1
|
Imran M, Junaid M, Shafiq S, Liu S, Chen X, Wang J, Tang X. Multiomics analysis reveals a substantial decrease in nanoplastics uptake and associated impacts by nano zinc oxide in fragrant rice (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134640. [PMID: 38810581 DOI: 10.1016/j.jhazmat.2024.134640] [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: 03/16/2024] [Revised: 04/28/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
Nanoplastics (NPs) have emerged as global environmental pollutants with concerning implications for sustainable agriculture. Understanding the underlying mechanisms of NPs toxicity and devising strategies to mitigate their impact is crucial for crop growth and development. Here, we investigated the nanoparticles of zinc oxide (nZnO) to mitigate the adverse effects of 80 nm NPs on fragrant rice. Our results showed that optimized nZnO (25 mg L-1) concentration rescued root length and structural deficits by improving oxidative stress response, antioxidant defense mechanism and balanced nutrient levels, compared to seedlings subjected only to NPs stress (50 mg L-1). Consequently, microscopy observations, Zeta potential and Fourier transform infrared (FTIR) results revealed that NPs were mainly accumulated on the initiation joints of secondary roots and between cortical cells that blocks the nutrients uptake, while the supplementation of nZnO led to the formation of aggregates with NPs, which effectively impedes the uptake of NPs by the roots of fragrant rice. Transcriptomic analysis identified a total of 3973, 3513 and 3380 differentially expressed genes (DEGs) in response to NPs, nZnO and NPs+nZnO, respectively, compared to the control. Moreover, DEGs were significantly enriched in multiple pathways including biosynthesis of secondary metabolite, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, carotenoid biosynthesis, plant-pathogen interactions, MAPK signaling pathway, starch and sucrose metabolism, and plant hormone signal transduction. These pathways could play a significant role in alleviating NPs toxicity and restoring fragrant rice roots. Furthermore, metabolomic analysis demonstrated that nZnO application restored 2-acetyl-1-pyrroline (2-AP) pathways genes expression, enzymatic activities, and the content of essential precursors related to 2-AP biosynthesis under NPs toxicity, which ultimately led to the restoration of 2-AP content in the leaves. In conclusion, this study shows that optimized nZnO application effectively alleviates NPs toxic effects and restores both root structure and aroma production in fragrant rice leaves. This research offers a sustainable and practical strategy to enhance crop production under NPs toxicity while emphasizing the pivotal role of essential micronutrient nanomaterials in agriculture.
Collapse
Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Muhammad Junaid
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Sarfraz Shafiq
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Shulin Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyuan Chen
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
2
|
Chen R, Wang M, Keasling JD, Hu T, Yin X. Expanding the structural diversity of terpenes by synthetic biology approaches. Trends Biotechnol 2024; 42:699-713. [PMID: 38233232 DOI: 10.1016/j.tibtech.2023.12.006] [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: 08/22/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible five-carbon (C5) isoprene units. New approaches have recently been developed to expand their structural diversity. This review systematically explores the combinatorial biosynthesis of noncanonical building blocks via the coexpression of the canonical mevalonate (MVA) pathway and C-methyltransferases (C-MTs), or by using the lepidopteran mevalonate (LMVA) pathway. Unnatural terpenoids can be created from farnesyl diphosphate (FPP) analogs by chemobiological synthesis and terpene cyclopropanation by artificial metalloenzymes (ArMs). Advanced technologies to accelerate terpene biosynthesis are discussed. This review provides a valuable reference for increasing the diversity of valuable terpenoids and their derivatives, as well as for expanding their potential applications.
Collapse
Affiliation(s)
- Rong Chen
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
| | - Ming Wang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tianyuan Hu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China
| | - Xiaopu Yin
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China.
| |
Collapse
|
3
|
Ishikawa E, Kanai S, Shinozawa A, Hyakutake M, Sue M. Hordeum vulgare CYP76M57 catalyzes C 2 shortening of tryptophan side chain by C-N bond rearrangement in gramine biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:892-904. [PMID: 38281119 DOI: 10.1111/tpj.16644] [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: 10/06/2023] [Revised: 12/25/2023] [Accepted: 01/07/2024] [Indexed: 01/29/2024]
Abstract
The indole alkaloid gramine, 3-(dimethylaminomethyl)indole, is a defensive specialized metabolite found in some barley cultivars. In its biosynthetic process, the tryptophan (Trp) side chain is shortened by two carbon atoms to produce 3-(aminomethyl)indole (AMI), which is then methylated by N-methyltransferase (HvNMT) to produce gramine. Although side chain shortening is one of the crucial scaffold formation steps of alkaloids originating from aromatic amino acids, the gene and enzyme involved in the Trp-AMI conversion reactions are unknown. In this study, through RNA-seq analysis, 35 transcripts were shown to correlate with gramine production; among them, an uncharacterized cytochrome P450 (CYP) gene, CYP76M57, and HvNMT were identified as candidate genes for gramine production. Transgenic Arabidopsis thaliana and rice overexpressing CYP and HvNMT accumulate AMI, N-methyl-AMI, and gramine. CYP76M57, heterologously expressed in Pichia pastoris, was able to act on Trp to produce AMI. Furthermore, the amino group nitrogen of Trp was retained during the CYP76M57-catalyzed reaction, indicating that the C2 shortening of Trp proceeds with an unprecedented biosynthetic process, the removal of the carboxyl group and Cα and the rearrangement of the nitrogen atom to Cβ. In some gramine-non-accumulating barley cultivars, arginine 104 in CYP76M57 is replaced by threonine, which abolished the catalytic activity of CYP76M57 to convert Trp into AMI. These results uncovered the missing committed enzyme of gramine biosynthesis in barley and contribute to the elucidation of the potential functions of CYPs in plants and undiscovered specialized pathways.
Collapse
Affiliation(s)
- Erika Ishikawa
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Shion Kanai
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Akihisa Shinozawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
- The NODAI Genome Research Center (NGRC), Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Mami Hyakutake
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| | - Masayuki Sue
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan
| |
Collapse
|
4
|
Liu W, Tian X, Huang X, Malit JJL, Wu C, Guo Z, Tang JW, Qian PY. Discovery of P450-Modified Sesquiterpenoids Levinoids A-D through Global Genome Mining. JOURNAL OF NATURAL PRODUCTS 2024; 87:876-883. [PMID: 38377956 DOI: 10.1021/acs.jnatprod.3c01136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Cytochrome P450-modified bacterial terpenoids remain in a vast chemical space to be explored. In the present study, we conducted global genome mining of 223,829 bacterial genomes and identified 2892 bacterial terpenoid biosynthetic gene clusters (BGCs) with cytochrome P450 genes. Among these, we selected 562 with multiple P450 enzymes, which were further clustered as 355 gene cluster families by sequence similarity analysis. We then chose lev, a BGC from Streptomyces levis MCCC1A01616, for heterologous expression and discovered four new α-amorphene-type sesquiterpenoids, levinoids A-D (1-4). The structures and absolute configurations of these four new compounds were determined by employing extensive NMR analysis, NMR chemical shift calculations with DP4+, and ECD calculations. Furthermore, levinoid C (3) exhibited a moderate level of neuroprotective activity (EC50 = 21 μM) in the glutamate-induced excitotoxicity cell model. Our findings highlight the untapped chemical diversity of P450-modified bacterial terpenoids, opening new avenues for further exploration and discovery.
Collapse
Affiliation(s)
- Wenchao Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Xueying Tian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xin Huang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | | | - Chuanhai Wu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhihong Guo
- Department of Chemistry, Department of Physics, and Bioengineering Program, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wei Tang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| |
Collapse
|
5
|
Wang YC, Wei Y, Li XY, Zhang HM, Meng X, Duan CQ, Pan QH. Ethylene-responsive VviERF003 modulates glycosylated monoterpenoid synthesis by upregulating VviGT14 in grapes. HORTICULTURE RESEARCH 2024; 11:uhae065. [PMID: 38689696 PMCID: PMC11059816 DOI: 10.1093/hr/uhae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/18/2024] [Indexed: 05/02/2024]
Abstract
Terpenoids are important contributors to the aroma of grapes and wines. Grapes contain terpenoids in both volatile free form and non-volatile glycosidic form, with the latter being more abundant. Glycosylated terpenoids are deemed as latent aromatic potentials for their essential role in adding to the flowery and fruity bouquet of wines. However, the transcriptional regulatory mechanism underlying glycosylated terpenoid biosynthesis remains poorly understood. Our prior study identified an AP2/ERF transcription factor, VviERF003, through DNA pull-down screening using the promoter of terpenoid glycosyltransferase VviGT14 gene. This study demonstrated that both genes were co-expressed and synchronized with the accumulation of glycosylated monoterpenoids during grape maturation. VviERF003 can bind to the VviGT14 promoter and promote its activity according to yeast one-hybrid and dual-luciferase assays. VviERF003 upregulated VviGT14 expression in vivo, leading to increased production of glycosylated monoterpenoids based on the evidence from overexpression or RNA interference in leaves, berry skins, and calli of grapes, as well as tomato fruits. Additionally, VviERF003 and VviGT14 expressions and glycosylated monoterpenoid levels were induced by ethylene in grapes. The findings suggest that VviERF003 is ethylene-responsive and stimulates glycosylated monoterpenoid biosynthesis through upregulating VviGT14 expression.
Collapse
Affiliation(s)
- Ya-Chen Wang
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Yi Wei
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Xiang-Yi Li
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui-Min Zhang
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Xiao Meng
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Chang-Qing Duan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Qiu-Hong Pan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| |
Collapse
|
6
|
Dias SL, Chuang L, Liu S, Seligmann B, Brendel FL, Chavez BG, Hoffie RE, Hoffie I, Kumlehn J, Bültemeier A, Wolf J, Herde M, Witte CP, D'Auria JC, Franke J. Biosynthesis of the allelopathic alkaloid gramine in barley by a cryptic oxidative rearrangement. Science 2024; 383:1448-1454. [PMID: 38547266 DOI: 10.1126/science.adk6112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024]
Abstract
The defensive alkaloid gramine not only protects barley and other grasses from insects but also negatively affects their palatability to ruminants. The key gene for gramine formation has remained elusive, hampering breeding initiatives. In this work, we report that a gene encoding cytochrome P450 monooxygenase CYP76M57, which we name AMI synthase (AMIS), enables the production of gramine in Nicotiana benthamiana, Arabidopsis thaliana, and Saccharomyces cerevisiae. We reconstituted gramine production in the gramine-free barley (Hordeum vulgare) variety Golden Promise and eliminated it from cultivar Tafeno by Cas-mediated gene editing. In vitro experiments unraveled that an unexpected cryptic oxidative rearrangement underlies this noncanonical conversion of an amino acid to a chain-shortened biogenic amine. The discovery of the genetic basis of gramine formation now permits tailor-made optimization of gramine-linked traits in barley by plant breeding.
