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Bai X, Zhang R, Zeng Q, Yang W, Fang F, Sun Q, Yan C, Li F, Liu X, Li B. The RNA-Binding Protein BoRHON1 Positively Regulates the Accumulation of Aliphatic Glucosinolates in Cabbage. Int J Mol Sci 2024; 25:5314. [PMID: 38791354 PMCID: PMC11120748 DOI: 10.3390/ijms25105314] [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: 03/23/2024] [Revised: 04/29/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Aliphatic glucosinolates are an abundant group of plant secondary metabolites in Brassica vegetables, with some of their degradation products demonstrating significant anti-cancer effects. The transcription factors MYB28 and MYB29 play key roles in the transcriptional regulation of aliphatic glucosinolates biosynthesis, but little is known about whether BoMYB28 and BoMYB29 are also modulated by upstream regulators or how, nor their gene regulatory networks. In this study, we first explored the hierarchical transcriptional regulatory networks of MYB28 and MYB29 in a model plant, then systemically screened the regulators of the three BoMYB28 homologs in cabbage using a yeast one-hybrid. Furthermore, we selected a novel RNA binding protein, BoRHON1, to functionally validate its roles in modulating aliphatic glucosinolates biosynthesis. Importantly, BoRHON1 induced the accumulation of all detectable aliphatic and indolic glucosinolates, and the net photosynthetic rates of BoRHON1 overexpression lines were significantly increased. Interestingly, the growth and biomass of these overexpression lines of BoRHON1 remained the same as those of the control plants. BoRHON1 was shown to be a novel, potent, positive regulator of glucosinolates biosynthesis, as well as a novel regulator of normal plant growth and development, while significantly increasing plants' defense costs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Baohua Li
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (X.B.); (R.Z.); (Q.Z.); (W.Y.); (F.F.); (Q.S.); (C.Y.); (F.L.); (X.L.)
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Zhou J, Zou X, Deng Z, Duan L. Analysing a Group of Homologous BAHD Enzymes Provides Insights into the Evolutionary Transition of Rosmarinic Acid Synthases from Hydroxycinnamoyl-CoA:Shikimate/Quinate Hydroxycinnamoyl Transferases. PLANTS (BASEL, SWITZERLAND) 2024; 13:512. [PMID: 38498481 PMCID: PMC10892161 DOI: 10.3390/plants13040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
The interplay of various enzymes and compounds gives rise to the intricate secondary metabolic networks observed today. However, the current understanding of their formation and expansion remains limited. BAHD acyltransferases play important roles in the biosynthesis of numerous significant secondary metabolites. In plants, they are widely distributed and exhibit a diverse range of activities. Among them, rosmarinic acid synthase (RAS) and hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) have gained significant recognition and have been extensively investigated as prominent members of the BAHD acyltransferase family. Here, we conducted a comprehensive study on a unique group of RAS homologous enzymes in Mentha longifolia that display both catalytic activities and molecular features similar to HCT and Lamiaceae RAS. Subsequent phylogenetic and comparative genome analyses revealed their derivation from expansion events within the HCT gene family, indicating their potential as collateral branches along the evolutionary trajectory, leading to Lamiaceae RAS while still retaining certain ancestral vestiges. This discovery provides more detailed insights into the evolution from HCT to RAS. Our collective findings indicate that gene duplication is the driving force behind the observed evolutionary pattern in plant-specialized enzymes, which probably originated from ancestral enzyme promiscuity and were subsequently shaped by principles of biological adaptation.
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Affiliation(s)
| | | | | | - Lian Duan
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430071, China; (J.Z.); (X.Z.); (Z.D.)
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Ali S, Bai Y, Zhang J, Zada S, Khan N, Hu Z, Tang Y. Discovering Nature's shield: Metabolomic insights into green zinc oxide nanoparticles Safeguarding Brassica parachinensis L. from cadmium stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108126. [PMID: 38147709 DOI: 10.1016/j.plaphy.2023.108126] [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: 04/28/2023] [Revised: 08/06/2023] [Accepted: 10/19/2023] [Indexed: 12/28/2023]
Abstract
Heavy metal cadmium (Cd) hinders plants' growth and productivity by causing different morphological and physiological changes. Nanoparticles (NPs) are promising for raising plant yield and reducing Cd toxicity. Nonetheless, the fundamental mechanism of nanoparticle-interfered Cd toxicity in Brassica parachineses L. remains unknown. A novel ZnO nanoparticle (ZnO-NPs) was synthesized using a microalgae strain (Chlorella pyrenoidosa) through a green process and characterized by different standard parameters through TEM, EDX, and XRD. This study examines the effect of different concentrations of ZnO-NPs (50 and 100 mgL-1) in B. parachineses L. under Cd stress through ultra-high-performance liquid chromatography/high-resolution mass spectrometry-based untargeted metabolomics profiling. In the presence of Cd toxicity, foliar spraying with ZnO-NPs raised Cu, Fe, Zn, and Mg levels in the roots and/or leaves, improved seedling development, as demonstrated by increased plant height, root length, and shoot and root fresh weight. Furthermore, the ZnO-NPs significantly enhanced the photosynthetic pigments and changed the antioxidant activities of the Cd-treated plants. Based on a metabolomics analysis, 481 untargeted metabolites were accumulated in leaves under normal and Cd-stressed conditions. These metabolites were highly enriched in producing organic acids, amino acids, glycosides, flavonoids, nucleic acids, and vitamin biosynthesis. Surprisingly, ZnO-NPs restored approximately 60% of Cd stress metabolites to normal leaf levels. Our findings suggest that green synthesized ZnO-NPs can balance ions' absorption, modulate the antioxidant activities, and restore more metabolites associated with plant growth to their normal levels under Cd stress. It can be applied as a plant growth regulator to alleviate heavy metal toxicity and improve crop yield in heavy metal-contaminated regions.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Junliang Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Shah Zada
- Guangdong Laboratory of Artificial Intelligence & Digital Economy (SZ), Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL32611, USA
| | - Zhangli Hu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform of Collaborative Innovation for Marine Algae Industry, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong, China.
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4
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Chen L, Zeng Q, Zhang J, Li C, Bai X, Sun F, Kliebenstein DJ, Li B. Large-scale identification of novel transcriptional regulators of the aliphatic glucosinolate pathway in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:300-315. [PMID: 37738614 DOI: 10.1093/jxb/erad376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023]
Abstract
Aliphatic glucosinolates are a large group of plant secondary metabolites characteristic of Brassicaceae, including the model plant Arabidopsis. The diverse and complex degradation products of aliphatic glucosinolates contribute to plant responses to herbivory, pathogen attack, and environmental stresses. Most of the biosynthesis genes in the aliphatic glucosinolate pathway have been cloned in Arabidopsis, and the research focus has recently shifted to the regulatory mechanisms controlling aliphatic glucosinolate accumulation. Up till now, more than 40 transcriptional regulators have been identified as regulating the aliphatic glucosinolate pathway, but many more novel regulators likely remain to be discovered based on research evidence over the past decade. In the current study, we took a systemic approach to functionally test 155 candidate transcription factors in Arabidopsis identified by yeast one-hybrid assay, and successfully validated at least 30 novel regulators that could significantly influence the accumulation of aliphatic glucosinolates in our experimental set-up. We also showed that the regulators of the aliphatic glucosinolate pathway have balanced positive and negative effects, and glucosinolate metabolism and plant development can be coordinated. Our work is the largest scale effort so far to validate transcriptional regulators of a plant secondary metabolism pathway, and provides new insights into how the highly diverse plant secondary metabolism is regulated at the transcriptional level.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Qi Zeng
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jiahao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xue Bai
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Fengli Sun
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Baohua Li
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
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5
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Li S, Chiu TY, Jin X, Cao D, Xu M, Zhu M, Zhou Q, Liu C, Zong Y, Wang S, Yu K, Zhang F, Bai M, Liu G, Liang Y, Zhang C, Simonsen HT, Zhao J, Liu B, Zhao S. Integrating genomic and multiomic data for Angelica sinensis provides insights into the evolution and biosynthesis of pharmaceutically bioactive compounds. Commun Biol 2023; 6:1198. [PMID: 38001348 PMCID: PMC10674023 DOI: 10.1038/s42003-023-05569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Angelica sinensis roots (Angelica roots) are rich in many bioactive compounds, including phthalides, coumarins, lignans, and terpenoids. However, the molecular bases for their biosynthesis are still poorly understood. Here, an improved chromosome-scale genome for A. sinensis var. Qinggui1 is reported, with a size of 2.16 Gb, contig N50 of 4.96 Mb and scaffold N50 of 198.27 Mb, covering 99.8% of the estimated genome. Additionally, by integrating genome sequencing, metabolomic profiling, and transcriptome analysis of normally growing and early-flowering Angelica roots that exhibit dramatically different metabolite profiles, the pathways and critical metabolic genes for the biosynthesis of these major bioactive components in Angelica roots have been deciphered. Multiomic analyses have also revealed the evolution and regulation of key metabolic genes for the biosynthesis of pharmaceutically bioactive components; in particular, TPSs for terpenoid volatiles, ACCs for malonyl CoA, PKSs for phthalide, and PTs for coumarin biosynthesis were expanded in the A. sinensis genome. These findings provide new insights into the biosynthesis of pharmaceutically important compounds in Angelica roots for exploration of synthetic biology and genetic improvement of herbal quality.
