024] [Accepted: 01/29/2025] [Indexed: 03/04/2025]
Abstract
Fritillaria unibracteata var. wabuensis is an important resource plant for the famous traditional Chinese medicine Fritillariae cirrhosae bulbus ("Chuanbeimu" in Chinese). F. cirrhosae bulbus is the dried bulbs of several species from Fritillaria genus, with isosteroidal alkaloids components assumed as the bioactive ingredients. However, the biosynthesis pathway of isosteroidal alkaloids remains elusive. Here, we adopted F. unibracteata var. wabuensis as a material to identify genes involved in the biosynthesis of isosteroidal alkaloids. We first constructed the multi-tissue metabolome and transcriptome dataset of F. unibracteata var. wabuensis. Interestingly, imperialine-3-β-d-glucoside, an isosteroidal glycoalkaloid, was found to be the major tissue-specific accumulated alkaloid. Through phylogenetic and co-expression analysis, we identified two UDP-glucosyltransferases from UGT73 family catalyzing 3-O-glucosylation of isosteroidal and steroidal alkaloids: imperialine 3-O-glucosyltransferase (FuwI3GT) can use both isosteroidal alkaloid imperialine and steroidal alkaloid solanidine as substrates, while solanidine 3-O-glucosyltransferase (FuwS3GT) can only use steroidal alkaloid solanidine as a substrate. We further approved that the W201 residue of FuwI3GT determined its substrate preference of isosteroidal alkaloids. Overall, our results identified enzymes involved in 3-O-glucosylation of isosteroidal and steroidal alkaloids in F. unibracteata var. wabuensis and paved the way to fully elucidate the isosteroidal alkaloid biosynthesis pathway in Fritillaria species.
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Affiliation(s)
- Jingjin Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zikun Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Hsihua Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mingxin Pai
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Tingting Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Hengyang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Bengui Ye
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- College of Medical, Tibet University, Lasa, 850002, China
| | - Lin Tang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Gharat SA, Tamhane VA, Giri AP, Aharoni A. Navigating the challenges of engineering composite specialized metabolite pathways in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70100. [PMID: 40089911 PMCID: PMC11910955 DOI: 10.1111/tpj.70100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 02/26/2025] [Accepted: 02/28/2025] [Indexed: 03/17/2025]
Abstract
Plants are a valuable source of diverse specialized metabolites with numerous applications. However, these compounds are often produced in limited quantities, particularly under unfavorable ecological conditions. To achieve sufficient levels of target metabolites, alternative strategies such as pathway engineering in heterologous systems like microbes (e.g., bacteria and fungi) or cell-free systems can be employed. Another approach is plant engineering, which aims to either enhance the native production in the original plant or reconstruct the target pathway in a model plant system. Although increasing metabolite production in the native plant is a promising strategy, these source plants are often exotic and pose significant challenges for genetic manipulation. Effective pathway engineering requires comprehensive prior knowledge of the genes and enzymes involved, as well as the precursor, intermediate, branching, and final metabolites. Thus, a thorough elucidation of the biosynthetic pathway is closely linked to successful metabolic engineering in host or model systems. In this review, we highlight recent advances in strategies for biosynthetic pathway elucidation and metabolic engineering. We focus on efforts to engineer complex, multi-step pathways that require the expression of at least eight genes for transient and three genes for stable transformation. Reports on the engineering of complex pathways in stably transformed plants remain relatively scarce. We discuss the major hurdles in pathway elucidation and strategies for overcoming them, followed by an overview of achievements, challenges, and solutions in pathway reconstitution through metabolic engineering. Recent advances including computer-based predictions offer valuable platforms for the sustainable production of specialized metabolites in plants.