Collapse
Affiliation(s)
- Sara Leite Dias
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Ling Chuang
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Shenyu Liu
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Benedikt Seligmann
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Fabian L Brendel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Benjamin G Chavez
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Robert E Hoffie
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Iris Hoffie
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Jochen Kumlehn
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Arne Bültemeier
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Johanna Wolf
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - John C D'Auria
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Jakob Franke
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| |
Collapse
|
7
|
Hou Y, Zeng W, Ao C, Huang J. Integrative analysis of the transcriptome and metabolome reveals Bacillus atrophaeus WZYH01-mediated salt stress mechanism in maize (Zea mays L.). J Biotechnol 2024; 383:39-54. [PMID: 38346451 DOI: 10.1016/j.jbiotec.2024.02.004] [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: 12/17/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Maize is an important food crop that is affected by salt stress during growth, which can hinder plant growth and result in a significant decrease in yield. The application of plant growth-promoting rhizobacteria can improve this situation to a certain extent. However, the gene network of rhizosphere-promoting bacteria regulating the response of maize to salt stress remains elusive. Here, we used metabolomics and transcriptomics techniques to elucidate potential gene networks and salt-response pathways in maize. Phenotypic analysis showed that the Bacillus atrophaeus treatment improved the plant height, leaf area, biomass, ion, nutrient and stomatal indicators of maize. Metabolomic analysis identified that differentially expressed metabolites (DEMs) were primarily concentrated in the arginine, proline and phytohormone signaling metabolic pathways. 4-Hydroxyphenylacetylglutamic acid, L-histidinol, oxoglutaric acid, L-glutamic acid, L-arginine, and L-tyrosine were significantly increased in the Bacillus atrophaeus treatment. Weighted gene coexpression network analysis (WGCNA) identified several hub genes associated with salt response: Zm00001eb155540 and Zm00001eb088790 (ABC transporter family), Zm00001eb419060 (extra-large GTP-binding protein family), Zm00001eb317200 (calcium-transporting ATPase), Zm00001eb384800 (aquaporin NIP1-4) and Zm00001eb339170 (cytochrome P450). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that genes related to plant hormone signal transduction and the MAPK signaling pathway were involved in the response to the effect of Bacillus atrophaeus under salt stress. In the plant hormone signal transduction pathway, 3 differentially expressed genes (DEGs) encoding EIN3/EILs protein, 3 DEGs encoding GH3, 1 DEG encoding PYR/PYL and 6 DEGs encoding PP2C were all upregulated in Bacillus atrophaeus treatment. In the MAPK signaling pathway, 2 DEGs encoding CAT1 and 2 DEGs encoding WRKY22/WRKY29 were significantly upregulated, and the expression of DEGs encoding RbohD was downregulated by the application of Bacillus atrophaeus. In conclusion, the application of Bacillus atrophaeus under salt stress regulated key physiological and molecular processes in plants, which could stimulate the expression of genes related to ion transport and nutrients in maize, alleviate salt stress and promote maize growth to some extent, deepening our understanding of the application of Bacillus atrophaeus under salt stress to improve the salt-response gene network of maize growth.
Collapse
Affiliation(s)
- Yaling Hou
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei Province, China
| | - Wenzhi Zeng
- College of Agricultural Science and Engineering, Hohai University, Nanjing, Jiangsu Province, China.
| | - Chang Ao
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei Province, China.
| | - Jiesheng Huang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei Province, China
| |
Collapse
|
8
|
Frey M, Bathe U, Meink L, Balcke GU, Schmidt J, Frolov A, Soboleva A, Hassanin A, Davari MD, Frank O, Schlagbauer V, Dawid C, Tissier A. Combinatorial biosynthesis in yeast leads to over 200 diterpenoids. Metab Eng 2024; 82:193-200. [PMID: 38387676 DOI: 10.1016/j.ymben.2024.02.006] [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: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. The modular character of diterpene biosynthesis and the promiscuity of the enzymes involved make combinatorial biosynthesis a promising approach to generate libraries of diverse diterpenoids. Here, we report on the combinatorial assembly in yeast of ten diterpene synthases producing (+)-copalyl diphosphate-derived backbones and four cytochrome P450 oxygenases (CYPs) in diverse combinations. This resulted in the production of over 200 diterpenoids. Based on literature and chemical database searches, 162 of these compounds can be considered new-to-Nature. The CYPs accepted most substrates they were given but remained regioselective with few exceptions. Our results provide the basis for the systematic exploration of the diterpenoid chemical space in yeast using sequence databases.
Collapse
Affiliation(s)
- Maximilian Frey
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ulschan Bathe
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
| | - Luca Meink
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Gerd U Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Jürgen Schmidt
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Alena Soboleva
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ahmed Hassanin
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mehdi D Davari
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Oliver Frank
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Verena Schlagbauer
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Martin-Luther University Halle-Wittenberg, Institute of Pharmacy, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
| |
Collapse
|
9
|
Petersen SD, Levassor L, Pedersen CM, Madsen J, Hansen LG, Zhang J, Haidar AK, Frandsen RJN, Keasling JD, Weber T, Sonnenschein N, K. Jensen M. teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. PLoS Comput Biol 2024; 20:e1011929. [PMID: 38457467 PMCID: PMC10954146 DOI: 10.1371/journal.pcbi.1011929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/20/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024] Open
Abstract
Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.
Collapse
Affiliation(s)
- Søren D. Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lucas Levassor
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christine M. Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jan Madsen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lea G. Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ahmad K. Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, United States of America
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
10
|
Jiang B, Gao L, Wang H, Sun Y, Zhang X, Ke H, Liu S, Ma P, Liao Q, Wang Y, Wang H, Liu Y, Du R, Rogge T, Li W, Shang Y, Houk KN, Xiong X, Xie D, Huang S, Lei X, Yan J. Characterization and heterologous reconstitution of Taxus biosynthetic enzymes leading to baccatin III. Science 2024; 383:622-629. [PMID: 38271490 DOI: 10.1126/science.adj3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Paclitaxel is a well known anticancer compound. Its biosynthesis involves the formation of a highly functionalized diterpenoid core skeleton (baccatin III) and the subsequent assembly of a phenylisoserinoyl side chain. Despite intensive investigation for half a century, the complete biosynthetic pathway of baccatin III remains unknown. In this work, we identified a bifunctional cytochrome P450 enzyme [taxane oxetanase 1 (TOT1)] in Taxus mairei that catalyzes an oxidative rearrangement in paclitaxel oxetane formation, which represents a previously unknown enzyme mechanism for oxetane ring formation. We created a screening strategy based on the taxusin biosynthesis pathway and uncovered the enzyme responsible for the taxane oxidation of the C9 position (T9αH1). Finally, we artificially reconstituted a biosynthetic pathway for the production of baccatin III in tobacco.
Collapse
Affiliation(s)
- Bin Jiang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lei Gao
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Haijun Wang
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yaping Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaolin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Han Ke
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shengchao Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pengchen Ma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yue Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huan Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yugeng Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Torben Rogge
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xingyao Xiong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Daoxin Xie
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
11
|
Li KL, Liang YM, Chen Z, Zheng PJ, Zhang GQ, Yan B, Elshikh MS, Rizwana H, Chen B, Xu Q. Genome-wide identification of the alkaloid synthesis gene family CYP450, gives new insights into alkaloid resource utilization in medicinal Dendrobium. Int J Biol Macromol 2024; 259:129229. [PMID: 38211913 DOI: 10.1016/j.ijbiomac.2024.129229] [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: 09/12/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
The medicinal Dendrobium species of Orchidaceae possess significant pharmaceutical value, and modern pharmacological research has shown that Dendrobium contains many important active ingredients. Alkaloids, the crucial components of medicinal Dendrobium, demonstrate beneficial healing properties in cardiovascular, cataract, gastrointestinal, and respiratory diseases. Members of the cytochrome P450 monooxygenase (CYP) gene family play essential roles in alkaloid synthesis, participating in alkaloid terpene skeleton construction and subsequent modifications. Although studies of the CYP family have been conducted in some species, genome-wide characterization and systematic analysis of the CYP family in medicinal Dendrobium remain underexplored. In this study, we identified CYP gene family members in the genomes of four medicinal Dendrobium species recorded in the Pharmacopoeia: D. nobile, D. chrysotoxum, D. catenatum, and D. huoshanense. Further, we analyzed the motif composition, gene replication events, and selection pressure of this family. Syntenic analysis revealed that members of the clan 710 were present on chromosome 18 in three medicinal Dendrobium species, except for D. nobile, indicating a loss of clan 710 occurring in D. nobile. We also conducted an initial screening of the CYP genes involved in alkaloid synthesis through transcriptome sequencing. Quantitative real-time reverse transcription PCR showed that the expression of DnoNew43 and DnoNew50, homologs of secologanin synthase involved in the alkaloid synthesis pathway, was significantly higher in the stems than in the leaves. This result coincided with the distribution of dendrobine content in Dendrobium stems and leaves, indicating that these two genes might be involved in the dendrobine synthesis pathway. Our results give insights into the CYP gene family evolution analysis in four medicinal Dendrobium species for the first time and identify two related genes that may be involved in alkaloid synthesis, providing a valuable resource for further investigations into alkaloid synthesis pathway in Dendrobium and other medicinal plants.
Collapse
Affiliation(s)
- Kang-Li Li
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Yu-Min Liang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhi Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Pei-Ji Zheng
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binghua Yan
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mohamed Soliman Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Humaira Rizwana
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - BingJie Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China.
| | - Qing Xu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China.
| |
Collapse
|
12
|
Kwon T, Hovde BT. Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures. Sci Rep 2024; 14:1534. [PMID: 38233413 PMCID: PMC10794256 DOI: 10.1038/s41598-023-50095-3] [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: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.
Collapse
Affiliation(s)
- Taehyung Kwon
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Blake T Hovde
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| |
Collapse
|
13
|
Zhao Y, Liang Y, Luo G, Li Y, Han X, Wen M. Sequence-Structure Analysis Unlocking the Potential Functional Application of the Local 3D Motifs of Plant-Derived Diterpene Synthases. Biomolecules 2024; 14:120. [PMID: 38254720 PMCID: PMC10813164 DOI: 10.3390/biom14010120] [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: 12/12/2023] [Revised: 12/31/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Plant-derived diterpene synthases (PdiTPSs) play a critical role in the formation of structurally and functionally diverse diterpenoids. However, the specificity or functional-related features of PdiTPSs are not well understood. For a more profound insight, we collected, constructed, and curated 199 functionally characterized PdiTPSs and their corresponding 3D structures. The complex correlations among their sequences, domains, structures, and corresponding products were comprehensively analyzed. Ultimately, our focus narrowed to the geometric arrangement of local structures. We found that local structural alignment can rapidly localize product-specific residues that have been validated by mutagenesis experiments. Based on the 3D motifs derived from the residues around the substrate, we successfully searched diterpene synthases (diTPSs) from the predicted terpene synthases and newly characterized PdiTPSs, suggesting that the identified 3D motifs can serve as distinctive signatures in diTPSs (I and II class). Local structural analysis revealed the PdiTPSs with more conserved amino acid residues show features unique to class I and class II, whereas those with fewer conserved amino acid residues typically exhibit product diversity and specificity. These results provide an attractive method for discovering novel or functionally equivalent enzymes and probing the product specificity in cases where enzyme characterization is limited.