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Affiliation(s)
- Shiming Li
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Tsan-Yu Chiu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Dong Cao
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Meng Xu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Mingzhi Zhu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, Hunan, China
| | - Qi Zhou
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Chun Liu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Yuan Zong
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Shujie Wang
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Feng Zhang
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Mingzhou Bai
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
- Department of Biotechnology and Biomedicine, The Technical University of Denmark, 2800, Kongens, Lyngby, Denmark
| | - Guangrui Liu
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Yunlong Liang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China
| | - Chi Zhang
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Henrik Toft Simonsen
- Department of Biotechnology and Biomedicine, The Technical University of Denmark, 2800, Kongens, Lyngby, Denmark
- Laboratory of Plant Biotechnology, Université Jean Monnet, 23 Rue du Dr Michelon, 42000, Saint-Etienne, France
| | - Jian Zhao
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, Hunan, China.
| | - Baolong Liu
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, Qinghai, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, 810008, Xining, Qinghai, China.
| | - Shancen Zhao
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.
- Beijing Life Science Academy, 102200, Beijing, China.
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Tsipinana S, Husseiny S, Alayande KA, Raslan M, Amoo S, Adeleke R. Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1248319. [PMID: 37771494 PMCID: PMC10522919 DOI: 10.3389/fpls.2023.1248319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.
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Affiliation(s)
- Sinawo Tsipinana
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Samah Husseiny
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Kazeem A. Alayande
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mai Raslan
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Stephen Amoo
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- Agricultural Research Council – Vegetables, Industrial and Medicinal Plants, Roodeplaat, Pretoria, South Africa
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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7
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Conneely LJ, Berkowitz O, Lewsey MG. Emerging trends in genomic and epigenomic regulation of plant specialised metabolism. PHYTOCHEMISTRY 2022; 203:113427. [PMID: 36087823 DOI: 10.1016/j.phytochem.2022.113427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Regulation of specialised metabolism genes is multilayered and complex, influenced by an array of genomic, epigenetic and epigenomic mechanisms. Here, we review the most recent knowledge in this field, drawing from discoveries in several plant species. Our aim is to improve understanding of how plant genome structure and function influence specialised metabolism. We also highlight key areas for future exploration. Gene regulatory mechanisms influencing specialised metabolism include gene duplication and neo-functionalization, conservation of operon-like clusters of specialised metabolism genes, local chromatin modifications, and the organisation of higher order chromatin structures within the nucleus. Genomic and epigenomic research to-date in the discipline have focused on a relatively small number of plant species, primarily at whole organ or tissue level. This is largely due to the technical demands of the experimental methods needed. However, a high degree of cell-type specificity of function exists in specialised metabolism, driven by similarly specific gene regulation. In this review we focus on the genomic characteristics of genes that are found in different types of clusters within the genome. We propose that acquisition of cell-resolution epigenomic datasets in emerging models, such as the glandular trichomes of Cannabis sativa, will yield important advances. Data such as chromatin accessibility and histone modification profiles can pinpoint which regulatory sequences are active in individual cell types and at specific times in development. These could provide fundamental biological insight as well as novel targets for genetic engineering and crop improvement.
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Affiliation(s)
- Lee J Conneely
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
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Yu J, Tu X, Huang AC. Functions and biosynthesis of plant signaling metabolites mediating plant-microbe interactions. Nat Prod Rep 2022; 39:1393-1422. [PMID: 35766105 DOI: 10.1039/d2np00010e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2015-2022Plants and microbes have coevolved since their appearance, and their interactions, to some extent, define plant health. A reasonable fraction of small molecules plants produced are involved in mediating plant-microbe interactions, yet their functions and biosynthesis remain fragmented. The identification of these compounds and their biosynthetic genes will open up avenues for plant fitness improvement by manipulating metabolite-mediated plant-microbe interactions. Herein, we integrate the current knowledge on their chemical structures, bioactivities, and biosynthesis with the view of providing a high-level overview on their biosynthetic origins and evolutionary trajectory, and pinpointing the yet unknown and key enzymatic steps in diverse biosynthetic pathways. We further discuss the theoretical basis and prospects for directing plant signaling metabolite biosynthesis for microbe-aided plant health improvement in the future.
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Affiliation(s)
- Jingwei Yu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Xingzhao Tu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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Zou C, Lu T, Wang R, Xu P, Jing Y, Wang R, Xu J, Wan J. Comparative physiological and metabolomic analyses reveal that Fe 3O 4 and ZnO nanoparticles alleviate Cd toxicity in tobacco. J Nanobiotechnology 2022; 20:302. [PMID: 35761340 PMCID: PMC9235244 DOI: 10.1186/s12951-022-01509-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Heavy metals repress tobacco growth and quality, and engineered nanomaterials have been used for sustainable agriculture. However, the underlying mechanism of nanoparticle-mediated cadmium (Cd) toxicity in tobacco remains elusive. RESULTS Herein, we investigated the effects of Fe3O4 and ZnO nanoparticles (NPs) on Cd stress in tobacco cultivar 'Yunyan 87' (Nicotiana tabacum). Cd severely repressed tobacco growth, whereas foliar spraying with Fe3O4 and ZnO NPs promoted plant growth, as indicated by enhancing plant height, root length, shoot and root fresh weight under Cd toxicity. Moreover, Fe3O4 and ZnO NPs increased, including Zn, K and Mn contents, in the roots and/or leaves and facilitated seedling growth under Cd stress. Metabolomics analysis showed that 150 and 76 metabolites were differentially accumulated in roots and leaves under Cd stress, respectively. These metabolites were significantly enriched in the biosynthesis of amino acids, nicotinate and nicotinamide metabolism, arginine and proline metabolism, and flavone and flavonol biosynthesis. Interestingly, Fe3O4 and ZnO NPs restored 50% and 47% in the roots, while they restored 70% and 63% in the leaves to normal levels, thereby facilitating plant growth. Correlation analysis further indicated that these metabolites, including proline, 6-hydroxynicotinic acid, farrerol and quercetin-3-O-sophoroside, were significantly correlated with plant growth. CONCLUSIONS These results collectively indicate that metal nanoparticles can serve as plant growth regulators and provide insights into using them for improving crops in heavy metal-contaminated areas.
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Affiliation(s)
- Congming Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Tianquan Lu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- Center of Economic Botany, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruting Wang
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- Center of Economic Botany, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Yifen Jing
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- Center of Economic Botany, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Ruling Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- Center of Economic Botany, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Jinpeng Wan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- Center of Economic Botany, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Sun L, Liu L, Wang Y, Feng Y, Yang W, Wang D, Gao S, Miao X, Sun W. Integration of Metabolomics and Transcriptomics for Investigating the Tolerance of Foxtail Millet ( Setaria italica) to Atrazine Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:890550. [PMID: 35755691 PMCID: PMC9226717 DOI: 10.3389/fpls.2022.890550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Foxtail millet (Setaria italica) is a monotypic species widely planted in China. However, residual atrazine, a commonly used maize herbicide, in soil, is a major abiotic stress to millet. Here, we investigated atrazine tolerance in millet based on the field experiments, then obtained an atrazine-resistant variety (Gongai2, GA2) and an atrazine-sensitive variety (Longgu31, LG31). To examine the effects of atrazine on genes and metabolites in millet plants, we compared the transcriptomic and metabolomic profiles between GA2 and LG31 seedling leaves. The results showed that 2,208 differentially expressed genes (DEGs; 501 upregulated, 1,707 downregulated) and 192 differentially expressed metabolites (DEMs; 82 upregulated, 110 downregulate) were identified in atrazine-treated GA2, while in atrazine-treated LG31, 1,773 DEGs (761 upregulated, 1,012 downregulated) and 215 DEMs (95 upregulated, 120 downregulated) were identified. The bioinformatics analysis of DEGs and DEMs showed that many biosynthetic metabolism pathways were significantly enriched in GA2 and LG31, such as glutathione metabolism (oxiglutatione, γ-glutamylcysteine; GSTU6, GSTU1, GSTF1), amino acid biosynthesis (L-cysteine, N-acetyl-L-glutamic acid; ArgB, GS, hisC, POX1), and phenylpropanoid biosynthesis [trans-5-o-(4-coumaroyl)shikimate; HST, C3'H]. Meanwhile, the co-expression analysis indicated that GA2 plants had enhanced atrazine tolerance owing to improved glutathione metabolism and proline biosynthesis, and the enrichment of scopoletin may help LG31 plants resist atrazine stress. Herein, we screened an atrazine-resistant millet variety and generated valuable information that may deepen our understanding of the complex molecular mechanism underlying the response to atrazine stress in millet.