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Affiliation(s)
- Sachin A. Gharat
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovot7610001Israel
| | - Vaijayanti A. Tamhane
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovot7610001Israel
- Department of Biotechnology (Merged With Institute of Bioinformatics and Biotechnology)Savitribai Phule Pune UniversityPuneMaharashtra411007India
| | - Ashok P. Giri
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovot7610001Israel
- Biochemical Sciences DivisionCSIR‐National Chemical LaboratoryPune411008India
- Academy of Scientific and Innovative Research (AcSIR)Ghaziabad201002India
| | - Asaph Aharoni
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovot7610001Israel
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Ye X, Tao Y, Pu XL, Hu H, Chen J, Tan CL, Tan X, Li SH, Liu Y. The genus Paris: a fascinating resource for medicinal and botanical studies. HORTICULTURE RESEARCH 2025; 12:uhae327. [PMID: 40051578 PMCID: PMC11883231 DOI: 10.1093/hr/uhae327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 11/15/2024] [Indexed: 03/09/2025]
Abstract
The genus Paris, comprising a series of distinctive medicinal plants, has been utilized globally for its therapeutic properties over centuries. Modern pharmacological studies have demonstrated that secondary metabolites from Paris species exhibit significant pharmacological activities, including anticancer, hemostatic, anti-inflammatory, antimicrobial, and other effects. Additionally, the unique morphological traits and large genome size of Paris species have continuously captured the interest of botanists and horticulturalists. Nonetheless, the conservation of wild Paris populations is threatened due to the lengthy reproductive cycle and overexploitation, posing considerable challenges to their development and sustainable use. This review provides a comprehensive overview of the botanical characteristics, historical medicinal uses, pharmacological effects, and toxicity evaluation of secondary metabolites in Paris species. It also covers the molecular biological research conducted on the genus Paris and proposes key research questions and important directions for future solutions. We advocate the expansion and implementation of multi-omics approaches, as well as molecular and genetic technologies recently advanced in model plant research, to intensively study Paris species. This will facilitate the comprehensive understanding of gene function and molecular mechanisms underlying specialized metabolite formation in Paris.
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Affiliation(s)
- Xiao Ye
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
- Chengdu Medical College, Chengdu 610500, China
| | - Yang Tao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiu-Lan Pu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hong Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jing Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Chun-Lin Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xin Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Sheng-Hong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Xu P, Mi Q, Zhang X, Zhang X, Yu M, Gao Y, Wan X, Chen Y, Li Q, Chen J, Zheng G. Dissection of transcriptome and metabolome insights into the polyphyllin biosynthesis in Paris. BMC PLANT BIOLOGY 2025; 25:206. [PMID: 39955498 PMCID: PMC11829371 DOI: 10.1186/s12870-025-06219-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Accepted: 02/07/2025] [Indexed: 02/17/2025]
Abstract
BACKGROUND Polyphyllins are significant medicinal compounds found in Paris species, with different polyphyllins fulfilling distinct medicinal roles. Although some genes involved in polyphyllin synthesis have been identified, further exploration of the genes in the polyphyllin synthesis pathway is necessary due to the extensive genome of Paris species. The content and composition of polyphyllins vary among different Paris species, and the variations in specific polyphyllin levels across these plants make them promising candidates for identifying metabolites and genes associated with the biosynthesis of specific polyphyllins. RESULTS In this study, we investigate the global metabolic and transcriptomic profiles of three types of Paris polyphylla var. yunnanensis (Franch.) Hand.-Mazz, one Paris fargesii Franch, and one Paris forrestii (Takht.) H. Li. The rhizome of P. polyphylla is rich in polyphyllin I and II, while P. forrestii is abundant in polyphyllin III, and P. fargesii contains high levels of polyphyllin VI, VII and H. The three Paris species exhibit distinct metabolomic and transcriptomic profiles. Through an integrated analysis of metabolic and transcriptomic data, along with a phylogenetic analysis of genes related to polyphyllin synthesis in Paris, we annotated a total of six 2,3-oxidosqualene cyclases (OSCs), 120 cytochrome P450s (CYPs), and 138 UDP glycosyltransferases (UGTs). Phylogenetic tree analysis of the obtained data assisted in refining the candidate gene pool for OSC, CYP, and UGT. Subsequently, we identified 6, 12, and 26 candidate genes for OSC, CYP, and UGT, respectively. Finally, by combining the analyses of metabolic and genetic differences, we identified a total of 17 candidate genes, including 2 CAS, 4 CYP, and 11 UGT. CONCLUSIONS P. fargesii and P. forrestii are candidate medicinal plants for the development and application of specific polyphyllins. Transcripts from the UGT91 subfamily in Paris may play dual roles, contributing to both the synthesis of polyphyllin II and the catabolism of polyphyllin V and VI. The homologous genes of PpUGT73CE1 may regulate the synthesis of polyphyllin VI in P. fargesii. This study provides new insights into the investigation of biosynthetic pathways in medicinal plants that lack gene clusters.