Collapse
Affiliation(s)
- Yalan Zhao
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yupeng Liang
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Gan Luo
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Xiulin Han
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Mengliang Wen
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; (Y.Z.); (Y.L.); (G.L.); (X.H.)
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| |
Collapse
|
14
|
Lin X, Tang B, Li Z, Shi L, Zhu H. Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.). BMC Genomics 2024; 25:58. [PMID: 38218763 PMCID: PMC10787477 DOI: 10.1186/s12864-024-09965-x] [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: 09/28/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Cytochrome P450 monooxygenases (CYP450s) play a crucial role in various biochemical reactions involved in the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds in plants. As sweet potato (Ipomoea batatas L.) holds significant economic importance, a comprehensive analysis of CYP450 genes in this plant species can offer valuable insights into the evolutionary relationships and functional characteristics of these genes. RESULTS In this study, we successfully identified and categorized 95 CYP450 genes from the sweet potato genome into 5 families and 31 subfamilies. The predicted subcellular localization results indicate that CYP450s are distributed in the cell membrane system. The promoter region of the IbCYP450 genes contains various cis-acting elements related to plant hormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) have been identified in the IbCYP450 family proteins, with 5 genes lacking introns and only one exon. We observed extensive duplication events within the CYP450 gene family, which may account for its expansion. The gene duplication analysis results showed the presence of 15 pairs of genes with tandem repeats. Interaction network analysis reveals that IbCYP450 families can interact with multiple target genes and there are protein-protein interactions within the family. Transcription factor interaction analysis suggests that IbCYP450 families interact with multiple transcription factors. Furthermore, gene expression analysis revealed tissue-specific expression patterns of CYP450 genes in sweet potatoes, as well as their response to abiotic stress and plant hormones. Notably, quantitative real-time polymerase chain reaction (qRT‒PCR) analysis indicated the involvement of CYP450 genes in the defense response against nonbiological stresses in sweet potatoes. CONCLUSIONS These findings provide a foundation for further investigations aiming to elucidate the biological functions of CYP450 genes in sweet potatoes.
Collapse
Affiliation(s)
- Xiongjian Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Binquan Tang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhenqin Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Lei Shi
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.
| |
Collapse
|
15
|
Roy P, Rutter A, Gainer A, Haack E, Zeeb BA. Phytotoxicity of weathered petroleum hydrocarbons in soil to boreal plant species. ENVIRONMENTAL RESEARCH 2023; 238:117136. [PMID: 37717802 DOI: 10.1016/j.envres.2023.117136] [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: 07/18/2023] [Revised: 08/25/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Canada has extensive petroleum hydrocarbon (PHC) contamination in northern areas and the boreal forest region from historical oil and gas activities. Since the 2013 standardization of boreal forest species for plant toxicity testing in Canada, there has been a need to build the primary literature of the toxicity of weathered PHCs to these species. A series of toxicity experiments were carried out using fine-grained (<0.005-0.425 mm) background (100 total mg/kg total PHCs) and weathered contaminated soil (11,900 mg/kg total PHCs) collected from a contaminated site in northern Ontario, Canada. The PHC mixture in the contaminated site soil was characterized through Canadian Council of Ministers of the Environment Fractions, as indicated by the number equivalent normal straight-chain hydrocarbons (nC). The soil was highly contaminated with Fraction 2 (>nC10 to nC16) at 4790 mg/kg and Fraction 3 (>nC16 to nC34) at 4960 mg/kg. Five plant species (Elymus trachycaulus, Achillea millefolium, Picea mariana, Salix bebbiana, and Alnus viridis) were grown from seed in 0%, 25%, 50%, 75%, and 100% relative contamination mixtures of the PHC-contaminated and background soil from the site over 2-6 weeks. All five species showed significant inhibition in shoot length, shoot weight, root length, and/or root weight (Kruskal-Wallis Tests: p < 0.05, df = 4.0). Measurements of 25% inhibitory concentrations (IC25) following PHC toxicity experiments revealed that S. bebbiana was most significantly impaired by the PHC-contaminated soil (410-990 mg/kg total PHCs), where it showed <35% germination. This study indicates that natural weathering of Fraction 2- and Fraction 3-concentrated soil did not eliminate phytotoxicity to boreal plant species. Furthermore, it builds on the limited existing literature for toxicity of PHCs on boreal plants and supports site remediation to existing Canadian provincial PHC guidelines.
Collapse
Affiliation(s)
- Prama Roy
- School of Environmental Studies, Queen's University, Kingston, ON, K7L 3N6, Canada.
| | - Allison Rutter
- School of Environmental Studies, Queen's University, Kingston, ON, K7L 3N6, Canada.
| | - Amy Gainer
- Clear-Site Solutions (formerly with Advisian/Worley Canada Services), 9807 83 Ave Edmonton, AB, Canada.
| | - Elizabeth Haack
- Ecometrix Incorporated, 6800 Campobello Road, Mississauga, ON, L5N 2L8, Canada.
| | - Barbara A Zeeb
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, K7K 7B4, Canada.
| |
Collapse
|
16
|
de Lima Silva MG, Santos da Silva LY, Torres Pessoa R, de Oliveira MRC, Batista FLA, Alcântara IS, Bezerra Martins AOBP, Ribeiro-Filho J, Coutinho HDM, de Menezes IRA. Antiedematogenic and Analgesic Activities of Abietic Acid in Mice. Chem Biodivers 2023; 20:e202300906. [PMID: 37795905 DOI: 10.1002/cbdv.202300906] [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: 06/20/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/06/2023]
Abstract
Exacerbated inflammatory responses to harmful stimuli can lead to significant pain, edema, and other complications that require pharmacological intervention. Abietic acid (AA) is a diterpene found as a significant constituent in pine species, and evidence has identified its biological potential. The present study aimed to evaluate abietic acid's antiedematogenic and anti-inflammatory activity in mice. Swiss mice (Mus musculus) weighing 20-30 g were treated with AA at 50, 100, and 200 mg/kg. The central nervous system (CNS) effects were evaluated using open-field and rotarod assays. The antinociceptive and anti-inflammatory screening was assessed by the acetic acid and formalin tests. The antiedematogenic activity was investigated by measuring paw edema induced by carrageenan, dextran, histamine, arachidonic acid, and prostaglandin, in addition to using a granuloma model. The oral administration of abietic acid (200 mg/Kg) showed no evidence of CNS effects. The compound also exhibited significant antiedematogenic and anti-inflammatory activities in the carrageenan and dextran models, mostly related to the inhibition of myeloperoxidase (MOP) activity and histamine action and, to a lesser extent, the inhibition of eicosanoid-dependent pathways. In the granuloma model, abietic acid's effect was less expressive than in the acute models investigated in this study. In conclusion, abietic acid has analgesic and antiedematogenic activities related to anti-inflammatory mechanisms.
Collapse
Affiliation(s)
- Maria Gabriely de Lima Silva
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | - Lucas Yure Santos da Silva
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | - Renata Torres Pessoa
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | - Maria Rayane Correia de Oliveira
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | - Francisco Lucas Alves Batista
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | - Isabel Sousa Alcântara
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | | | - Jaime Ribeiro-Filho
- Oswaldo Cruz Foundation (Fiocruz), Fiocruz Ceará, Eusébio, CE-60180-900, Brazil
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology, Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| | - Irwin Rose Alencar de Menezes
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato, CE-63105-000, Brazil
| |
Collapse
|
17
|
Zhang Y, Kashkooli AB, Blom S, Zhao T, Bouwmeester HJ, Kappers IF. The Capsicum terpenoid biosynthetic module is affected by spider-mite herbivory. PLANT MOLECULAR BIOLOGY 2023; 113:303-321. [PMID: 37995005 PMCID: PMC10721696 DOI: 10.1007/s11103-023-01390-0] [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: 04/23/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
In response to herbivory, Capsicum annuum leaves adapt their specialized metabolome that may protect the plant against herbivore feeding either directly or indirectly through volatile metabolites acting as cues for natural enemies of the herbivore. The volatile blend of spider-mite infested leaves differs from non-challenged leaves predominantly by a higher contribution of mono- and sesquiterpenes. In addition to these terpenoids released into the headspace, the terpenoid composition of the leaves alters upon herbivory. All this suggests an important role for terpenoids and their biosynthetic machinery in the defence against herbivory. Here, we show that the C. annuum genome contains a terpene synthase (TPS) gene family of 103 putative members of which structural analysis revealed that 27 encode functional enzymes. Transcriptome analysis showed that several TPS loci were differentially expressed upon herbivory in leaves of two C. annuum genotypes, that differ in susceptibility towards spider mites. The relative expression of upstream biosynthetic genes from the mevalonate and the methylerythritol phosphate pathway also altered upon herbivory, revealing a shift in the metabolic flux through the terpene biosynthetic module. The expression of multiple genes potentially acting downstream of the TPSs, including cytochrome P450 monooxygenases, UDP-glucosyl transferases, and transcription factors strongly correlated with the herbivory-induced TPS genes. A selection of herbivory-induced TPS genes was functionally characterized through heterologous expression and the products that these enzymes catalysed matched with the volatile and non-volatile terpenoids induced in response to herbivory.
Collapse
Affiliation(s)
- Yuanyuan Zhang
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Arman B Kashkooli
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- Tarbiat Modares University, Tehran, Iran
| | - Suze Blom
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Tao Zhao
- Biosystematics, Wageningen University, Wageningen, The Netherlands
- Northwest Agriculture and Forestry University, Xi'an, China
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iris F Kappers
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
18
|
de Lima Silva MG, de Lima LF, Alencar Fonseca VJ, Santos da Silva LY, Calixto Donelardy AC, de Almeida RS, de Morais Oliveira-Tintino CD, Pereira Bezerra Martins AOB, Ribeiro-Filho J, Bezerra Morais-Braga MF, Tintino SR, Alencar de Menezes IR. Enhancing the Antifungal Efficacy of Fluconazole with a Diterpene: Abietic Acid as a Promising Adjuvant to Combat Antifungal Resistance in Candida spp. Antibiotics (Basel) 2023; 12:1565. [PMID: 37998767 PMCID: PMC10668680 DOI: 10.3390/antibiotics12111565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
The increasing antifungal resistance rates against conventional drugs reveal the urgent need to search for new therapeutic alternatives. In this context, natural bioactive compounds have a critical role in antifungal drug development. Since evidence demonstrates that abietic acid, a diterpene found in Pinus species, has significant antimicrobial properties, this study aimed to evaluate the antifungal activity of abietic acid against Candida spp and its ability to potentiate the activity of fluconazole. Abietic acid was tested both individually and in combination with fluconazole against Candida albicans (CA INCQS 40006), Candida krusei (CK INCQS 40095), and Candida tropicalis (CT INCQS 40042). The microdilution method was used to determine the IC50 and the cell viability curve. Minimum Fungicidal Concentration (MFC) was determined by subculture in a solid medium. The plasma membrane permeability was measured using a fluorescent SYTOX Green probe. While the IC50 of the drugs alone ranged between 1065 and 3255 μg/mL, the IC50 resulting from the combination of abietic acid and fluconazole ranged between 7563 and 160.1 μg/mL. Whether used in combination with fluconazole or isolated, abietic acid exhibited Minimum Fungicidal Concentration (MFC) values exceeding 1024 μg/mL against Candida albicans, Candida krusei and Candida tropicalis. However, it was observed that the antifungal effect of fluconazole was enhanced when used in combination with abietic acid against Candida albicans and Candida tropicalis. These findings suggest that while abietic acid alone has limited inherent antifungal activity, it can enhance the effectiveness of fluconazole, thereby reducing antifungal resistance.