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Affiliation(s)
- Lifang Sun
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Libin Liu
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yuting Wang
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanfei Feng
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Yang
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Di Wang
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shuren Gao
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xingfen Miao
- Key Laboratory of Crop Germplasm Improvement and Cultivation in Cold Regions, Key Laboratory of Low Carbon Green Agriculture of Northeast Plain in Ministry of Agriculture and Rural Affairs, Agronomy College of Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wentao Sun
- Heilongjiang HYHC Company, Daqing, China
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11
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Alonso AM, Reyes-Maldonado OK, Puebla-Pérez AM, Arreola MPG, Velasco-Ramírez SF, Zúñiga-Mayo V, Sánchez-Fernández RE, Delgado-Saucedo JI, Velázquez-Juárez G. GC/MS Analysis, Antioxidant Activity, and Antimicrobial Effect of Pelargonium peltatum (Geraniaceae). Molecules 2022; 27:molecules27113436. [PMID: 35684374 PMCID: PMC9181846 DOI: 10.3390/molecules27113436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 12/05/2022] Open
Abstract
In recent years, the increase in antibiotic resistance demands searching for new compounds with antimicrobial activity. Phytochemicals found in plants offer an alternative to this problem. The genus Pelargonium contains several species; some have commercial use in traditional medicine such as P. sinoides, and others such as P. peltatum are little studied but have promising potential for various applications such as phytopharmaceuticals. In this work, we characterized the freeze-dried extracts (FDEs) of five tissues (root, stem, leaf, and two types of flowers) and the ethyl acetate fractions from leaf (Lf-EtOAc) and flower (Fwr-EtOAc) of P. peltatum through the analysis by thin-layer chromatography (T.L.C.), gas chromatography coupled to mass spectrometry (GC-MS), phytochemicals quantification, antioxidant capacity, and antimicrobial activity. After the first round of analysis, it was observed that the FDE-Leaf and FDE-Flower showed higher antioxidant and antimicrobial activities compared to the other FDEs, for which FDE-Leaf and FDE-Flower were fractionated and analyzed in a second round. The antioxidant activity determined by ABTS showed that Lf-EtOAc and Fwr-EtOAc had the lowest IC50 values with 27.15 ± 1.04 and 28.11 ± 1.3 µg/mL, respectively. The content of total polyphenols was 264.57 ± 7.73 for Lf-EtOAc and 105.39 ± 4.04 mg G.A./g FDE for Fwr-EtOAc. Regarding the content of flavonoid, Lf-EtOAc and Fw-EtOAc had the highest concentration with 34.4 ± 1.06 and 29.45 ± 1.09 mg Q.E./g FDE. In addition, the minimum inhibitory concentration (M.I.C.) of antimicrobial activity was evaluated: Lf-EtOAc and Fwr-EtOAc were effective at 31.2 µg/mL for Staphylococcus aureus and 62.5 µg/mL for Salmonella enterica, while for the Enterococcus feacalis strain, Fwr-EtOAc presented 31.2 µg/mL of M.I.C. According to the GC-MS analysis, the main compounds were 1,2,3-Benzenetriol (Pyrogallol), with 77.38% of relative abundance in the Lf-EtOAc and 71.24% in the Fwr-EtOAc, followed by ethyl gallate (13.10%) in the Fwr-EtOAc and (Z)-9-Octadecenamide (13.63% and 6.75%) in both Lf-EtOAc and Fwr-EtOAc, respectively.
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Affiliation(s)
- Alan-Misael Alonso
- Doctorado en Ciencias en Procesos Biotecnológicos, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, Guadalajara CP 44340, Jalisco, Mexico;
| | - Oscar Kevin Reyes-Maldonado
- Centro Universitario de Ciencias Exactas e Ingenierías, Laboratorio de Bioquímica Avanzada, Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, Guadalajara CP 44430, Jalisco, Mexico; (O.K.R.-M.); (S.F.V.-R.)
| | - Ana María Puebla-Pérez
- Centro Universitario de Ciencias Exactas e Ingenierías, Departamento de Farmacobiología, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, Guadalajara CP 44430, Jalisco, Mexico;
| | - Martha Patricia Gallegos Arreola
- Centro de Investigación Biomédica de Occidente, División de Genética, I.M.S.S., Sierra Mojada 800, Independencia Oriente, Guadalajara CP 44340, Jalisco, Mexico;
| | - Sandra Fabiola Velasco-Ramírez
- Centro Universitario de Ciencias Exactas e Ingenierías, Laboratorio de Bioquímica Avanzada, Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, Guadalajara CP 44430, Jalisco, Mexico; (O.K.R.-M.); (S.F.V.-R.)
| | - Victor Zúñiga-Mayo
- Campus Montecillo, CONACyT-Instituto de Fitosanidad, Colegio de Postgraduados, Texcoco CP 56230, Estado de Mexico, Mexico;
| | - Rosa E. Sánchez-Fernández
- Laboratorio Nacional de Investigación y Servicio Agroalimentario y Forestal (LANISAF), Universidad Autónoma Chapingo, Mexico-Texcoco km 38.5, Texcoco CP 56230, Mexico;
| | - Jorge-Iván Delgado-Saucedo
- Centro Universitario de Ciencias Exactas e Ingenierías, Departamento de Farmacobiología, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, Guadalajara CP 44430, Jalisco, Mexico;
- Correspondence: (J.-I.D.-S.); (G.V.-J.)
| | - Gilberto Velázquez-Juárez
- Centro Universitario de Ciencias Exactas e Ingenierías, Laboratorio de Bioquímica Avanzada, Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, Guadalajara CP 44430, Jalisco, Mexico; (O.K.R.-M.); (S.F.V.-R.)
- Correspondence: (J.-I.D.-S.); (G.V.-J.)
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12
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Noushahi HA, Khan AH, Noushahi UF, Hussain M, Javed T, Zafar M, Batool M, Ahmed U, Liu K, Harrison MT, Saud S, Fahad S, Shu S. Biosynthetic pathways of triterpenoids and strategies to improve their Biosynthetic Efficiency. PLANT GROWTH REGULATION 2022; 97:439-454. [PMID: 35382096 PMCID: PMC8969394 DOI: 10.1007/s10725-022-00818-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/18/2022] [Indexed: 05/13/2023]
Abstract
"Triterpenoids" can be considered natural products derived from the cyclization of squalene, yielding 3-deoxytriterpenes (hydrocarbons) or 3-hydroxytriterpenes. Triterpenoids are metabolites of these two classes of triterpenes, produced by the functionalization of their carbon skeleton. They can be categorized into different groups based on their structural formula/design. Triterpenoids are an important group of compounds that are widely used in the fields of pharmacology, food, and industrial biotechnology. However, inadequate synthetic methods and insufficient knowledge of the biosynthesis of triterpenoids, such as their structure, enzymatic activity, and the methods used to produce pure and active triterpenoids, are key problems that limit the production of these active metabolites. Here, we summarize the derivatives, pharmaceutical properties, and biosynthetic pathways of triterpenoids and review the enzymes involved in their biosynthetic pathway. Furthermore, we concluded the screening methods, identified the genes involved in the pathways, and highlighted the appropriate strategies used to enhance their biosynthetic production to facilitate the commercial process of triterpenoids through the synthetic biology method.
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Affiliation(s)
- Hamza Armghan Noushahi
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
- Plant Breeding and Phenomic Centre, Faculty of Agricultural Sciences, University of Talca, 3460000 Talca, Chile
| | - Aamir Hamid Khan
- National Key Lab of Crop Genetics Improvement, College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Usama Farhan Noushahi
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, 54000 Lahore, Pakistan
| | - Mubashar Hussain
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Maimoona Zafar
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Umair Ahmed
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ke Liu
- Tasmanian Institute of Agriculture, University of Tasmania, 7250 Burnie, Tasmania Australia
| | - Matthew Tom Harrison
- Tasmanian Institute of Agriculture, University of Tasmania, 7250 Burnie, Tasmania Australia
| | - Shah Saud
- College of Life Science, Linyi University, 276000 Linyi, Shandong China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, 570228 Haikou, China
- Department of Agronomy, The University of Haripur, 22620 Haripur, Pakistan
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
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13
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Activation of Cryptic Secondary Metabolite Biosynthesis in Bamboo Suspension Cells by a Histone Deacetylase Inhibitor. Appl Biochem Biotechnol 2021; 193:3496-3511. [PMID: 34287751 DOI: 10.1007/s12010-021-03629-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Plants have evolved a diverse array of secondary metabolite biosynthetic pathways. Undifferentiated plant cells, however, tend to biosynthesize secondary metabolites to a lesser extent and sometimes not at all. This phenomenon in cultured cells is associated with the transcriptional suppression of biosynthetic genes due to epigenetic alterations, such as low histone acetylation levels and/or high DNA methylation levels. Here, using cultured cells of bamboo (Bambusa multiplex; Bm) as a model system, we investigated the effect of histone deacetylase (HDAC) inhibitors on the activation of cryptic secondary metabolite biosynthesis. The Bm suspension cells cultured in the presence of an HDAC inhibitor, suberoyl bis-hydroxamic acid (SBHA), exhibited strong biosynthesis of some compounds that are inherently present at very low levels in Bm cells. Two major compounds induced by SBHA were isolated and were identified as 3-O-p-coumaroylquinic acid (1) and 3-O-feruloylquinic acid (2). Their productivities depended on the type of basal culture medium, initial cell density, and culture period, as well as the SBHA concentration. The biosynthesis of these two compounds was also induced by another HDAC inhibitor, trichostatin A. These results demonstrate the usefulness of HDAC inhibitors to activate cryptic secondary metabolite biosynthesis in cultured plant cells.