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Affiliation(s)
- Ping Xu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Qi Mi
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Xiaoye Zhang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Xuan Zhang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Mengwen Yu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Yingsi Gao
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Xiheng Wan
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Yichun Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Qiaoyuan Li
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China
| | - Jia Chen
- College of Ethnic Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China.
| | - Guowei Zheng
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, People's Republic of China.
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Hu K, Feng Y, Li P, Chen M, Shen ZJ, Sun XQ, Lu RS. Haplotype-resolved genome and population genomics provide insights into dioscin biosynthesis and evolutionary history of the medicinal species Dioscorea nipponica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e17237. [PMID: 39935194 DOI: 10.1111/tpj.17237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 11/24/2024] [Accepted: 12/18/2024] [Indexed: 02/13/2025]
Abstract
Dioscorea nipponica, a perennial herb widely distributed in the Sino-Japanese Floristic Region, is renowned for its medicinal properties, particularly its ability to produce dioscin. Here, we present a haplotype-resolved genome assembly of the diploid D. nipponica, comprising 511.41 Mb for Haplotype A and 498.29 Mb for Haplotype B, each organized into 10 chromosomes. The two haplotypes exhibited high similarity, with only 2.75% of the allelic genes exhibiting specific expression. Key genes in the dioscin biosynthesis pathway were identified, and expression analysis revealed that the majority (16/21) of genes involved in the first two stages were highly expressed in rhizomes. Notably, significant expansion of the CYP90, CYP94, and UGT73 gene families was observed in dioscin-producing species, highlighting their critical roles in dioscin biosynthesis. Additionally, genome size estimation and population genomic analyses of diverse D. nipponica accessions identified four principal clades in D. nipponica, corresponding to diploid, di-tetra-octoploid, tetraploid, and hexaploid accessions from various geographic regions, with clade A (diploids) further divided into five subclades. Demographic analysis of the diploid D. nipponica revealed a prolonged decline in effective population size from the Pleistocene to the Last Glacial Maximum, with population splits occurring during the mid-to-late Pleistocene. Selective sweep analysis identified key genes, including HD-Zip I, ADH1, SMT1, and CYPs that may contribute to adaptation to high-latitude environments and the geographical variations in dioscin content. Overall, this study enhances our understanding of the genomic architecture, biosynthetic pathways, and evolutionary dynamics of D. nipponica, providing valuable insights into its medicinal potential and evolution.
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Affiliation(s)
- Ke Hu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yu Feng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Min Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zi-Jie Shen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xiao-Qin Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Rui-Sen Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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10
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Fan B, Ji Z, Zhu M, Chen Y, Liang J, Li Y, Yi R, Liu C, Wang L, Shi N, Yang T, Huang R, Yang L, Ji A, Liu Z, Duan L. Elucidation of the biosynthetic pathways of timosaponins reveals the antifungal mechanisms in Anemarrhena asphodeloides. J Adv Res 2025:S2090-1232(25)00068-2. [PMID: 39889822 DOI: 10.1016/j.jare.2025.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 12/19/2024] [Accepted: 01/27/2025] [Indexed: 02/03/2025] Open
Abstract
INTRODUCTION Timosaponins, as steroidal saponins, are the primary active constituents and quality biomarkers in Anemarrhena asphodeloides Bunge. Despite their significance, the biosynthetic pathways of timosaponins have not been thoroughly investigated. OBJECTIVES This study aims to delineate the biosynthetic pathway of timosaponins in A. asphodeloides, elucidate the catalytic mechanisms of the key cycloartenol synthase (CAS), and investigate the antifungal properties of timosaponins. METHODS Genes were cloned from A. asphodeloides and heterologous expressed in yeast, tobacco or bacillus coli. Site-directed mutagenesis and molecular docking were used to elucidate the catalytic mechanism of CAS. Antifungal assays were conducted to evaluate the antifungal activities of timosaponins. RESULTS In this study, we elucidated the biochemical functions of seven genes involved in timosaponins biosynthesis in A. asphodeloides. Among three candidate OSC genes, AaOSCR12 was identified as the gene encoding cycloartenol synthase, which is responsible for the skeleton cyclization in timosaponin biosynthesis. Six residues (257H, 369N, 448T, 507V, 558P, 616Y) were identified as the critical catalytic active sites of CAS (AaOSCR12). Sterol methyltransferase (AaSMT1) and sterol side-chain reductase (AaSSR2) were found to be the subsequent enzymes and the branching points leading to phytosterol and cholesterol biosynthesis, respectively. Two oxide reductase genes, AaCYP90B27 and AaCYP90B2, were responsible for post-modification of cholesterol, serving as a precursor of timosaponins. A key 26-O-β-glucosidase (AaF26G1) was identified as facilitating the conversion of furostanol-type timosaponins into spirostanol-type timosaponins. Antifungal assays revealed that spirostanol-type timosaponin III exhibits superior antifungal activity compared to furostanol-type timosaponin II, potentially linked to plant defense mechanisms involving AaF26G1. CONCLUSION This study utilized a multi-chassis cross-identification strategy, revealing key enzymes in the timosaponin biosynthetic pathway and offering novel insights into plant defense mechanisms against microbial pathogens.