Collapse
Affiliation(s)
- Maria Gabriely de Lima Silva
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (M.G.d.L.S.); (L.Y.S.d.S.); (A.C.C.D.); (A.O.B.P.B.M.)
| | - Luciene Ferreira de Lima
- Laboratory of Applied Mycology of Cariri (LMAC), Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (L.F.d.L.); (V.J.A.F.); (M.F.B.M.-B.)
| | - Victor Juno Alencar Fonseca
- Laboratory of Applied Mycology of Cariri (LMAC), Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (L.F.d.L.); (V.J.A.F.); (M.F.B.M.-B.)
| | - Lucas Yure Santos da Silva
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (M.G.d.L.S.); (L.Y.S.d.S.); (A.C.C.D.); (A.O.B.P.B.M.)
| | - Ana Cecília Calixto Donelardy
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (M.G.d.L.S.); (L.Y.S.d.S.); (A.C.C.D.); (A.O.B.P.B.M.)
| | - Ray Silva de Almeida
- Laboratory of Microbiology and Molecular Biology (LMBM), Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (R.S.d.A.); (C.D.d.M.O.-T.)
| | | | - Anita Oliveira Brito Pereira Bezerra Martins
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (M.G.d.L.S.); (L.Y.S.d.S.); (A.C.C.D.); (A.O.B.P.B.M.)
| | - Jaime Ribeiro-Filho
- Oswaldo Cruz Foundation (Fiocruz), Fiocruz Ceará, Eusébio 61773-270, Ceará, Brazil;
| | - Maria Flaviana Bezerra Morais-Braga
- Laboratory of Applied Mycology of Cariri (LMAC), Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (L.F.d.L.); (V.J.A.F.); (M.F.B.M.-B.)
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (R.S.d.A.); (C.D.d.M.O.-T.)
| | - Irwin Rose Alencar de Menezes
- Laboratory of Pharmacology and Molecular Chemistry (LFQM), Department of Biological Chemistry, Regional University of Cariri (URCA), Crato 63105-000, Ceará, Brazil; (M.G.d.L.S.); (L.Y.S.d.S.); (A.C.C.D.); (A.O.B.P.B.M.)
| |
Collapse
|
19
|
Mazzotta S, Rositano V, Senaldi L, Bernardi A, Allegrini P, Appendino G. Scalemic natural products. Nat Prod Rep 2023; 40:1647-1671. [PMID: 37439042 DOI: 10.1039/d3np00014a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Covering: up to the end of 2022The area of scalemic natural products is often enigmatic from a mechanistic standpoint, since low optical purity is observed in compounds having multiple contiguous stereogenic centers resulting from mechanistically distinct biogenetic steps. A scalemic state is rarely the result of a sloppy enzymatic activity, rather resulting from the expression of antipodal enzymes/directing proteins or from the erosion of optical purity by enzymatic or spontaneous reactions. Evidence for these processes is critically reviewed, identifying the mechanisms most often associated to the enzymatic generation of scalemic natural products and also discussing analytical exploitations of natural products' scalemicity.
Collapse
Affiliation(s)
- Sarah Mazzotta
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Vincenzo Rositano
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
- Indena SpA, Via Don Minzoni 6, 20049 Settala, MI, Italy
| | - Luca Senaldi
- Indena SpA, Via Don Minzoni 6, 20049 Settala, MI, Italy
| | - Anna Bernardi
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | | | - Giovanni Appendino
- Dipartimento di Scienze del Farmaco, Largo Donegani 2, 28100 Novara, Italy.
| |
Collapse
|
20
|
Jing SX, Ferreira D, Pandey P, Klein LL, Chittiboyina AG, McAlpine JB, Lankin DC, Alania Y, Reis-Havlat M, Bedran-Russo AK, Chen SN, Pauli GF. Unprecedented Benzoquinone Motifs Reveal Post-Oligomerizational Modification of Proanthocyanidins. J Org Chem 2023; 88:13490-13503. [PMID: 37748101 PMCID: PMC10921432 DOI: 10.1021/acs.joc.3c00950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Proanthocyanidins (PACs) are complex flavan-3-ol polymers with stunning chemical complexity due to oxygenation patterns, oxidative phenolic ring linkages, and intricate stereochemistry of their heterocycles and inter-flavan linkages. Being promising candidates for dental restorative biomaterials, trace analysis of dentin bioactive cinnamon PACs now yielded novel trimeric (1 and 2) and tetrameric (3) PACs with unprecedented o- and p-benzoquinone motifs (benzoquinonoid PACs). Challenges in structural characterization, especially their absolute configuration, prompted the development of a new synthetic-analytical approach involving comprehensive spectroscopy, including NMR with quantum mechanics-driven 1H iterative functionalized spin analysis (HifSA) plus experimental and computational electronic circular dichroism (ECD). Vital stereochemical information was garnered from synthesizing 4-(2,5-benzoquinone)flavan-3-ols and a truncated analogue of trimer 2 as ECD models. Discovery of the first natural benzoquinonoid PACs provides new evidence to the experimentally elusive PAC biosynthesis as their formation requires two oxidative post-oligomerizational modifications (POMs) that are distinct and occur downstream from both quinone-methide-driven oligomerization and A-type linkage formation. While Nature is known to achieve structural diversity of many major compound classes by POMs, this is the first indication of PACs also following this common theme.
Collapse
Affiliation(s)
- Shu-Xi Jing
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Daneel Ferreira
- Department of Biomolecular Sciences, The University of Mississippi, University, Mississippi 38677, USA
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA
| | - Pankaj Pandey
- Department of Biomolecular Sciences, The University of Mississippi, University, Mississippi 38677, USA
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA
| | - Larry L. Klein
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Amar Gopal Chittiboyina
- Department of Biomolecular Sciences, The University of Mississippi, University, Mississippi 38677, USA
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA
| | - James B. McAlpine
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - David C. Lankin
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yvette Alania
- Department of General Dental Sciences, School of Dentistry, Marquette University, Milwaukee, Wisconsin 53233, USA
| | - Mariana Reis-Havlat
- Department of General Dental Sciences, School of Dentistry, Marquette University, Milwaukee, Wisconsin 53233, USA
| | - Ana K. Bedran-Russo
- Department of General Dental Sciences, School of Dentistry, Marquette University, Milwaukee, Wisconsin 53233, USA
| | - Shao-Nong Chen
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Guido F. Pauli
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| |
Collapse
|
21
|
Shi J, Zhang F, Wang Y, Zhang S, Wang F, Ma Y. The cytochrome P450 gene, MdCYP716B1, is involved in regulating plant growth and anthracnose resistance in apple. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111832. [PMID: 37586420 DOI: 10.1016/j.plantsci.2023.111832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/21/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
Apple is one of the main cultivated fruit trees worldwide. Both biotic and abiotic stresses, especially fungal diseases, have serious effects on the growth and fruit quality of apples. Cytochrome P450, the largest protein family in plants, is critical for plant growth and stress responses. However, the function of apple P450 remains poorly understood. In our previous study, 'Hanfu' autotetraploid showed dwarfism and fungal resistance phenotypes compared to 'Hanfu' diploid. Digital gene expression sequencing analysis revealed that the transcript level of MdCYP716B1 was significantly downregulated in the autotetraploid apple cultivar 'Hanfu'. In this study, we identified and cloned the MdCYP716B1 gene from 'Hanfu' apples. The MdCYP716B1 protein fused to a green fluorescent protein was localized in the cytoplasm. We constructed the plant overexpression vector and RNAi vector of MdCYP716B1, and the apple 'GL-3' was transformed by Agrobacterium-mediated transformation to obtain transgenic plants. Overexpressing and RNAi silencing transgenic plants exhibited an increase and decrease in plant height to 'GL-3', respectively. RNAi silencing transgenic plants displayed increased resistance to Colletotrichum gloeosporioides, whereas overexpression transgenic plants were more sensitive to C. gloeosporioides. According to transcriptome analysis, the transcript levels of gibberellin biosynthesis genes were upregulated in MdCYP716B1-overexpression plants. In contrast with 'GL-3', GA3 accumulation was rose in MdCYP716B1-OE lines and impaired in MdCYP716B1-RNAi lines. Collectively, our data indicate that MdCYP716B1 regulates plant growth and resistance to fungal stress.
Collapse
Affiliation(s)
- Jiajun Shi
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Feng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yangshu Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Shuyuan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Feng Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, PR China.
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China.
| |
Collapse
|
22
|
Bie H, Li Y, Zhao Y, Fang W, Chen C, Wang X, Wu J, Wang L, Cao K. Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111778. [PMID: 37353009 DOI: 10.1016/j.plantsci.2023.111778] [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: 02/15/2023] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
Gene presence/absence variation (PAV) is an important contributor to the studies of genetic diversity, gene identification, and molecular marker development in plants. In the present study, 100 peach (Prunus persica) accessions were used for genome resequencing to identify PAVs. Alignmentwith a reference genome yielded a total of 2.52 Mb non-reference sequences and 923 novel genes were identified. The dispensable PAVs were enriched in resistance, perhaps reflecting their roles in plant adaptation to various environments. Furthermore, selection sweeps associated with peach domestication and improvement were identified based on PAV data. Only 4.3% and 13.4% of domestication and improvement sweeps, respectively, were identified simultaneously using single nucleotide polymorphism (SNP) data, suggesting flexible identification between the different methods. To further verify the applicability of PAV identification, a genome-wide association study was conducted using 21 agronomic traits. Some of the identified loci were consistent with those reported in previous studies, while some were mapped for the first time; the latter included petiole length, petiole gland shape, and petiole gland number. Through tissue-specific expression analysis and gene transformation experiments, a novel gene, evm.model.Contig322_A94.1, was identified and found to be involved in chilling requirements. We speculated that this novel gene might regulate the trait by participating in the ABA signaling pathway. The PAVs identified in P. persica provide valuable resources for mapping the entire gene set and identifying optional markers for molecular selection in future studies.