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14
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Kawasaki A, Chikugo A, Tamura K, Seki H, Muranaka T. Characterization of UDP-glucose dehydrogenase isoforms in the medicinal legume Glycyrrhiza uralensis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:205-218. [PMID: 34393599 PMCID: PMC8329271 DOI: 10.5511/plantbiotechnology.21.0222a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 02/22/2021] [Indexed: 06/13/2023]
Abstract
Uridine 5'-diphosphate (UDP)-glucose dehydrogenase (UGD) produces UDP-glucuronic acid from UDP-glucose as a precursor of plant cell wall polysaccharides. UDP-glucuronic acid is also a sugar donor for the glycosylation of various plant specialized metabolites. Nevertheless, the roles of UGDs in plant specialized metabolism remain poorly understood. Glycyrrhiza species (licorice), which are medicinal legumes, biosynthesize triterpenoid saponins, soyasaponins and glycyrrhizin, commonly glucuronosylated at the C-3 position of the triterpenoid scaffold. Often, several different UGD isoforms are present in plants. To gain insight into potential functional differences among UGD isoforms in triterpenoid saponin biosynthesis in relation to cell wall component biosynthesis, we identified and characterized Glycyrrhiza uralensis UGDs (GuUGDs), which were discovered to comprise five isoforms, four of which (GuUGD1-4) showed UGD activity in vitro. GuUGD1-4 had different biochemical properties, including their affinity for UDP-glucose, catalytic constant, and sensitivity to feedback inhibitors. GuUGD2 had the highest catalytic constant and highest gene expression level among the GuUGDs, suggesting that it is the major isoform contributing to the transition from UDP-glucose to UDP-glucuronic acid in planta. To evaluate the contribution of GuUGD isoforms to saponin biosynthesis, we compared the expression patterns of GuUGDs with those of saponin biosynthetic genes in methyl jasmonate (MeJA)-treated cultured stolons. GuUGD1-4 showed delayed responses to MeJA compared to those of saponin biosynthetic genes, suggesting that MeJA-responsive expression of GuUGDs compensates for the decreased UDP-glucuronic acid pool due to consumption during saponin biosynthesis.
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Affiliation(s)
- Ayumi Kawasaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Ayaka Chikugo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Keita Tamura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
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15
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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16
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Liu Z, Wang H, Xie J, Lv J, Zhang G, Hu L, Luo S, Li L, Yu J. The Roles of Cruciferae Glucosinolates in Disease and Pest Resistance. PLANTS 2021; 10:plants10061097. [PMID: 34070720 PMCID: PMC8229868 DOI: 10.3390/plants10061097] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022]
Abstract
With the expansion of the area under Cruciferae vegetable cultivation, and an increase in the incidence of natural threats such as pests and diseases globally, Cruciferae vegetable losses caused by pathogens, insects, and pests are on the rise. As one of the key metabolites produced by Cruciferae vegetables, glucosinolate (GLS) is not only an indicator of their quality but also controls infestation by numerous fungi, bacteria, aphids, and worms. Today, the safe and pollution-free production of vegetables is advocated globally, and environmentally friendly pest and disease control strategies, such as biological control, to minimize the adverse impacts of pathogen and insect pest stress on Cruciferae vegetables, have attracted the attention of researchers. This review explores the mechanisms via which GLS acts as a defensive substance, participates in responses to biotic stress, and enhances plant tolerance to the various stress factors. According to the current research status, future research directions are also proposed.
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Affiliation(s)
- Zeci Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China;
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Huiping Wang
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Jianming Xie
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Jian Lv
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Guobin Zhang
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Linli Hu
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Shilei Luo
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Lushan Li
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua 617000, China
| | - Jihua Yu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China;
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
- Correspondence: ; Tel.: +86-931-763-2188
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Allemailem KS. Antimicrobial Potential of Naturally Occurring Bioactive Secondary Metabolites. J Pharm Bioallied Sci 2021; 13:155-162. [PMID: 34349474 PMCID: PMC8291113 DOI: 10.4103/jpbs.jpbs_753_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/01/2020] [Accepted: 12/25/2020] [Indexed: 11/04/2022] Open
Abstract
The use of traditional medicines of natural origin has been prevalent since ancient times globally as the plants produce a great diversity in their secondary metabolites. The naturally occurring bioactive constituents in food and other plant materials have shown widespread attention for their use as alternative medicine to prevent and cure microbial growth with the least toxic manifestations. The inclusion of these contents revealed their crucial role to improve the therapeutic efficacy of the classical drugs against various pathogenic microorganisms. Furthermore, several metabolites have also been explored in combination with antimicrobial agents to overcome the problems associated with drug resistance. This current review discusses the antimicrobial activities of secondary metabolites as well as their role in drug sensitivity against multiple-drug resistant pathogenic microbes.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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18
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Parra-Galindo MA, Soto-Sedano JC, Mosquera-Vásquez T, Roda F. Pathway-based analysis of anthocyanin diversity in diploid potato. PLoS One 2021; 16:e0250861. [PMID: 33914830 PMCID: PMC8084248 DOI: 10.1371/journal.pone.0250861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
Anthocyanin biosynthesis is one of the most studied pathways in plants due to the important ecological role played by these compounds and the potential health benefits of anthocyanin consumption. Given the interest in identifying new genetic factors underlying anthocyanin content we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses. By using an expanded SNP dataset, we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein. Importantly, a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS. Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters. We identified multiple anthocyanin homologs in this genomic region, including four transcription factors and five enzymes that could be governing anthocyanin variation. For instance, a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured. Finally, we combined a pathway analysis and GWAS of other agronomic traits to identify pathways related to anthocyanin biosynthesis in potatoes. We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis. The results contribute to the understanding of anthocyanins regulation in potatoes and can be used in future breeding programs focused on nutraceutical food.
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Affiliation(s)
| | - Johana Carolina Soto-Sedano
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Teresa Mosquera-Vásquez
- Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Federico Roda
- Max Planck Tandem Group, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
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Transcriptomic Analyses Shed Light on Critical Genes Associated with Bibenzyl Biosynthesis in Dendrobium officinale. PLANTS 2021; 10:plants10040633. [PMID: 33810588 PMCID: PMC8065740 DOI: 10.3390/plants10040633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
The Dendrobium plants (members of the Orchidaceae family) are used as traditional Chinese medicinal herbs. Bibenzyl, one of the active compounds in Dendrobium officinale, occurs in low amounts among different tissues. However, market demands require a higher content of thes compounds to meet the threshold for drug production. There is, therefore, an immediate need to dissect the physiological and molecular mechanisms underlying how bibenzyl compounds are biosynthesized in D. officinale tissues. In this study, the accumulation of erianin and gigantol in tissues were studied as representative compounds of bibenzyl. Exogenous application of Methyl-Jasmonate (MeJA) promotes the biosynthesis of bibenzyl compounds; therefore, transcriptomic analyses were conducted between D. officinale-treated root tissues and a control. Our results show that the root tissues contained the highest content of bibenzyl (erianin and gigantol). We identified 1342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes in our transcriptome dataset. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. We also identified two candidate cytochrome P450 genes and nine other enzymatic genes functionally involved in bibenzyl biosynthesis. Our study provides insights on the identification of critical genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, paving the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as guide genetic engineering for the improvement of Dendrobium varieties through increasing bibenzyl content for drug production and industrialization.
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Andargie M, Vinas M, Rathgeb A, Möller E, Karlovsky P. Lignans of Sesame ( Sesamum indicum L.): A Comprehensive Review. Molecules 2021; 26:883. [PMID: 33562414 PMCID: PMC7914952 DOI: 10.3390/molecules26040883] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Major lignans of sesame sesamin and sesamolin are benzodioxol--substituted furofurans. Sesamol, sesaminol, its epimers, and episesamin are transformation products found in processed products. Synthetic routes to all lignans are known but only sesamol is synthesized industrially. Biosynthesis of furofuran lignans begins with the dimerization of coniferyl alcohol, followed by the formation of dioxoles, oxidation, and glycosylation. Most genes of the lignan pathway in sesame have been identified but the inheritance of lignan content is poorly understood. Health-promoting properties make lignans attractive components of functional food. Lignans enhance the efficiency of insecticides and possess antifeedant activity, but their biological function in plants remains hypothetical. In this work, extensive literature including historical texts is reviewed, controversial issues are critically examined, and errors perpetuated in literature are corrected. The following aspects are covered: chemical properties and transformations of lignans; analysis, purification, and total synthesis; occurrence in Seseamum indicum and related plants; biosynthesis and genetics; biological activities; health-promoting properties; and biological functions. Finally, the improvement of lignan content in sesame seeds by breeding and biotechnology and the potential of hairy roots for manufacturing lignans in vitro are outlined.