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Affiliation(s)
- Baolian Fan
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Zhongju Ji
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China; Chinese Medicine Guangdong Laboratory, Hengqin 519031 China
| | - Min Zhu
- The Third People's Hospital of Hubei Province, Wuhan 430000 China
| | - Yidu Chen
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Jincai Liang
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Yu Li
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Runxiang Yi
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Chenxu Liu
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Lijun Wang
- Yiyang Normal College, Yiyang 413000 China
| | - Ningwei Shi
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Tingxing Yang
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Ruoshi Huang
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Lu Yang
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China
| | - Aijia Ji
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China.
| | - Zhongqiu Liu
- Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China.
| | - Lixin Duan
- Chinese Medicine Guangdong Laboratory, Hengqin 519031 China; Guangdong Engineering Research Center of Biosynthesis and Metabolism of Effective Components of Chinese Medicine, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006 China.
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11
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Deng YJ, Duan AQ, Liu H, Xu ZS, Xiong AS. Generation of high purity capsanthin and capsorubin through synthetic metabolic engineering in carrot germplasm. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:7202-7216. [PMID: 39140865 DOI: 10.1093/jxb/erae351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/13/2024] [Indexed: 08/15/2024]
Abstract
Capsanthin and capsorubin are red κ-xanthophylls exclusively found in a handful of other plant species. Currently, capsanthin and capsorubin are extracted from red pepper (Capsicum annuum L.). Here, high purity production of capsanthin and capsorubin was achieved in carrot (Daucus carota L.) taproot by a synthetic metabolic engineering strategy. Expression of a capsanthin-capsorubin synthase gene (CaCCS) from pepper resulted in dominant production of capsanthin, whereas expression of a LiCCS gene from tiger lily (Lilium lancifolium Thunb.) resulted in production of both capsanthin and capsorubin in carrot taproot. The highest content of capsanthin and capsorubin was obtained in LiC-1 carrot taproot hosting the LiCCS gene. Co-expression of DcBCH1 with CCS could improve the purity of capsanthin and capsorubin by eliminating the non-target carotenoids (e.g. α-carotene and β-carotene). The highest purity of capsanthin and capsorubin was obtained in BLiC-1 carrot taproot hosting DcBCH1+LiCCS genes, 91.10% of total carotenoids. The non-native pigments were esterified partially and stored in the globular chromoplast of carrot taproot. Our results demonstrated the use of carrot taproot as green factories for high purity production of capsanthin and capsorubin. The capsanthin/capsorubin carrot germplasms are also valuable materials for breeding colorful carrots cultivars.
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Affiliation(s)
- Yuan-Jie Deng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ao-Qi Duan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
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12
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Xu P, Chen J, Mi Q, Li W, Lu Y, Luo W, Yu M, Zhang X, Tu Z, Xu H, Zheng G. Metabolomics and transcriptomics profiling of three Paris species with varied polyphyllin compositions. Sci Data 2024; 11:1293. [PMID: 39604406 PMCID: PMC11603173 DOI: 10.1038/s41597-024-04066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 10/31/2024] [Indexed: 11/29/2024] Open
Abstract
Most of the species in Paris have important medicinal values in China. Polyphyllins are the key components in Paris, with varying levels and compositions among different species. This study investigated polyphyllin compositions of 206 Paris samples from 16 different producing areas. 9 Paris polyphylla var. yunnanensis, 3 Paris fargesii, and 3 Paris forrestii were selected based on polyphyllin levels and composition for metabolome and transcriptome analysis. A total of 1,243 metabolites were identified among these samples, along with 92.11 Gb of full-length transcriptome data. This study provides potential candidate genes involved in polyphyllins synthesis in Paris, aiming to facilitate the biosynthesis of different polyphyllins.