Collapse
Affiliation(s)
- Hangling Bie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China; The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Yalin Zhao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jinlong Wu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Ke Cao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China; The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| |
Collapse
|
23
|
Zhao S, Zhang Q, Xiao W, Chen D, Hu J, Gao N, Huang M, Ye X. Comparative transcriptome analysis reveals key genes and coordinated mechanisms in two rice cultivars differing in cadmium accumulation. CHEMOSPHERE 2023; 338:139489. [PMID: 37451631 DOI: 10.1016/j.chemosphere.2023.139489] [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: 05/24/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Although Cd accumulation varies among rice varieties is recognized, the underlying mechanisms are not well clarified. In this study, comparative transcriptome analysis were performed by hydroponic culture system with two rice varieties, Y1540 (high Cd accumulator) and Y15 (low Cd accumulator) under 20 μM Cd stress. Results revealed 17,320 differentially expressed genes (DEGs) in roots of Y15 (7,655 upregulated and 9,665 downregulated) and 17,386 DEGs in roots of Y1540 (8,823 upregulated and 8,563 downregulated) expose to 20 μM Cd stress. Gene ontology (GO) analysis enriched 24 and 26 terms in Y15 and Y1540 respectively, including 23 common terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed 27 and 28 significant pathways in Y15 and Y1540 respectively, with 19 common pathways. Different responses to Cd stress between cultivars were not only reflected in differently enriched GO terms and KEGG pathways but also in different DEGs of 23 common GO terms and significant sequences represented by p-values of 19 common KEGG pathways. Both cultivars resist Cd through common processes with different weights; hence glutathione metabolism, mineral absorption, biosynthesis of secondary metabolites, and degradation of aromatic compounds could be playing a more important role in Y1540, whereas ribosome biogenesis in eukaryotes, mismatch repair, aminoacyl-tRNA biosynthesis, and the cell cycle maybe playing a more important role in Y15. Weighted gene co-expression network analysis (WGCNA) showed that five and three modules were clustered in Y15 and Y1540, respectively, with yellow and brown modules in Y15 and brown modules in Y1540 being significantly related to Cd stress. Further analysis showed that most of hub genes in Y15 were related to signal transduction or transcription factors, while most of hub genes in Y1540 were related to binding, metabolic, and secondary metabolic processes, which demonstrated their different response patterns at transcriptomic level to Cd stress.
Collapse
Affiliation(s)
- Shouping Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wendan Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - De Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jing Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Na Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Miaojie Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xuezhu Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
24
|
Qiu T, Li Y, Wu H, Yang H, Peng Z, Du Z, Wu Q, Wang H, Shen Y, Huang L. Tandem duplication and sub-functionalization of clerodane diterpene synthase originate the blooming of clerodane diterpenoids in Scutellaria barbata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:375-388. [PMID: 37395679 DOI: 10.1111/tpj.16377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
Scutellaria barbata is a traditional Chinese herb medicine and a major source of bioactive clerodane diterpenoids. However, barely clerodanes have been isolated from the closely related S. baicalensis. Here we assembled a chromosome-level genome of S. barbata and identified three class II clerodane diterpene synthases (SbarKPS1, SbarKPS2 and SbaiKPS1) from these two organisms. Using in vitro and in vivo assays, SbarKPS1 was characterized as a monofunctional (-)-kolavenyl diphosphate synthases ((-)-KPS), while SbarKPS2 and SbaiKPS1 produced major neo-cleroda-4(18),13E-dienyl diphosphate with small amount of (-)-KPP. SbarKPS1 and SbarKPS2 shared a high protein sequence identity and formed a tandem gene pair, indicating tandem duplication and sub-functionalization probably led to the evolution of monofunctional (-)-KPS in S. barbata. Additionally, SbarKPS1 and SbarKPS2 were primarily expressed in the leaves and flowers of S. barbata, which was consistent with the distribution of major clerodane diterpenoids scutebarbatine A and B. In contrast, SbaiKPS1 was barely expressed in any tissue of S. baicalensis. We further explored the downstream class I diTPS by functional characterizing of SbarKSL3 and SbarKSL4. Unfortunately, no dephosphorylated product was detected in the coupled assays with SbarKSL3/KSL4 and four class II diTPSs (SbarKPS1, SbarKPS2, SbarCPS2 and SbarCPS4) when a phosphatase inhibitor cocktail was included. Co-expression of SbarKSL3/KSL4 with class II diTPSs in yeast cells did not increase the yield of the corresponding dephosphorylated products, either. Together, these findings elucidated the involvement of two class II diTPSs in clerodane biosynthesis in S. barbata, while the class I diTPS is likely not responsible for the subsequent dephosphorylation step.
Collapse
Affiliation(s)
- Ting Qiu
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - YangYan Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Haisheng Wu
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hui Yang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ziqiu Peng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Zuying Du
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Qingwen Wu
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hongbin Wang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yanting Shen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lili Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| |
Collapse
|
25
|
Shen C, Li X. Genome-wide analysis of the P450 gene family in tea plant (Camellia sinensis) reveals functional diversity in abiotic stress. BMC Genomics 2023; 24:535. [PMID: 37697232 PMCID: PMC10494425 DOI: 10.1186/s12864-023-09619-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Cytochrome P450 (Cytochrome P450s) genes are involved in the catalysis of various reactions, including growth, development, and secondary metabolite biosynthetic pathways. However, little is known about the characteristics and functions of the P450 gene family in Camellia sinensis (C. sinensis). RESULTS To reveal the mechanisms of tea plant P450s coping with abiotic stresses, analyses of the tea plant P450 gene family were conducted using bioinformatics-based methods. In total, 273 putative P450 genes were identified from the genome database of C. sinensis. The results showed that P450s were well-balanced across the chromosomes I to XV of entire genome, with amino acid lengths of 268-612 aa, molecular weights of 30.95-68.5 kDa, and isoelectric points of 4.93-10.17. Phylogenetic analysis divided CsP450s into 34 subfamilies, of which CYP71 was the most abundant. The predicted subcellular localization results showed that P450 was distributed in a variety of organelles, with chloroplasts, plasma membrane,,and cytoplasm localized more frequently. The promoter region of CsP450s contained various cis-acting elements related to phytohormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) were identified in the CsP450 family proteins, with 27 genes lacking introns and only one exon. The results of genome large segment duplication showed that there were 37 pairs of genes with tandem duplication. Interaction network analysis showed that CsP450 could interact with multiple types of target genes, and there are protein interactions within the family. Tissue expression analysis showed that P450 was highly expressed in roots and stems. Moreover, qPCR analysis of the relative expression level of the gene under drought and cold stress correlated with the sequencing results. CONCLUSIONS This study lays the foundation for resolving the classification and functional study of P450 family genes and provides a reference for the molecular breeding of C. sinensis.
Collapse
Affiliation(s)
- Chuan Shen
- Shaannan Eco-Economy Research Center, Ankang University, Ankang, 725000, China.
| | - Xia Li
- Department of Electronic and Information Engineering, Ankang University, Ankang, 725000, China
| |
Collapse
|
26
|
Ye RY, Song J, Zhang ZJ, Yu HL. Prokaryotic expression and characterization of artificial self-sufficient CYP120A monooxygenases. Appl Microbiol Biotechnol 2023; 107:5727-5737. [PMID: 37477695 DOI: 10.1007/s00253-023-12678-y] [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: 01/30/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Cytochrome P450 monooxygenases CYP120As are the unique non-membrane P450s, which are extensively involved in retinoid biodegradation. As the O-functionalized 1,3,3-trimethylcyclohex-1-ene moiety exists in many bioactive compounds which could only be catalyzed by Class II P450s, exploration of the catalytic repertoire of CYP120As is therefore highly attractive. However, up to date, only one bacteriogenic candidate (CYP120A1) was demonstrated for the hydroxylation of C16 and C17 of retinoic acid, by utilizing the integral membrane protein cytochrome P450 reductase redox partner for the electron transfer. Herein, we provided an efficient prokaryotic functional expression system of CYP120As in E. coli by expression of the CYP120A1 coupled with several reductase partners. Fusion redox partners to the C-terminal of the heme-domain are also working on other CYP120A members. Among them, the fusion protein of CYP120A29 and FAD/FMN reductase from Bacillus megaterium P450BM3 (CYP101A2) showed the highest expression level. Based on the available translational fusion systems, the regioselectivity and the substrate scope of the CYP120As have also been explored. This work represents a good starting point for further expanding the catalytic potential of CYP120 family. KEY POINTS: • Characterization of CYP120As in E. coli is firstly achieved by constructing fusion proteins. • The feasibility of three P450 reductase domains to CYP120As was evaluated. • Hydroxylated products of retinoic acid by six CYP120As were sorted and analyzed.
Collapse
Affiliation(s)
- Ru-Yi Ye
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Juan Song
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| |
Collapse
|
27
|
Liu J, Hua J, Wang Y, Guo X, Luo S. Caterpillars Detoxify Diterpenoid from Nepeta stewartiana by the Molting Hormone Gene CYP306A1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37331015 DOI: 10.1021/acs.jafc.3c02779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Herbivorous insects are well known for detoxifying a broad range of the defense compounds produced by the plants that they feed on, but knowledge of the mechanisms of detoxification is still very limited. Here, we describe a system in which two species of lepidopteran caterpillars metabolize an abietane diterpene from the plants of Nepeta stewartiana Diels to an oxygenated derivative that is less active biologically. We found that this transformation could be catalyzed by a cytochrome P450 enzyme in caterpillars, which are associated with molting. Most interestingly, abietane diterpene targets the molting-associated gene CYP306A1 to alter the content of molting hormones in the insect at specific developmental stages and competitively inhibit molting hormone metabolism. These findings identify the mechanism by which caterpillars are able to detoxify abietane diterpenoid through hydroxylation at the C-19 position, which may be opening up exciting research questions into the mechanisms of interaction between plants and insects.
Collapse
Affiliation(s)
- Jiayi Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Juan Hua
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Yangyang Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Xuanyue Guo
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Shihong Luo
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| |
Collapse
|
28
|
Ritz M, Ahmad N, Brueck T, Mehlmer N. Differential RNA-Seq Analysis Predicts Genes Related to Terpene Tailoring in Caryopteris × clandonensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:2305. [PMID: 37375930 DOI: 10.3390/plants12122305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/17/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Enzymatic terpene functionalization is an essential part of plant secondary metabolite diversity. Within this, multiple terpene-modifying enzymes are required to enable the chemical diversity of volatile compounds essential in plant communication and defense. This work sheds light on the differentially transcribed genes within Caryopteris × clandonensis that are capable of functionalizing cyclic terpene scaffolds, which are the product of terpene cyclase action. The available genomic reference was subjected to further improvements to provide a comprehensive basis, where the number of contigs was minimized. RNA-Seq data of six cultivars, Dark Knight, Grand Bleu, Good as Gold, Hint of Gold, Pink Perfection, and Sunny Blue, were mapped on the reference, and their distinct transcription profile investigated. Within this data resource, we detected interesting variations and additionally genes with high and low transcript abundancies in leaves of Caryopteris × clandonensis related to terpene functionalization. As previously described, different cultivars vary in their modification of monoterpenes, especially limonene, resulting in different limonene-derived molecules. This study focuses on predicting the cytochrome p450 enzymes underlying this varied transcription pattern between investigated samples. Thus, making them a reasonable explanation for terpenoid differences between these plants. Furthermore, these data provide the basis for functional assays and the verification of putative enzyme activities.