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Affiliation(s)
- Mebeaselassie Andargie
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| | - Maria Vinas
- Centro para Investigaciones en Granos y Semillas (CIGRAS), University of Costa Rica, 2060 San Jose, Costa Rica;
| | - Anna Rathgeb
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| | - Evelyn Möller
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
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21
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Dar MS, Dholakia BB, Kulkarni AP, Oak PS, Shanmugam D, Gupta VS, Giri AP. Influence of domestication on specialized metabolic pathways in fruit crops. PLANTA 2021; 253:61. [PMID: 33538903 DOI: 10.1007/s00425-020-03554-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/23/2020] [Indexed: 05/08/2023]
Abstract
During the process of plant domestication, the selection and traditional breeding for desired characters such as flavor, juiciness and nutritional value of fruits, probably have resulted in gain or loss of specialized metabolites contributing to these traits. Their appearance in fruits is likely due to the acquisition of novel and specialized metabolic pathways and their regulation, driven by systematic molecular evolutionary events facilitated by traditional breeding. Plants change their armory of specialized metabolism to adapt and survive in diverse ecosystems. This may occur through molecular evolutionary events, such as single nucleotide polymorphism, gene duplication and transposition, leading to convergent or divergent evolution of biosynthetic pathways producing such specialized metabolites. Breeding and selection for improved specific and desired traits (fruit size, color, taste, flavor, etc.) in fruit crops through conventional breeding approaches may further alter content and profile of specialized metabolites. Biosynthetic routes of these metabolites have been studied in various plants. Here, we explore the influence of plant domestication and breeding processes on the selection of biosynthetic pathways of favorable specialized metabolites in fruit crops. An orderly clustered arrangement of genes associated with their production is observed in many fruit crops. We further analyzed selection-based acquisition of specialized metabolic pathways comparing first the metabolic profiles and genes involved in their biosynthesis, followed by the genomic organization of such genes between wild and domesticated horticultural crops. Domestication of crop plants favored the acquisition and retention of metabolic pathways that enhanced the fruit value while eliminated those which produced toxic or unfavorable metabolites. Interestingly, unintentional reorganization of complex metabolic pathways by selection and traditional breeding processes has endowed us with flavorful, juicy and nutritionally rich fruits.
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Affiliation(s)
- M Saleem Dar
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Bhushan B Dholakia
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
| | - Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS, 411007, India
| | - Pranjali S Oak
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Dhanasekaran Shanmugam
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India.
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22
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Jacoby RP, Koprivova A, Kopriva S. Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:57-69. [PMID: 32995888 PMCID: PMC7816845 DOI: 10.1093/jxb/eraa424] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/10/2020] [Indexed: 05/02/2023]
Abstract
One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.
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Affiliation(s)
- Richard P Jacoby
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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23
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Delli-Ponti R, Shivhare D, Mutwil M. Using Gene Expression to Study Specialized Metabolism-A Practical Guide. FRONTIERS IN PLANT SCIENCE 2021; 11:625035. [PMID: 33510763 PMCID: PMC7835209 DOI: 10.3389/fpls.2020.625035] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/30/2020] [Indexed: 05/25/2023]
Abstract
Plants produce a vast array of chemical compounds that we use as medicines and flavors, but these compounds' biosynthetic pathways are still poorly understood. This paucity precludes us from modifying, improving, and mass-producing these specialized metabolites in suitable bioreactors. Many of the specialized metabolites are expressed in a narrow range of organs, tissues, and cell types, suggesting a tight regulation of the responsible biosynthetic pathways. Fortunately, with unprecedented ease of generating gene expression data and with >200,000 publicly available RNA sequencing samples, we are now able to study the expression of genes from hundreds of plant species. This review demonstrates how gene expression can elucidate the biosynthetic pathways by mining organ-specific genes, gene expression clusters, and applying various types of co-expression analyses. To empower biologists to perform these analyses, we showcase these analyses using recently published, user-friendly tools. Finally, we analyze the performance of co-expression networks and show that they are a valuable addition to elucidating multiple the biosynthetic pathways of specialized metabolism.
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Affiliation(s)
| | | | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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24
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Zhao DK, Zhao Y, Chen SY, Kennelly EJ. Solanum steroidal glycoalkaloids: structural diversity, biological activities, and biosynthesis. Nat Prod Rep 2021; 38:1423-1444. [DOI: 10.1039/d1np00001b] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical structures of typical Solanum steroidal glycoalkaloids from eggplant, tomato, and potato.
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Affiliation(s)
- Da-Ke Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environment, Yunnan University, Kunming, 650504, P. R. China
| | - Yi Zhao
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, 10468, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, 10016, USA
| | - Sui-Yun Chen
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environment, Yunnan University, Kunming, 650504, P. R. China
| | - Edward J. Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, 10468, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, 10016, USA
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25
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Yi S, Song X, Yu W, Zhang R, Wang W, Zhao Y, Han B, Gai Y. De novo assembly and Transcriptome Analysis of the Momordica charantia Seedlings Responding to methyl jasmonate using 454 pyrosequencing. Gene Expr Patterns 2020; 40:119160. [PMID: 33253895 DOI: 10.1016/j.gep.2020.119160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
Momordica charantia, a medicinal and edible species of the Cucurbitaceae family, has been widely used as a vegetable around the world. Hundreds of pharmacological compounds isolated from the M. charantia have been reported. However, the mechanism of action of the secondary metabolites has not been fully elucidated. In this study, 118,590 unigenes were gained by de novo assembly based on the raw data from high-throughput sequencing of mRNA (RNA-Sequencing) upon systemic analysis, among which, 51,860 (43.73%) could be annotated to the public sequence databases such as Nr, GO, Swiss-Prot, KEGG and KOG. The transcriptomic changes of M. charantia seedlings treated with or without methyl jasmonate (MeJA) were analyzed to identify key genes involved in MeJA treatment. Additionally, 554 differentially expressed genes (DEGs), including 328 up-regulated ones and 226 down-regulated genes, have been identified. Most DEGs were associated with secondary metabolism and stress responses. Meanwhile, six DEGs were further confirmed by quantitative real-time RT-PCR (qRT-PCR) analysis, resulting in similar expression patterns as compared to those of RNA-Sequencing. Nine significantly enriched pathways including 11 DEGs were identified to be possibly involved in the MeJA-responsive biosynthesis of secondary metabolites based on the transcriptome sequencing analysis. Among them, 4 DEGs, encoding two peroxidases, one cinnamyl alcohol dehydrogenase and one hypothetical protein Csa, might play important roles in the process of phenylpropanoid biosynthesis. In addition, 9 transcription factors (TFs) were also detected as DEGs from 1899 unigenes. Most of them up-regulated by MeJA treatment might be potentially involved in regulating secondary metabolites biosynthesis. This work is the first research on the large-scale assessment of M. charantia transcriptomic resources and the analysis of DEGs and TFs in secondary metabolites biosynthesis of M. charantia seedings treated with or without MeJA, which will be conducive to the further applications of M. charantia.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, Anhui, PR China; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an 237012, Anhui, PR China.
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, Anhui, PR China; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an 237012, Anhui, PR China.
| | - Wangyang Yu
- Anhui Qiansouyan Biotechnology Co., Ltd, Lu'an 237200, Anhui, PR China.
| | - Rongfei Zhang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, PR China.
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, Anhui, PR China; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an 237012, Anhui, PR China.
| | - Yucheng Zhao
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, PR China.
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, Anhui, PR China; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an 237012, Anhui, PR China.
| | - Yanan Gai
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, PR China.
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26
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Elekhnawy E, Sonbol F, Abdelaziz A, Elbanna T. Potential impact of biocide adaptation on selection of antibiotic resistance in bacterial isolates. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020. [DOI: 10.1186/s43094-020-00119-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
Antibiotic resistance in pathogenic bacterial isolates has increased worldwide leading to treatment failures.
Main body
Many concerns are being raised about the usage of biocidal products (including disinfectants, antiseptics, and preservatives) as a vital factor that contributes to the risk of development of antimicrobial resistance which has many environmental and economic impacts.
Conclusion
Consequently, it is important to recognize the different types of currently used biocides, their mechanisms of action, and their potential impact to develop cross-resistance and co-resistance to various antibiotics. The use of biocides in medical or industrial purposes should be monitored and regulated. In addition, new agents with biocidal activity should be investigated from new sources like phytochemicals in order to decrease the emergence of resistance among bacterial isolates.