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Affiliation(s)
- Ping Xu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Jia Chen
- College of Ethnic Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Qi Mi
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Wenchun Li
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - You Lu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Wenxiu Luo
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Mengwen Yu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Xuan Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Zhenhua Tu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Honggao Xu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China
| | - Guowei Zheng
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, People's Republic of China.
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13
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Fang Y, Tai Z, Hu K, Luo L, Yang S, Liu M, Xie X. Comprehensive Review on Plant Cytochrome P450 Evolution: Copy Number, Diversity, and Motif Analysis From Chlorophyta to Dicotyledoneae. Genome Biol Evol 2024; 16:evae240. [PMID: 39506518 PMCID: PMC11586672 DOI: 10.1093/gbe/evae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 10/17/2024] [Accepted: 11/04/2024] [Indexed: 11/08/2024] Open
Abstract
Cytochrome P450 enzymes (CYPs) are widely distributed among various plant groups and constitute approximately 1% of the total number of protein-coding genes. Extensive studies suggest that CYPs are involved in nearly all molecular processes that occur in plants. Over the past two decades, the identification of CYP genes has expanded rapidly, with more than 40,000 CYP genes and 819 CYP families being discovered. Copy number variation is a significant evolutionary characteristic of gene families, yet a systematic characterization of the copy evolution patterns in plant CYP gene families has been lacking, resulting in confusion and challenges in understanding CYP functions. To address these concerns, this review provides comprehensive statistics and analyses of the copy number and diversity of almost all plant CYP gene families, focusing on CYP evolution from Chlorophyta to Dicotyledoneae. Additionally, we examined the subfamily characteristics of certain CYP families with restricted copy changes and identified several CYP subfamilies that play pivotal roles in this event. Furthermore, we analyzed the structural conservation of CYPs across different taxa and compiled a comprehensive database to support plant CYP studies. Our analysis revealed differences in the six core conserved motifs of plant CYP proteins among various clans and plant taxa, while demonstrating similar conservation patterns for the ERR (glutamic acid-arginine-arginine) triad motifs. These findings will significantly facilitate the understanding of plant CYP gene evolution and metabolic diversity and serve as a valuable reference for researchers studying CYP enzymes.
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Affiliation(s)
- Yuanpeng Fang
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Zheng Tai
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Keyi Hu
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Lingfeng Luo
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Sanwei Yang
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Mengmeng Liu
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Xin Xie
- College of Agriculture, Guizhou University, Guiyang 550025, PR China
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Golubova D, Tansley C, Su H, Patron NJ. Engineering Nicotiana benthamiana as a platform for natural product biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102611. [PMID: 39098308 DOI: 10.1016/j.pbi.2024.102611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/06/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Nicotiana benthamiana is a model plant, widely used for research. The susceptibility of young plants to Agrobacterium tumefaciens has been utilised for transient gene expression, enabling the production of recombinant proteins at laboratory and commercial scales. More recently, this technique has been used for the rapid prototyping of synthetic genetic circuits and for the elucidation and reconstruction of metabolic pathways. In the last few years, many complex metabolic pathways have been successfully reconstructed in this species. In addition, the availability of improved genomic resources and efficient gene editing tools have enabled the application of sophisticated metabolic engineering approaches to increase the purity and yield of target compounds. In this review, we discuss recent advances in the use of N. benthamiana for understanding and engineering plant metabolism, as well as efforts to improve the utility of this species as a production chassis for natural products.