Collapse
Affiliation(s)
- Manfred Ritz
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Nadim Ahmad
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Thomas Brueck
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| |
Collapse
|
29
|
Lanier ER, Andersen TB, Hamberger B. Plant terpene specialized metabolism: complex networks or simple linear pathways? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1178-1201. [PMID: 36891828 PMCID: PMC11166267 DOI: 10.1111/tpj.16177] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.
Collapse
Affiliation(s)
| | | | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, Molecular Plant Sciences Building, 1066 Bogue Street, East Lansing, Michigan, 48824, USA
| |
Collapse
|
30
|
Wang D, Yu Z, Guan M, Cai Q, Wei J, Ma P, Xue Z, Ma R, Oksman-Caldentey KM, Rischer H. Comparative transcriptome analysis of Veratrum maackii and Veratrum nigrum reveals multiple candidate genes involved in steroidal alkaloid biosynthesis. Sci Rep 2023; 13:8198. [PMID: 37211560 DOI: 10.1038/s41598-023-35429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
Veratrum (Melanthiaceae; Liliales) is a genus of perennial herbs known for the production of unique bioactive steroidal alkaloids. However, the biosynthesis of these compounds is incompletely understood because many of the downstream enzymatic steps have yet to be resolved. RNA-Seq is a powerful method that can be used to identify candidate genes involved in metabolic pathways by comparing the transcriptomes of metabolically active tissues to controls lacking the pathway of interest. The root and leaf transcriptomes of wild Veratrum maackii and Veratrum nigrum plants were sequenced and 437,820 clean reads were assembled into 203,912 unigenes, 47.67% of which were annotated. We identified 235 differentially expressed unigenes potentially involved in the synthesis of steroidal alkaloids. Twenty unigenes, including new candidate cytochrome P450 monooxygenases and transcription factors, were selected for validation by quantitative real-time PCR. Most candidate genes were expressed at higher levels in roots than leaves but showed a consistent profile across both species. Among the 20 unigenes putatively involved in the synthesis of steroidal alkaloids, 14 were already known. We identified three new CYP450 candidates (CYP76A2, CYP76B6 and CYP76AH1) and three new transcription factor candidates (ERF1A, bHLH13 and bHLH66). We propose that ERF1A, CYP90G1-1 and CYP76AH1 are specifically involved in the key steps of steroidal alkaloid biosynthesis in V. maackii roots. Our data represent the first cross-species analysis of steroidal alkaloid biosynthesis in the genus Veratrum and indicate that the metabolic properties of V. maackii and V. nigrum are broadly conserved despite their distinct alkaloid profiles.
Collapse
Affiliation(s)
- Dan Wang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
- College of Agricultural Sciences, Yanbian University, Yanji, 133000, Jilin Province, People's Republic of China
| | - Zhijing Yu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Meng Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin, People's Republic of China
| | - Qinan Cai
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Pengda Ma
- College of Life Sciences, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Zheyong Xue
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin, People's Republic of China
| | - Rui Ma
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China.
| | | | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd., P. O. Box 1000, 02044 VTT, Espoo, Finland.
| |
Collapse
|
31
|
Habán M, Korczyk-Szabó J, Čerteková S, Ražná K. Lavandula Species, Their Bioactive Phytochemicals, and Their Biosynthetic Regulation. Int J Mol Sci 2023; 24:ijms24108831. [PMID: 37240177 DOI: 10.3390/ijms24108831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Lavandula species are one of the most useful aromatic and medicinal plants and have great economic potential. The phytopharmaceutical contribution of the secondary metabolites of the species is unquestionable. Most recent studies have been focusing on the elucidation of the genetic background of secondary metabolite production in lavender species. Therefore, knowledge of not only genetic but especially epigenetic mechanisms for the regulation of secondary metabolites is necessary for the modification of those biosynthesis processes and the understanding of genotypic differences in the content and compositional variability of these products. The review discusses the genetic diversity of Lavandula species in relation to the geographic area, occurrence, and morphogenetic factors. The role of microRNAs in secondary-metabolites biosynthesis is described.
Collapse
Affiliation(s)
- Miroslav Habán
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Pharmacognosy and Botany, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 83232 Bratislava, Slovakia
| | - Joanna Korczyk-Szabó
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Simona Čerteková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| |
Collapse
|
32
|
Zhou M, Jiang Y, Liu X, Kong W, Zhang C, Yang J, Ke S, Li Y. Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice ( Oryza sativa). Int J Mol Sci 2023; 24:ijms24108522. [PMID: 37239869 DOI: 10.3390/ijms24108522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice.
Collapse
Affiliation(s)
- Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yifei Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Shenzhen Branch, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China
| | - Jian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Simin Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
33
|
Wei J, Yang Y, Peng Y, Wang S, Zhang J, Liu X, Liu J, Wen B, Li M. Biosynthesis and the Transcriptional Regulation of Terpenoids in Tea Plants ( Camellia sinensis). Int J Mol Sci 2023; 24:ijms24086937. [PMID: 37108101 PMCID: PMC10138656 DOI: 10.3390/ijms24086937] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Terpenes, especially volatile terpenes, are important components of tea aroma due to their unique scents. They are also widely used in the cosmetic and medical industries. In addition, terpene emission can be induced by herbivory, wounding, light, low temperature, and other stress conditions, leading to plant defense responses and plant-plant interactions. The transcriptional levels of important core genes (including HMGR, DXS, and TPS) involved in terpenoid biosynthesis are up- or downregulated by the MYB, MYC, NAC, ERF, WRKY, and bHLH transcription factors. These regulators can bind to corresponding cis-elements in the promoter regions of the corresponding genes, and some of them interact with other transcription factors to form a complex. Recently, several key terpene synthesis genes and important transcription factors involved in terpene biosynthesis have been isolated and functionally identified from tea plants. In this work, we focus on the research progress on the transcriptional regulation of terpenes in tea plants (Camellia sinensis) and thoroughly detail the biosynthesis of terpene compounds, the terpene biosynthesis-related genes, the transcription factors involved in terpene biosynthesis, and their importance. Furthermore, we review the potential strategies used in studying the specific transcriptional regulation functions of candidate transcription factors that have been discriminated to date.
Collapse
Affiliation(s)
- Junchi Wei
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Yun Yang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Ye Peng
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Shaoying Wang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Jing Zhang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Xiaobo Liu
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Jianjun Liu
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Beibei Wen
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Meifeng Li
- College of Tea Science, Guizhou University, Guiyang 550025, China
| |
Collapse
|
34
|
Du Z, Peng Z, Yang H, Wu H, Sun J, Huang L. Identification and functional characterization of three cytochrome P450 genes for the abietane diterpenoid biosynthesis in Isodon lophanthoides. PLANTA 2023; 257:90. [PMID: 36991182 DOI: 10.1007/s00425-023-04125-z] [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: 11/29/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
We identify two ferruginol synthases and a 11-hydroxyferruginol synthase from a traditional Chinese medicinal herb Isodon lophanthoides and propose their involvement in two independent abietane diterpenoids biosynthetic pathways. Isodon lophanthoides is a traditional Chinese medicinal herb rich in highly oxidized abietane-type diterpenoids. These compounds exhibit a wide range of pharmaceutical activities, yet the biosynthesis is barely known. Here, we describe the screening and functional characterization of P450s that oxidize the abietane skeleton abietatriene. We mainly focused on CYP76 family and identified 12 CYP76AHs by mining the RNA-seq data of I. lophanthoides. Among the 12 CYP76AHs, 6 exhibited similar transcriptional expression features as upstream diterpene synthases, including root or leaf-preferential expression pattern and highly MeJA inducibility. These six P450s were considered as first-tier candidates and functionally characterized in yeast and plant cells. In yeast assays showed that both CYP76AH42 and CYP76AH43 were ferruginol synthases hydroxylating the C12 position of abietatriene, whereas CYP76AH46 was characterized as a 11-hydroxyferruginol synthase which catalyzes two successive oxidations at C12 and C11 of abietatriene. Heterologous expression of three CYP76AHs in Nicotiana benthamiana resulted in the formation of ferruginol. qPCR analysis showed CYP76AH42 and CYP76AH43 were mainly expressed in the root, which was consistent with the distribution of ferruginol in the root periderms. CYP76AH46 was primarily expressed in the leaves where barely ferruginol or 11-hydroxyferruginol was detected. In addition to distinct organ-specific expression pattern, three CYP76AHs exhibited different genomic structures (w or w/o introns), low protein sequence identities (51-63%) and were placed in separate subclades in the phylogenetic tree. These results suggest that the identified CYP76AHs may be involved in at least two independent abietane biosynthetic pathways in the aerial and underground parts of I. lophanthoides.
Collapse
Affiliation(s)
- Zuying Du
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ziqiu Peng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hui Yang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Haisheng Wu
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jie Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Lili Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| |
Collapse
|
35
|
Sun Y, Shao J, Liu H, Wang H, Wang G, Li J, Mao Y, Chen Z, Ma K, Xu L, Wang Y. A chromosome-level genome assembly reveals that tandem-duplicated CYP706V oxidase genes control oridonin biosynthesis in the shoot apex of Isodon rubescens. MOLECULAR PLANT 2023; 16:517-532. [PMID: 36518072 DOI: 10.1016/j.molp.2022.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/17/2022] [Accepted: 12/08/2022] [Indexed: 06/09/2023]
Abstract
The ent-kaurenoids (e.g., oridonin and enmein) from the Isodon genus (Lamiaceae) are one class of diterpenoids with rich structural diversity and intriguing pharmaceutical activity. In contrast to the well-established gibberellin pathway, oxidative modifications diversifying the ent-kaurene skeleton in Isodon have remained undetermined for half a century. Here we report a chromosome-level genome assembly of I. rubescens, a well-recognized oridonin producer long favored by Asian people as a traditional herb with antitumor effects. The shoot apex was confirmed to be the actual region actively producing ent-kaurene diterpenoids. Through comparative genomics and phylogenetic analyses, we discovered a cluster of tandem-duplicated CYP706V oxygenase-encoding genes located on an ancient genomic block widely distributed in eudicots, whereas almost exclusively emerged in Isodon plants. In the shoot apex, IrCYP706V2 and IrCYP706V7 oxidized the ent-kaurene core in the initial stage of oridonin biosynthesis. Loss of CYP706Vs in other Lamiaceae plants offered an explanation for the specific kaurenoid production in Isodon plants. Moreover, we found that the Isodon genomes encode multiple diterpenoid synthases that are potentially involved in generating diterpenoid diversity. These findings provided new insights into the evolution of the lineage-specific diterpenoid pathway and laid a foundation for improving production of bioactive ent-kaurene-type diterpenoids by molecular breeding and synthetic biology approaches.