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27
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Guo Y, Zhang T, Zhong J, Ba T, Xu T, Zhang Q, Sun M. Identification of the Volatile Compounds and Observation of the Glandular Trichomes in Opisthopappus taihangensis and Four Species of Chrysanthemum. PLANTS 2020; 9:plants9070855. [PMID: 32640748 PMCID: PMC7412243 DOI: 10.3390/plants9070855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 11/23/2022]
Abstract
Opisthopappus taihangensis (Ling) Shih, a wild relative germplasm of chrysanthemum, releases a completely different fragrance from chrysanthemum species. We aimed to identify the volatile compounds of the leaves of O. taihangensis and four other Chrysanthemum species using headspace solid-phase micro-extraction combined with gas chromatography-mass spectrometry (HS-SPME-GC/MS). In total, 70 compounds were detected, and terpenoids accounted for the largest percentage in these five species. Many specific compounds were only emitted from O. taihangensis and not from the other four species. In particular, 1,8-cineole could be responsible for the special leaf fragrance of O. taihangensis as it accounted for the largest proportion of the compounds in O. taihangensis but a small or no proportion at all in other species. The glandular trichomes (GTs) in the leaves are the main organs responsible for the emission of volatiles. To explore the relationship between the emissions and the density of the GTs on the leaf epidermis, the shape and density of the GTs were observed and calculated, respectively. The results showed that the trichomes have two shapes in these leaves: T-shaped non-glandular trichomes and capitate trichomes. Histochemical staining analyses indicated that terpenoids are mainly emitted from capitate glandular trichomes. Correlation analysis showed that the volatile amount of terpenoids is highly related to the density of capitate trichomes. In O. taihangensis, the terpenoids content and density of capitate trichomes are the highest. We identified the diversity of leaf volatiles from O. taihangensis and four other Chrysanthemum species and found a possible relationship between the content of volatile compounds and the density of capitate trichomes, which explained the cause of the fragrance of O. taihangensis leaves.
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Affiliation(s)
- Yanhong Guo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
| | - Tengxun Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
| | - Jian Zhong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
| | - Tingting Ba
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
| | - Ting Xu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Ming Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.G.); (T.Z.); (J.Z.); (T.B.); (T.X.); (Q.Z.)
- Correspondence:
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28
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Fernie AR, Wen W. Editorial overview: Evolution of metabolic diversity. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:A1-A4. [PMID: 32546303 DOI: 10.1016/j.pbi.2020.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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29
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Mutwil M. Computational approaches to unravel the pathways and evolution of specialized metabolism. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:38-46. [PMID: 32200228 DOI: 10.1016/j.pbi.2020.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/19/2020] [Accepted: 01/31/2020] [Indexed: 05/13/2023]
Abstract
Specialized metabolites serve as a chemical arsenal that protects plants from abiotic stress, pathogens, and herbivores, and they are an essential component of our nutrition and medicine. Despite their importance, we are still at the beginning of unravelling biosynthetic pathways that produce these compounds, which is needed to produce more resilient and nutritious crops, expand our inventory of useful biomolecules, and give valuable insights into plant evolution. This review focuses on the evolution of specialized metabolism in the plant kingdom and the state-of-the-art approaches used to identify the biosynthetic pathways of these useful compounds.
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Affiliation(s)
- Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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30
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Schuurink R, Tissier A. Glandular trichomes: micro-organs with model status? THE NEW PHYTOLOGIST 2020; 225:2251-2266. [PMID: 31651036 DOI: 10.1111/nph.16283] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/01/2019] [Indexed: 05/19/2023]
Abstract
Glandular trichomes are epidermal outgrowths that are the site of biosynthesis and storage of large quantities of specialized metabolites. Besides their role in the protection of plants against biotic and abiotic stresses, they have attracted interest owing to the importance of the compounds they produce for human use; for example, as pharmaceuticals, flavor and fragrance ingredients, or pesticides. Here, we review what novel concepts investigations on glandular trichomes have brought to the field of specialized metabolism, particularly with respect to chemical and enzymatic diversity. Furthermore, the next challenges in the field are understanding the metabolic network underlying the high productivity of glandular trichomes and the transport and storage of metabolites. Another emerging area is the development of glandular trichomes. Studies in some model species, essentially tomato, tobacco, and Artemisia, are now providing the first molecular clues, but many open questions remain: How is the distribution and density of different trichome types on the leaf surface controlled? When is the decision for an epidermal cell to differentiate into one type of trichome or another taken? Recent advances in gene editing make it now possible to address these questions and promise exciting discoveries in the near future.
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Affiliation(s)
- Robert Schuurink
- Swammerdam Institute for Life Sciences, Green Life Science Research Cluster, University of Amsterdam, Postbus 1210, 1000 BE, Amsterdam, the Netherlands
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
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31
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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32
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Cui J, Yang Y, Luo S, Wang L, Huang R, Wen Q, Han X, Miao N, Cheng J, Liu Z, Zhang C, Feng C, Zhu H, Su J, Wan X, Hu F, Niu Y, Zheng X, Yang Y, Shan D, Dong Z, He W, Dhillon NPS, Hu K. Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd ( Momordica spp.). HORTICULTURE RESEARCH 2020; 7:85. [PMID: 32528697 PMCID: PMC7261802 DOI: 10.1038/s41438-020-0305-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 05/06/2023]
Abstract
Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.
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Affiliation(s)
- Junjie Cui
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
| | - Yan Yang
- Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China
| | - Shaobo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Le Wang
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Rukui Huang
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China
| | - Qingfang Wen
- Crop Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, China
| | - Xiaoxia Han
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, 410125 Changsha, China
| | - Nansheng Miao
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200 Nanchang, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
| | - Ziji Liu
- Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China
| | - Changyuan Zhang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Chengcheng Feng
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, China
| | - Haisheng Zhu
- Crop Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, China
| | - Jianwen Su
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, 410125 Changsha, China
| | - Xinjian Wan
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200 Nanchang, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
| | - Yu Niu
- Tropical Crop Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, 571737 Danzhou, China
| | - Xiaoming Zheng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | | | - Weiming He
- BGI Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Narinder P. S. Dhillon
- World Vegetable Center, East and Southeast Asia, Research and Training Station, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, 510642 Guangzhou, China
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Shirai K, Hanada K. Contribution of Functional Divergence Through Copy Number Variations to the Inter-Species and Intra-Species Diversity in Specialized Metabolites. FRONTIERS IN PLANT SCIENCE 2019; 10:1567. [PMID: 31850041 PMCID: PMC6902010 DOI: 10.3389/fpls.2019.01567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
There is considerable diversity in the specialized metabolites within a single plant species (intra-species) and among different plant species (inter-species). The functional divergence associated with gene duplications largely contributes to the inter-species diversity in the specialized metabolites, whereas the intra-species diversity is due to gene dosage changes via gene duplications [i.e., copy number variants (CNVs)] at the intra-species level of evolution. This is because CNVs are thought to undergo associated with less functional divergence at the intra-species level of evolution. However, functional divergence caused by CNVs may induce specialized metabolite diversity at the intra-species and inter-species levels of evolution. We herein discuss the functional divergence of CNVs in metabolic quantitative trait genes (mQTGs). We focused on 5,654 previously identified mQTGs in 270 Arabidopsis thaliana accessions. The ratio of nonsynonymous to synonymous variations tends to be higher for mQTGs with CNVs than for mQTGs without CNVs within A. thaliana accessions, suggesting that CNVs are responsible for the functional divergence among mQTGs at the intra-species level of evolution. To evaluate the contribution of CNVs to inter-species diversity, we calculated the ratio of nonsynonymous to synonymous substitutions in the Arabidopsis lineage. The ratio tends to be higher for the mQTGs with CNVs than for the mQTGs without CNVs. Additionally, we determined that mQTGs with CNVs are subject to positive selection in the Arabidopsis lineage. Our data suggest that CNVs are closely related to functional divergence contributing to adaptations via the production of diverse specialized metabolites at the intra-species and inter-species levels of evolution.
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Marshall-Colón A, Kliebenstein DJ. Plant Networks as Traits and Hypotheses: Moving Beyond Description. TRENDS IN PLANT SCIENCE 2019; 24:840-852. [PMID: 31300195 DOI: 10.1016/j.tplants.2019.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Biology relies on the central thesis that the genes in an organism encode molecular mechanisms that combine with stimuli and raw materials from the environment to create a final phenotypic expression representative of the genomic programming. While conceptually simple, the genotype-to-phenotype linkage in a eukaryotic organism relies on the interactions of thousands of genes and an environment with a potentially unknowable level of complexity. Modern biology has moved to the use of networks in systems biology to try to simplify this complexity to decode how an organism's genome works. Previously, biological networks were basic ways to organize, simplify, and analyze data. However, recent advances are allowing networks to move beyond description and become phenotypes or hypotheses in their own right. This review discusses these efforts, like mapping responses across biological scales, including relationships among cellular entities, and the direct use of networks as traits or hypotheses.