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Affiliation(s)
- D Golubova
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - C Tansley
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - H Su
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - N J Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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15
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Li Y, Zhao ZA, Hu J, Lei T, Chen Q, Li J, Yang L, Hu D, Gao S. MeJA-induced hairy roots in Plumbago auriculata L. by RNA-seq profiling and key synthase provided new insights into the sustainable production of plumbagin and saponins. FRONTIERS IN PLANT SCIENCE 2024; 15:1411963. [PMID: 39070915 PMCID: PMC11272555 DOI: 10.3389/fpls.2024.1411963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/04/2024] [Indexed: 07/30/2024]
Abstract
Naturally synthesized secondary metabolites in plants are considered an important source of drugs, food additives, etc. Among them, research on natural plant medicinal components and their synthesis mechanisms has always been of high concern. We identified a novel medicinal floral crop, Plumbago auriculata L., that can be treated with methyl jasmonate (MeJA) for the rapid or sustainable production of natural bioactives from hairy roots. In the study, we globally analyzed the changes in the accumulation of plumbagin and others in the hairy roots of Plumbago auriculata L. hairy roots (PAHR) 15834 in P. auriculata L. based on 100 μmol/L of MeJA treatment by RNA-seq profiling, and we found that there was a significant increase in the accumulation of plumbagin and saponin before 24 h. To explain the principle of co-accumulation, it showed that MeJA induced JA signaling and the shikimic acid pathway, and the methylvaleric acid (MVA) pathway was activated downstream subsequently by the Mfuzz and weighted gene co-expression analysis. Under the shared metabolic pathway, the high expression of PAL3 and HMGR promoted the activity of the "gateway enzymes" phenylalanine ammonia lyase (PAL) and 3-hydroxy-3-methylglutaryl CoA reductase (HMGR), which respectively induced the high expression of key reaction enzyme genes, including chalcone synthase (CHS), isopentenyl diphosphate (IPP), and farnesyl pyrophosphate synthase (FPS), that led to the synthesis of plumbagin and saponin. We speculated that large amounts of ketones and/or aldehydes were formed under the action of these characteristic enzymes, ultimately achieving their co-accumulation through polyketone and high-level sugar and amino acid metabolism. The study results provided a theoretical basis for carrying out the factory refinement and biosynthesis of plumbagin and saponins and also provided new ideas for fully exploiting multifunctional agricultural crops and plants and developing new agricultural by-products.
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Affiliation(s)
- Yirui Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Zi-an Zhao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Ju Hu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Ting Lei
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Qibing Chen
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiani Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lijuan Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Di Hu
- School of Fine Arts and Calligraphy, Sichuan Normal University, Chengdu, China
| | - Suping Gao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
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16
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Kou C, Liu J, Yin X, He D, Liu J, Hua X, Ma R, Sun W, Xue Z, Ma P. Efficient heterologous biosynthesis of verazine, a metabolic precursor of the anti-cancer drug cyclopamine, in Nicotiana benthamiana. PLANT COMMUNICATIONS 2024; 5:100831. [PMID: 38308438 PMCID: PMC11211220 DOI: 10.1016/j.xplc.2024.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Chengxi Kou
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Jingling Liu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xue Yin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Di He
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jia Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Xin Hua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Rui Ma
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China.
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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Wang H, Abe I. Recent developments in the enzymatic modifications of steroid scaffolds. Org Biomol Chem 2024; 22:3559-3583. [PMID: 38639195 DOI: 10.1039/d4ob00327f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Steroids are an important family of bioactive compounds. Steroid drugs are renowned for their multifaceted pharmacological activities and are the second-largest category in the global pharmaceutical market. Recent developments in biocatalysis and biosynthesis have led to the increased use of enzymes to enhance the selectivity, efficiency, and sustainability for diverse modifications of steroids. This review discusses the advancements achieved over the past five years in the enzymatic modifications of steroid scaffolds, focusing on enzymatic hydroxylation, reduction, dehydrogenation, cascade reactions, and other modifications for future research on the synthesis of novel steroid compounds and related drugs, and new therapeutic possibilities.
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Affiliation(s)
- Huibin Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Lin J, Yin X, Zeng Y, Hong X, Zhang S, Cui B, Zhu Q, Liang Z, Xue Z, Yang D. Progress and prospect: Biosynthesis of plant natural products based on plant chassis. Biotechnol Adv 2023; 69:108266. [PMID: 37778531 DOI: 10.1016/j.biotechadv.2023.108266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
Plant-derived natural products are a specific class of active substances with numerous applications in the medical, energy, and industrial fields. Many of these substances are in high demand and have become the fundamental materials for various purposes. Recently, the use of synthetic biology to produce plant-derived natural products has become a significant trend. Plant chassis, in particular, offer unique advantages over microbial chassis in terms of cell structure, product affinity, safety, and storage. The development of the plant hairy root tissue culture system has accelerated the commercialization and industrialization of synthetic biology in the production of plant-derived natural products. This paper will present recent progress in the synthesis of various plant natural products using plant chassis, organized by the types of different structures. Additionally, we will summarize the four primary types of plant chassis used for synthesizing natural products from plant sources and review the enabling technologies that have contributed to the development of synthetic biology in recent years. Finally, we will present the role of isolated and combined use of different optimization strategies in breaking the upper limit of natural product production in plant chassis. This review aims to provide practical references for synthetic biologists and highlight the great commercial potential of plant chassis biosynthesis, such as hairy roots.