Collapse
Affiliation(s)
- Yuwei Sun
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Shao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Haili Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guangyi Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jianhua Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yaping Mao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhuo Chen
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ke Ma
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yong Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| |
Collapse
|
36
|
Li H, Wu S, Lin R, Xiao Y, Malaco Morotti AL, Wang Y, Galilee M, Qin H, Huang T, Zhao Y, Zhou X, Yang J, Zhao Q, Kanellis AK, Martin C, Tatsis EC. The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae. MOLECULAR PLANT 2023; 16:549-570. [PMID: 36639870 DOI: 10.1016/j.molp.2023.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/21/2022] [Accepted: 01/09/2023] [Indexed: 06/09/2023]
Abstract
The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata, although the molecular mechanisms behind clerodane biosynthesis are unknown. Here, we report a high-quality assembly of the 414.98 Mb genome of S. barbata into 13 pseudochromosomes. Using phylogenomic and biochemical data, we mapped the plastidial metabolism of kaurene (gibberellins), abietane, and clerodane diterpenes in three species of the family Lamiaceae (Scutellaria barbata, Scutellaria baicalensis, and Salvia splendens), facilitating the identification of genes involved in the biosynthesis of the clerodanes, kolavenol, and isokolavenol. We show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane metabolism. Despite the assumed monophyletic origin of clerodane biosynthesis, which is widespread in species of the Lamiaceae, our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family Lamiaceae. Our study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts.
Collapse
Affiliation(s)
- Haixiu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruoxi Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiren Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ya Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meytal Galilee
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haowen Qin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Huang
- Novogene Bioinformatics Institute, Beijing, China
| | - Yong Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xun Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Qing Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Lab. of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | | | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Shanghai 200032, China.
| |
Collapse
|
37
|
Wang Z, Nelson DR, Zhang J, Wan X, Peters RJ. Plant (di)terpenoid evolution: from pigments to hormones and beyond. Nat Prod Rep 2023; 40:452-469. [PMID: 36472136 PMCID: PMC9945934 DOI: 10.1039/d2np00054g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2014-2022.Diterpenoid biosynthesis in plants builds on the necessary production of (E,E,E)-geranylgeranyl diphosphate (GGPP) for photosynthetic pigment production, with diterpenoid biosynthesis arising very early in land plant evolution, enabling stockpiling of the extensive arsenal of (di)terpenoid natural products currently observed in this kingdom. This review will build upon that previously published in the Annual Review of Plant Biology, with a stronger focus on enzyme structure-function relationships, as well as additional insights into the evolution of (di)terpenoid metabolism since generated.
Collapse
Affiliation(s)
- Zhibiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China.,Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Juan Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, Research Center of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100024, China.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50014, USA.
| |
Collapse
|
38
|
Zhang Y, Gao J, Ma L, Tu L, Hu T, Wu X, Su P, Zhao Y, Liu Y, Li D, Zhou J, Yin Y, Tong Y, Zhao H, Lu Y, Wang J, Gao W, Huang L. Tandemly duplicated CYP82Ds catalyze 14-hydroxylation in triptolide biosynthesis and precursor production in Saccharomyces cerevisiae. Nat Commun 2023; 14:875. [PMID: 36797237 PMCID: PMC9936527 DOI: 10.1038/s41467-023-36353-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/27/2023] [Indexed: 02/18/2023] Open
Abstract
Triptolide is a valuable multipotent antitumor diterpenoid in Tripterygium wilfordii, and its C-14 hydroxyl group is often selected for modification to enhance both the bioavailability and antitumor efficacy. However, the mechanism for 14-hydroxylation formation remains unknown. Here, we discover 133 kb of tandem duplicated CYP82Ds encoding 11 genes on chromosome 12 and characterize CYP82D274 and CYP82D263 as 14-hydroxylases that catalyze the metabolic grid in triptolide biosynthesis. The two CYP82Ds catalyze the aromatization of miltiradiene, which has been repeatedly reported to be a spontaneous process. In vivo assays and evaluations of the kinetic parameters of CYP82Ds indicate the most significant affinity to dehydroabietic acid among multiple intermediates. The precursor 14-hydroxy-dehydroabietic acid is successfully produced by engineered Saccharomyces cerevisiae. Our study provides genetic elements for further elucidation of the downstream biosynthetic pathways and heterologous production of triptolide and of the currently intractable biosynthesis of other 14-hydroxyl labdane-type secondary metabolites.
Collapse
Affiliation(s)
- Yifeng Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jie Gao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lin Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lichan Tu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Tianyuan Hu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Xiaoyi Wu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ping Su
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China
| | - Yujun Zhao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Dan Li
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yan Yin
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Huan Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiadian Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China. .,Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China.
| |
Collapse
|
39
|
Ritz M, Ahmad N, Brueck T, Mehlmer N. Comparative Genome-Wide Analysis of Two Caryopteris x Clandonensis Cultivars: Insights on the Biosynthesis of Volatile Terpenoids. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030632. [PMID: 36771729 PMCID: PMC9921992 DOI: 10.3390/plants12030632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 05/31/2023]
Abstract
Caryopteris x Clandonensis, also known as bluebeard, is an ornamental plant containing a large variety of terpenes and terpene-like compounds. Four different cultivars were subjected to a principal component analysis to elucidate variations in terpenoid-biosynthesis and consequently, two representative cultivars were sequenced on a genomic level. Functional annotation of genes as well as comparative genome analysis on long read datasets enabled the identification of cultivar-specific terpene synthase and cytochrome p450 enzyme sequences. This enables new insights, especially since terpenoids in research and industry are gaining increasing interest due to their importance in areas such as food preservation, fragrances, or as active ingredients in pharmaceutical formulations. According to BUSCO assessments, the presented genomes have an average size of 355 Mb and about 96.8% completeness. An average of 52,090 genes could be annotated as putative proteins, whereas about 42 were associated with terpene synthases and about 1340 with cytochrome p450 enzymes.
Collapse
|
40
|
Zhang S, Qu-Bie JZ, Feng MK, Qu-Bie AX, Huang Y, Zhang ZF, Yan XJ, Liu Y. Illuminating the biosynthesis pathway genes involved in bioactive specific monoterpene glycosides in Paeonia veitchii Lynch by a combination of sequencing platforms. BMC Genomics 2023; 24:45. [PMID: 36698081 PMCID: PMC9878870 DOI: 10.1186/s12864-023-09138-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Paeonia veitchii Lynch, a well-known herb from the Qinghai-Tibet Plateau south of the Himalayas, can synthesize specific monoterpene glycosides (PMGs) with multiple pharmacological activities, and its rhizome has become an indispensable ingredient in many clinical drugs. However, little is known about the molecular background of P. veitchii, especially the genes involved in the biosynthetic pathway of PMGs. RESULTS A corrective full-length transcriptome with 30,827 unigenes was generated by combining next-generation sequencing (NGS) and single-molecule real-time sequencing (SMRT) of six tissues (leaf, stem, petal, ovary, phloem and xylem). The enzymes terpene synthase (TPS), cytochrome P450 (CYP), UDP-glycosyltransferase (UGT), and BAHD acyltransferase, which participate in the biosynthesis of PMGs, were systematically characterized, and their functions related to PMG biosynthesis were analysed. With further insight into TPSs, CYPs, UGTs and BAHDs involved in PMG biosynthesis, the weighted gene coexpression network analysis (WGCNA) method was used to identify the relationships between these genes and PMGs. Finally, 8 TPSs, 22 CYPs, 7 UGTs, and 2 BAHD genes were obtained, and these putative genes were very likely to be involved in the biosynthesis of PMGs. In addition, the expression patterns of the putative genes and the accumulation of PMGs in tissues suggested that all tissues are capable of biosynthesizing PMGs and that aerial plant parts could also be used to extract PMGs. CONCLUSION We generated a large-scale transcriptome database across the major tissues in P. veitchii, providing valuable support for further research investigating P. veitchii and understanding the genetic information of plants from the Qinghai-Tibet Plateau. TPSs, CYPs, UGTs and BAHDs further contribute to a better understanding of the biology and complexity of PMGs in P. veitchii. Our study will help reveal the mechanisms underlying the biosynthesis pathway of these specific monoterpene glycosides and aid in the comprehensive utilization of this multifunctional plant.
Collapse
Affiliation(s)
- Shaoshan Zhang
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People’s Republic of China, Chengdu, 610225 China ,Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225 China
| | - Jun-zhang Qu-Bie
- grid.412723.10000 0004 0604 889XCollege of Pharmacy, Southwest Minzu University, Chengdu, 610041 China
| | - Ming-kang Feng
- grid.412723.10000 0004 0604 889XCollege of Pharmacy, Southwest Minzu University, Chengdu, 610041 China
| | - A-xiang Qu-Bie
- grid.412723.10000 0004 0604 889XCollege of Pharmacy, Southwest Minzu University, Chengdu, 610041 China
| | - Yanfei Huang
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People’s Republic of China, Chengdu, 610225 China ,Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225 China
| | - Zhi-feng Zhang
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People’s Republic of China, Chengdu, 610225 China ,Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225 China
| | - Xin-jia Yan
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People’s Republic of China, Chengdu, 610225 China ,Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225 China
| | - Yuan Liu
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225 China
| |
Collapse
|
41
|
Bryson AE, Lanier ER, Lau KH, Hamilton JP, Vaillancourt B, Mathieu D, Yocca AE, Miller GP, Edger PP, Buell CR, Hamberger B. Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nat Commun 2023; 14:343. [PMID: 36670101 PMCID: PMC9860074 DOI: 10.1038/s41467-023-35845-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.