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Affiliation(s)
- Amy Marshall-Colón
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA; DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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35
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Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 2019; 16:731-744. [PMID: 30194403 DOI: 10.1038/s41579-018-0075-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.,Gladstone Institutes, San Francisco, CA, USA
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36
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Wang P, Niu B. Plant specialized metabolites modulate root microbiomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1111-1113. [PMID: 31290099 DOI: 10.1007/s11427-019-9579-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/12/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Pengchao Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China. .,College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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37
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Zlatić N, Jakovljević D, Stanković M. Temporal, Plant Part, and Interpopulation Variability of Secondary Metabolites and Antioxidant Activity of Inula helenium L. PLANTS 2019; 8:plants8060179. [PMID: 31213017 PMCID: PMC6630240 DOI: 10.3390/plants8060179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 11/14/2022]
Abstract
Variations in abiotic environmental factors have significant effects on quantity and quality of secondary metabolites, which is particularly important for plant species that possess biologically active compounds. The purpose of this study is determination of the total phenolic content, flavonoid concentration, and antioxidant activity of the different parts of Inula helenium L. (Asteraceae) sampled from different populations and in different time periods. The amounts obtained for the total phenolics varied from 16.73 to 89.85 mg of gallic acid (GA)/g. The concentration of flavonoids ranged from 9.32 to 376.22 mg of rutin (Ru)/g. The IC50 values of antioxidant activity determined using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical method varied from 161.60 to 1563.02 μg/ml. The inflorescence and roots possessed high concentration of phenolic compounds and significant antioxidant activity, while leaves contained the highest concentration of flavonoids. Additionally, the quantity of the phenolics, as well as antioxidant activity, significantly varied among the different populations due to different impacts of environmental factors. This research showed that I. helenium represents an abundant source of bioactive substances, and that the quantity of these compounds greatly differs among the different populations as well as in the same populations regarding the different time periods as well as plant parts.
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Affiliation(s)
- Nenad Zlatić
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Republic of Serbia.
| | - Dragana Jakovljević
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Republic of Serbia.
| | - Milan Stanković
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Republic of Serbia.
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38
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Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota. SCIENCE CHINA-LIFE SCIENCES 2019; 62:947-958. [PMID: 31079337 DOI: 10.1007/s11427-019-9521-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/25/2019] [Indexed: 01/04/2023]
Abstract
Land plants co-speciate with a diversity of continually expanding plant specialized metabolites (PSMs) and root microbial communities (microbiota). Homeostatic interactions between plants and root microbiota are essential for plant survival in natural environments. A growing appreciation of microbiota for plant health is fuelling rapid advances in genetic mechanisms of controlling microbiota by host plants. PSMs have long been proposed to mediate plant and single microbe interactions. However, the effects of PSMs, especially those evolutionarily new PSMs, on root microbiota at community level remain to be elucidated. Here, we discovered sesterterpenes in Arabidopsis thaliana, produced by recently duplicated prenyltransferase-terpene synthase (PT-TPS) gene clusters, with neo-functionalization. A single-residue substitution played a critical role in the acquisition of sesterterpene synthase (sesterTPS) activity in Brassicaceae plants. Moreover, we found that the absence of two root-specific sesterterpenoids, with similar chemical structure, significantly affected root microbiota assembly in similar patterns. Our results not only demonstrate the sensitivity of plant microbiota to PSMs but also establish a complete framework of host plants to control root microbiota composition through evolutionarily dynamic PSMs.
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39
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Henz Ryen A, Backlund A. Charting Angiosperm Chemistry: Evolutionary Perspective on Specialized Metabolites Reflected in Chemical Property Space. JOURNAL OF NATURAL PRODUCTS 2019; 82:798-812. [PMID: 30912945 DOI: 10.1021/acs.jnatprod.8b00767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plants possess an outstanding chemical diversity of specialized metabolites developed to adapt to environmental niches and increase fitness. The observed diversity is hypothesized to result from various evolutionary mechanisms, such as the continuous branching off and extension of existing biosynthetic pathways or enhanced levels of catalytic promiscuity in certain enzymes. In this study, ChemGPS-NP has been employed to chart the distribution and diversity of physicochemical properties for selected types of specialized metabolites from the angiosperms. Utilizing these charts, it is analyzed how different properties of various types of specialized metabolites change in different plant groups, and the chemical diversity from the volume they occupy in chemical property space is evaluated. In this context, possible underlying evolutionary mechanisms are discussed, which could explain the observed distribution and behavior in chemical property space. Based on these studies, it is demonstrated that evolutionary processes in plant specialized metabolism and the resultant metabolic diversification are reflected in chemical property space.
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Affiliation(s)
- Astrid Henz Ryen
- Research Group for Pharmacognosy, Department of Medicinal Chemistry , Uppsala University , BMC, Box 574, S-75123 Uppsala , Sweden
| | - Anders Backlund
- Research Group for Pharmacognosy, Department of Medicinal Chemistry , Uppsala University , BMC, Box 574, S-75123 Uppsala , Sweden
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40
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Shirai K, Matsuda F, Nakabayashi R, Okamoto M, Tanaka M, Fujimoto A, Shimizu M, Shinozaki K, Seki M, Saito K, Hanada K. A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions. Mol Biol Evol 2018; 34:3111-3122. [PMID: 28961930 DOI: 10.1093/molbev/msx234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs. We obtained 1,335 specialized metabolite signals from 53 worldwide A. thaliana accessions using liquid chromatography-quadrupole time-of-flight mass spectrometry. In this study, genes associated with specialized metabolites were inferred by either a generally authorized genome-wide association study (GWAS) approach or a novel analysis of the association between gene expression and metabolite accumulation. Genes qualified by both analyses are defined to be mQTGs. The integrated method enabled us to detect mQTGs with a low false positive rate (=5.71 × 10-4). We also identified 5,654 genes associated with 1,335 specialized metabolites. Of these genes, 4.4% were affected by CNVs, which was more than expected (χ2 test: P < 0.01). This result suggests that CNVs contribute to variations in specialized metabolites within a species. To assess the contribution of CNVs to adaptive evolution in A. thaliana, we examined the selective sweeps around the mQTGs. We observed that the mQTGs with CNVs tended to undergo selective sweeps. These observations imply that variations in specialized metabolites caused by CNVs contribute to the adaptive evolution of A. thaliana.
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Affiliation(s)
- Kazumasa Shirai
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan
| | - Fumio Matsuda
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Ryo Nakabayashi
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Masanori Okamoto
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Minami Shimizu
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuo Shinozaki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuki Saito
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kousuke Hanada
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan.,Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
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41
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Wang X, Chen Q, Wu Y, Lemmon ZH, Xu G, Huang C, Liang Y, Xu D, Li D, Doebley JF, Tian F. Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population. MOLECULAR PLANT 2018; 11:443-459. [PMID: 29275164 DOI: 10.1016/j.molp.2017.12.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 10/21/2017] [Accepted: 12/11/2017] [Indexed: 05/18/2023]
Abstract
Gene expression regulation plays an important role in controlling plant phenotypes and adaptation. Here, we report a comprehensive assessment of gene expression variation through the transcriptome analyses of a large maize-teosinte experimental population. Genome-wide mapping identified 25 660 expression quantitative trait loci (eQTL) for 17 311 genes, capturing an unprecedented range of expression variation. We found that local eQTL were more frequently mapped to adjacent genes, displaying a mode of expression piggybacking, which consequently created co-regulated gene clusters. Genes within the co-regulated gene clusters tend to have relevant functions and shared chromatin modifications. Distant eQTL formed 125 significant distant eQTL hotspots with their targets significantly enriched in specific functional categories. By integrating different sources of information, we identified putative trans- regulators for a variety of metabolic pathways. We demonstrated that the bHLH transcription factor R1 and hexokinase HEX9 might act as crucial regulators for flavonoid biosynthesis and glycolysis, respectively. Moreover, we showed that domestication or improvement has significantly affected global gene expression, with many genes targeted by selection. Of particular interest, the Bx genes for benzoxazinoid biosynthesis may have undergone coordinated cis-regulatory divergence between maize and teosinte, and a transposon insertion that inactivates Bx12 was under strong selection as maize spread into temperate environments with a distinct herbivore community.
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Affiliation(s)
- Xufeng Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qiuyue Chen
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yaoyao Wu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zachary H Lemmon
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Guanghui Xu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Cheng Huang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yameng Liang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dingyi Xu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dan Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Feng Tian
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China.