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Affiliation(s)
- Junjie Lin
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xue Yin
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin 150040, China
| | - Youran Zeng
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xinyu Hong
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Shuncang Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Beimi Cui
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Qinlong Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zongsuo Liang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin 150040, China..
| | - Dongfeng Yang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China; Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, China.
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19
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Li Y, Li Z, Zhang F, Li S, Gu Y, Tian W, Tian W, Wang J, Wen J, Li J. Integrated evolutionary pattern analyses reveal multiple origins of steroidal saponins in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:823-839. [PMID: 37522396 DOI: 10.1111/tpj.16411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/01/2023]
Abstract
Steroidal saponins are a class of specialized metabolites essential for plant's response to biotic and abiotic stresses. They are also important raw materials for the industrial production of steroid drugs. Steroidal saponins are present in some monocots, such as Dioscorea and Paris, but their distribution, origin, and evolution in plants remain poorly understood. By reconstructing the evolutionary history of the steroidal saponin-associated module (SSAM) in plants, we reveal that the steroidal saponin pathway has its origin in Asparagus and Dioscorea. Through evaluating the distribution and evolutionary pattern of steroidal saponins in angiosperms, we further show that steroidal saponins originated multiple times in angiosperms, and exist in early diverged lineages of certain monocot lineages including Asparagales, Dioscoreales, and Liliales. In these lineages, steroidal saponins are synthesized through the high copy and/or high expression mechanisms of key genes in SSAM. Together with shifts in gene evolutionary rates and amino acid usage, these molecular mechanisms shape the current distribution and diversity of steroidal saponins in plants. Consequently, our results provide new insights into the distribution, diversity and evolutionary history of steroidal saponins in plants, and enhance our understanding of plants' resistance to abiotic and biotic stresses. Additionally, fundamental understanding of the steroidal saponin biosynthesis will facilitate their industrial production and pharmacological applications.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zihao Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Furui Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Song Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongbing Gu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weijun Tian
- Yunnan Baotian Agricultural Technology Co., Ltd, Kunming, 650101, China
| | - Weirong Tian
- Yunnan Baotian Agricultural Technology Co., Ltd, Kunming, 650101, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, 20013-7012, DC, USA
| | - Jiaru Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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20
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Wang W, Hou L, Li S, Li J. The Functional Characterization of DzCYP72A12-4 Related to Diosgenin Biosynthesis and Drought Adaptability in Dioscorea zingiberensis. Int J Mol Sci 2023; 24:ijms24098430. [PMID: 37176134 PMCID: PMC10179397 DOI: 10.3390/ijms24098430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/02/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023] Open
Abstract
Dioscorea zingiberensis is a perennial herb famous for the production of diosgenin, which is a valuable initial material for the industrial synthesis of steroid drugs. Sterol C26-hydroxylases, such as TfCYP72A616 and PpCYP72A613, play an important role in the diosgenin biosynthesis pathway. In the present study, a novel gene, DzCYP72A12-4, was identified as C26-hydroxylase and was found to be involved in diosgenin biosynthesis, for the first time in D. zingiberensis, using comprehensive methods. Then, the diosgenin heterogenous biosynthesis pathway starting from cholesterol was created in stable transgenic tobacco (Nicotiana tabacum L.) harboring DzCYP90B71(QPZ88854), DzCYP90G6(QPZ88855) and DzCYP72A12-4. Meanwhile, diosgenin was detected in the transgenic tobacco using an ultra-performance liquid chromatography system (Vanquish UPLC 689, Thermo Fisher Scientific, Bremen, Germany) tandem MS (Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer, Thermo Fisher Scientific, Bremen, Germany). Further RT-qPCR analysis showed that DzCYP72A12-4 was highly expressed in both rhizomes and leaves and was upregulated under 15% polyethylene glycol (PEG) treatment, indicating that DzCYP72A12-4 may be related to drought resistance. In addition, the germination rate of the diosgenin-producing tobacco seeds was higher than that of the negative controls under 15% PEG pressure. In addition, the concentration of malonaldehyde (MDA) was lower in the diosgenin-producing tobacco seedlings than those of the control, indicating higher drought adaptability. The results of this study provide valuable information for further research on diosgenin biosynthesis in D. zingiberensis and its functions related to drought adaptability.
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Affiliation(s)
- Weipeng Wang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lixiu Hou
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Song Li
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiaru Li
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan 430072, China
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