Collapse
Affiliation(s)
- Abigail E Bryson
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Emily R Lanier
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Kin H Lau
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Davis Mathieu
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Garret P Miller
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Björn Hamberger
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
42
|
Feng M, Chen C, Qu-Bie J, Qu-Bie A, Bao X, Cui Q, Yan X, Li Y, Liu Y, Zhang S. Metabolome and transcriptome associated analysis of sesquiterpenoid metabolism in Nardostachys jatamansi. FRONTIERS IN PLANT SCIENCE 2022; 13:1041321. [PMID: 36523614 PMCID: PMC9746346 DOI: 10.3389/fpls.2022.1041321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Nardostachys jatamansi, an extremely endangered valuable plant of the alpine Himalayas, can synthesize specific sesquiterpenoids with multiple effective therapies and is widely exploited for the preparation of drugs, cosmetics and even religious functions (e.g., well-known spikenard). However, how accumulation trend of the sesquiterpenoids in tissues and the molecular mechanisms underlying the production of the active ingredients are not well understood. METHODS The single-molecule real-time (SMRT) and RNA-seq transcriptome sequencing were combined to analyse the roots, rhizomes, leaves, flowers and anthocaulus of N. jatamansi. The phytochemical analysis was performed by gas chromatography‒mass spectrometry (GC‒MS) and ultrahigh-performance liquid chromatography (UPLC). RESULTS A high-quality full-length reference transcriptome with 26,503 unigenes was generated for the first time. For volatile components, a total of sixty-five compounds were successfully identified, including fifty sesquiterpenoids. Their accumulation levels in five tissues were significantly varied, and most of the sesquiterpenoids were mainly enriched in roots and rhizomes. In addition, five aromatic compounds were only detected in flowers, which may help the plant attract insects for pollination. For nonvolatile ingredients, nardosinone-type sesquiterpenoids (nardosinone, kanshone C, and isonardosinone) were detected almost exclusively in roots and rhizomes. The candidate genes associated with sesquiterpenoid biosynthesis were identified by transcriptome analysis. Consistently, it was found that most biosynthesis genes were abundantly expressed in the roots and rhizomes according to the functional enrichment and expression patterns results. There was a positive correlation between the expression profile of genes related to the biosynthesis and the accumulation level of sesquiterpenoids in tissues. Gene family function analysis identified 28 NjTPSs and 43 NjCYPs that may be involved in the biosynthesis of the corresponding sesquiterpenoids. Furthermore, gene family functional analysis and gene coexpression network analysis revealed 28 NjTPSs and 43 NjCYPs associated with nardosinone-type sesquiterpenoid biosynthesis. CONCLUSION Our research results reveal the framework of sesquiterpenoids accumulation and biosynthesis in plant tissues and provide valuable support for further studies to elucidate the molecular mechanisms of sesquiterpenoid regulation and accumulation in N. jatamansi and will also contribute to the comprehensive utilization of this alpine plant.
Collapse
Affiliation(s)
- Mingkang Feng
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Chen Chen
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
| | - Junzhang Qu-Bie
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Axiang Qu-Bie
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Xiaoming Bao
- Analysis and Application Center, Shimadzu (China) Co., Ltd, Chengdu, China
| | - Qi Cui
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Xinjia Yan
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
| | - Ying Li
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Yuan Liu
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
| | - Shaoshan Zhang
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Southwest Minzu University, Chengdu, China
| |
Collapse
|
43
|
Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
Collapse
Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| |
Collapse
|
44
|
Ye J, Yang K, Li Y, Xu F, Cheng S, Zhang W, Liao Y, Yang X, Wang L, Wang Q. Genome-wide transcriptome analysis reveals the regulatory network governing terpene trilactones biosynthesis in Ginkgo biloba. TREE PHYSIOLOGY 2022; 42:2068-2085. [PMID: 35532090 DOI: 10.1093/treephys/tpac051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Ginkgo biloba L. is currently the only remaining gymnosperm of the Ginkgoaceae Ginkgo genus, and its history can be traced back to the Carboniferous 200 million years ago. Terpene trilactones (TTLs) are one of the main active ingredients in G. biloba, including ginkgolides and bilobalide. They have a good curative effect on cardiovascular and cerebrovascular diseases because of their special antagonistic effect on platelet-activating factors. Therefore, it is necessary to deeply mine genes related to TTLs and to analyze their transcriptional regulation mechanism, which will hold vitally important scientific and practical significance for quality improvement and regulation of G. biloba. In this study, we performed RNA-Seq on the root, stem, immature leaf, mature leaf, microstrobilus, ovulate strobilus, immature fruit and mature fruit of G. biloba. The TTL regulatory network of G. biloba in different organs was revealed by different transcriptomic analysis strategies. Weighted gene co-expression network analysis (WGCNA) revealed that the five modules were closely correlated with organs. The 12 transcription factors, 5 structural genes and 24 Cytochrome P450 (CYP450) were identified as candidate regulators for TTL accumulation by WGCNA and cytoscape visualization. Finally, 6 APETALA2/ethylene response factors, 2 CYP450s and bHLH were inferred to regulate the metabolism of TTLs by correlation analysis. This study is the comprehensive in authenticating transcription factors, structural genes and CYP450 involved in TTL biosynthesis, thereby providing molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.
Collapse
Affiliation(s)
- Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Ke Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yuting Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi, Hubei 445000, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Lina Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Qijian Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| |
Collapse
|
45
|
Kang J, Quynh Le T, Oh CH. Recent advances in abietane/icetexane synthesis. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
46
|
Malhotra K, Franke J. Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants. Beilstein J Org Chem 2022; 18:1289-1310. [PMID: 36225725 PMCID: PMC9520826 DOI: 10.3762/bjoc.18.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
The cytochrome P450 monooxygenase (CYP) superfamily comprises hemethiolate enzymes that perform remarkable regio- and stereospecific oxidative chemistry. As such, CYPs are key agents for the structural and functional tailoring of triterpenoids, one of the largest classes of plant natural products with widespread applications in pharmaceuticals, food, cosmetics, and agricultural industries. In this review, we provide a full overview of 149 functionally characterised CYPs involved in the biosynthesis of triterpenoids and steroids in primary as well as in specialised metabolism. We describe the phylogenetic distribution of triterpenoid- and steroid-modifying CYPs across the plant CYPome, present a structure-based summary of their reactions, and highlight recent examples of particular interest to the field. Our review therefore provides a comprehensive up-to-date picture of CYPs involved in the biosynthesis of triterpenoids and steroids in plants as a starting point for future research.
Collapse
Affiliation(s)
- Karan Malhotra
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jakob Franke
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| |
Collapse
|
47
|
Expanding the terpene biosynthetic code with non-canonical 16 carbon atom building blocks. Nat Commun 2022; 13:5188. [PMID: 36057727 PMCID: PMC9440906 DOI: 10.1038/s41467-022-32921-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
Humankind relies on specialized metabolites for medicines, flavors, fragrances, and numerous other valuable biomaterials. However, the chemical space occupied by specialized metabolites, and, thus, their application potential, is limited because their biosynthesis is based on only a handful of building blocks. Engineering organisms to synthesize alternative building blocks will bypass this limitation and enable the sustainable production of molecules with non-canonical chemical structures, expanding the possible applications. Herein, we focus on isoprenoids and combine synthetic biology with protein engineering to construct yeast cells that synthesize 10 non-canonical isoprenoid building blocks with 16 carbon atoms. We identify suitable terpene synthases to convert these building blocks into C16 scaffolds and a cytochrome P450 to decorate the terpene scaffolds and produce different oxygenated compounds. Thus, we reconstruct the modular structure of terpene biosynthesis on 16-carbon backbones, synthesizing 28 different non-canonical terpenes, some of which have interesting odorant properties.
Collapse
|
48
|
A gene cluster in Ginkgo biloba encodes unique multifunctional cytochrome P450s that initiate ginkgolide biosynthesis. Nat Commun 2022; 13:5143. [PMID: 36050299 PMCID: PMC9436924 DOI: 10.1038/s41467-022-32879-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 08/22/2022] [Indexed: 11/08/2022] Open
Abstract
The ginkgo tree (Ginkgo biloba) is considered a living fossil due to its 200 million year's history under morphological stasis. Its resilience is partly attributed to its unique set of specialized metabolites, in particular, ginkgolides and bilobalide, which are chemically complex terpene trilactones. Here, we use a gene cluster-guided mining approach in combination with co-expression analysis to reveal the primary steps in ginkgolide biosynthesis. We show that five multifunctional cytochrome P450s with atypical catalytic activities generate the tert-butyl group and one of the lactone rings, characteristic of all G. biloba trilactone terpenoids. The reactions include scarless C-C bond cleavage as well as carbon skeleton rearrangement (NIH shift) occurring on a previously unsuspected intermediate. The cytochrome P450s belong to CYP families that diversifies in pre-seed plants and gymnosperms, but are not preserved in angiosperms. Our work uncovers the early ginkgolide pathway and offers a glance into the biosynthesis of terpenoids of the Mesozoic Era.
Collapse
|
49
|
Hansen NL, Kjaerulff L, Heck QK, Forman V, Staerk D, Møller BL, Andersen-Ranberg J. Tripterygium wilfordii cytochrome P450s catalyze the methyl shift and epoxidations in the biosynthesis of triptonide. Nat Commun 2022; 13:5011. [PMID: 36008399 PMCID: PMC9411204 DOI: 10.1038/s41467-022-32667-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
The diterpenoid triepoxides triptolide and triptonide from Tripterygium wilfordii (thunder god wine) exhibit unique bioactivities with potential uses in disease treatment and as a non-hormonal male contraceptives. Here, we show that cytochrome P450s (CYPs) from the CYP71BE subfamily catalyze an unprecedented 18(4→3) methyl shift required for biosynthesis of the abeo-abietane core structure present in diterpenoid triepoxides and in several other plant diterpenoids. In combination with two CYPs of the CYP82D subfamily, four CYPs from T. wilfordii are shown to constitute the minimal set of biosynthetic genes that enables triptonide biosynthesis using Nicotiana benthamiana and Saccharomyces cerevisiae as heterologous hosts. In addition, co-expression of a specific T. wilfordii cytochrome b5 (Twcytb5-A) increases triptonide output more than 9-fold in S. cerevisiae and affords isolation and structure elucidation by NMR spectroscopic analyses of 18 diterpenoids, providing insights into the biosynthesis of diterpenoid triepoxides. Our findings pave the way for diterpenoid triepoxide production via fermentation. How triptonide is made in the medicinal plant Tripterygium wilfordii is largely unknown. Here, the authors report the identification and characterization of a suite of cytochrome P450s and show their function in catalyzing the formation of triptonide from miltriadiene in tobacco and baker’s yeast.
Collapse
Affiliation(s)
- Nikolaj Lervad Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Louise Kjaerulff
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Quinn Kalby Heck
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Victor Forman
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
| |
Collapse
|
50
|
Knoch E, Kovács J, Deiber S, Tomita K, Shanmuganathan R, Serra Serra N, Okada K, Becker C, Schandry N. Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification. BMC PLANT BIOLOGY 2022; 22:402. [PMID: 35974304 PMCID: PMC9382751 DOI: 10.1186/s12870-022-03780-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds. RESULTS In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis of Arabidopsis thaliana exposed to either the benzoxazinoid derivative 2-amino- 3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different Poaceae crop species. CONCLUSIONS Despite their distinct chemical nature, we observed similar molecular responses of A. thaliana to these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.
Collapse
Affiliation(s)
- Eva Knoch
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Judit Kovács
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sebastian Deiber
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Keisuke Tomita
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences (GSALS), The University of Tokyo, Tokyo, 113-8657, Japan
| | - Reshi Shanmuganathan
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Núria Serra Serra
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Kazunori Okada
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences (GSALS), The University of Tokyo, Tokyo, 113-8657, Japan
| | - Claude Becker
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany.
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria.
| | - Niklas Schandry
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany.
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria.
| |
Collapse
|