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42
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Rahikainen M, Alegre S, Trotta A, Pascual J, Kangasjärvi S. Trans-methylation reactions in plants: focus on the activated methyl cycle. PHYSIOLOGIA PLANTARUM 2018; 162:162-176. [PMID: 28815615 DOI: 10.1111/ppl.12619] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/02/2017] [Accepted: 08/10/2017] [Indexed: 05/11/2023]
Abstract
Trans-methylation reactions are vital in basic metabolism, epigenetic regulation, RNA metabolism, and posttranslational control of protein function and therefore fundamental in determining the physiological processes in all living organisms. The plant kingdom is additionally characterized by the production of secondary metabolites that undergo specific hydroxylation, oxidation and methylation reactions to obtain a wide array of different chemical structures. Increasing research efforts have started to reveal the enzymatic pathways underlying the biosynthesis of complex metabolites in plants. Further engineering of these enzymatic machineries offers significant possibilities in the development of bio-based technologies, but necessitates deep understanding of their potential metabolic and regulatory interactions. Trans-methylation reactions are tightly coupled with the so-called activated methyl cycle (AMC), an essential metabolic circuit that maintains the trans-methylation capacity in all living cells. Tight regulation of the AMC is crucial in ensuring accurate trans-methylation reactions in different subcellular compartments, cell types, developmental stages and environmental conditions. This review addresses the organization and posttranslational regulation of the AMC and elaborates its critical role in determining metabolic regulation through modulation of methyl utilization in stress-exposed plants.
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Affiliation(s)
- Moona Rahikainen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Sara Alegre
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Andrea Trotta
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
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43
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Krieger C, Roselli S, Kellner-Thielmann S, Galati G, Schneider B, Grosjean J, Olry A, Ritchie D, Matern U, Bourgaud F, Hehn A. The CYP71AZ P450 Subfamily: A Driving Factor for the Diversification of Coumarin Biosynthesis in Apiaceous Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:820. [PMID: 29971079 PMCID: PMC6018538 DOI: 10.3389/fpls.2018.00820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/28/2018] [Indexed: 05/19/2023]
Abstract
The production of coumarins and furanocoumarins (FCs) in higher plants is widely considered a model illustration of the adaptation of plants to their environment. In this report, we show that the multiplication of cytochrome P450 variants within the CYP71AZ subfamily has contributed to the diversification of these molecules. Multiple copies of genes encoding this enzyme family are found in Apiaceae, and their phylogenetic analysis suggests that they have different functions within these plants. CYP71AZ1 from Ammi majus and CYP71AZ3, 4, and 6 from Pastinaca sativa were functionally characterized. While CYP71AZ3 merely hydroxylated esculetin, the other enzymes accepted both simple coumarins and FCs. Superimposing in silico models of these enzymes led to the identification of different conformations of three regions in the enzyme active site. These sequences were subsequently utilized to mutate CYP71AZ4 to resemble CYP71AZ3. The swapping of these regions lead to significantly modified substrate specificity. Simultaneous mutations of all three regions shifted the specificity of CYP71AZ4 to that of CYP71AZ3, exclusively accepting esculetin. This approach may explain the evolution of this cytochrome P450 family regarding the appearance of FCs in parsnip and possibly in the Apiaceae.
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Affiliation(s)
- Célia Krieger
- Laboratoire Agronomie et Environnement, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
| | - Sandro Roselli
- Laboratoire Agronomie et Environnement, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
| | - Sandra Kellner-Thielmann
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Marburg, Germany
| | - Gianni Galati
- Laboratoire Agronomie et Environnement, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
| | | | - Jérémy Grosjean
- Laboratoire Agronomie et Environnement, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
| | - Alexandre Olry
- Laboratoire Agronomie et Environnement, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
| | - David Ritchie
- INRIA Nancy, Grand-Est Research Centre, Laboratoire Lorrain De Recherche En Informatique Et Ses Applications, Nancy, France
| | - Ulrich Matern
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Alain Hehn
- Laboratoire Agronomie et Environnement, Institut National de la Recherche Agronomique, Université de Lorraine, Nancy, France
- *Correspondence: Alain Hehn,
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44
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Zlatić NM, Stanković MS. Variability of Secondary Metabolites of the Species Cichorium intybus L. from Different Habitats. PLANTS 2017; 6:plants6030038. [PMID: 28891986 PMCID: PMC5620594 DOI: 10.3390/plants6030038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 01/03/2023]
Abstract
The principal aim of this paper is to show the influence of soil characteristics on the quantitative variability of secondary metabolites. Analysis of phenolic content, flavonoid concentrations, and the antioxidant activity was performed using the ethanol and ethyl acetate plant extracts of the species Cichorium intybus L. (Asteraceae). The samples were collected from one saline habitat and two non-saline habitats. The values of phenolic content from the samples taken from the saline habitat ranged from 119.83 to 120.83 mg GA/g and from non-saline habitats from 92.44 to 115.10 mg GA/g. The amount of flavonoids in the samples from the saline locality varied between 144.36 and 317.62 mg Ru/g and from non-saline localities between 86.03 and 273.07 mg Ru/g. The IC50 values of antioxidant activity in the samples from the saline habitat ranged from 87.64 to 117.73 μg/mL and from 101.44 to 125.76 μg/mL in the samples from non-saline habitats. The results confirmed that soil types represent a significant influence on the quantitative content of secondary metabolites. The greatest concentrations of phenols and flavonoids and the highest level of antioxidant activity were found in the samples from saline soil. This further corroborates the importance of saline soil as an ecological factor, as it is proven to give rise to increased biosynthesis of secondary metabolites and related antioxidant activity.
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Affiliation(s)
- Nenad M Zlatić
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia.
| | - Milan S Stanković
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia.
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Abstract
Plant metabolic studies have traditionally focused on the role and regulation of the enzymes catalyzing key reactions within specific pathways. Within the past 20 years, reverse genetic approaches have allowed direct determination of the effects of the deficiency, or surplus, of a given protein on the biochemistry of a plant. In parallel, top-down approaches have also been taken, which rely on screening broad, natural genetic diversity for metabolic diversity. Here, we compare and contrast the various strategies that have been adopted to enhance our understanding of the natural diversity of metabolism. We also detail how these approaches have enhanced our understanding of both specific and global aspects of the genetic regulation of metabolism. Finally, we discuss how such approaches are providing important insights into the evolution of plant secondary metabolism.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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46
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Roselli S, Olry A, Vautrin S, Coriton O, Ritchie D, Galati G, Navrot N, Krieger C, Vialart G, Bergès H, Bourgaud F, Hehn A. A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1119-1132. [PMID: 27943460 DOI: 10.1111/tpj.13450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 05/06/2023]
Abstract
Furanocoumarins are specialized metabolites that are involved in the defense of plants against phytophagous insects. The molecular and functional characterization of the genes involved in their biosynthetic pathway is only partially complete. Many recent reports have described gene clusters responsible for the biosynthesis of specialized metabolites in plants. To investigate possible co-localization of the genes involved in the furanocoumarin pathway, we sequenced parsnip BAC clones spanning two different gene loci. We found that two genes previously identified in this pathway, CYP71AJ3 and CYP71AJ4, were located on the same BAC, whereas a third gene, PsPT1, belonged to a different BAC clone. Chromosome mapping using fluorescence in situ hybridization (FISH) indicated that PsPT1 and the CYP71AJ3-CYP71AJ4 clusters are located on two different chromosomes. Sequencing the BAC clone harboring PsPT1 led to the identification of a gene encoding an Fe(II) α-ketoglutarate-dependent dioxygenase (PsDIOX) situated in the neighborhood of PsPT1 and confirmed the occurrence of a second gene cluster involved in the furanocoumarin pathway. This enzyme metabolizes p-coumaroyl CoA, leading exclusively to the synthesis of umbelliferone, an important intermediate compound in furanocoumarin synthesis. This work provides an insight into the genomic organization of genes from the furanocoumarin biosynthesis pathway organized in more than one gene cluster. It also confirms that the screening of a genomic library and the sequencing of BAC clones represent a valuable tool to identify genes involved in biosynthetic pathways dedicated to specialized metabolite synthesis.
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Affiliation(s)
- Sandro Roselli
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alexandre Olry
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales - INRA - 24 Chemin de Borde Rouge - Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
| | - Olivier Coriton
- Plate-Forme de Cytogénétique Moléculaire - UMR1349 IGEPP INRA - Agrocampus Ouest-Université de Rennes 1, 35653, Le Rheu, France
| | - Dave Ritchie
- INRIA Nancy Grand Est, 615 rue du Jardin Botanique, 54600, Villers-lès-Nancy, France
| | - Gianni Galati
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Nicolas Navrot
- Institut de biologie moléculaire des plantes - UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer - 67084, Strasbourg Cedex, France
| | - Célia Krieger
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Guilhem Vialart
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales - INRA - 24 Chemin de Borde Rouge - Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
| | - Frédéric Bourgaud
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alain Hehn
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
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47
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Nomura T. Function and application of a non-ester-hydrolyzing carboxylesterase discovered in tulip. Biosci Biotechnol Biochem 2017; 81:81-94. [DOI: 10.1080/09168451.2016.1240608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Plants have evolved secondary metabolite biosynthetic pathways of immense rich diversity. The genes encoding enzymes for secondary metabolite biosynthesis have evolved through gene duplication followed by neofunctionalization, thereby generating functional diversity. Emerging evidence demonstrates that some of those enzymes catalyze reactions entirely different from those usually catalyzed by other members of the same family; e.g. transacylation catalyzed by an enzyme similar to a hydrolytic enzyme. Tuliposide-converting enzyme (TCE), which we recently discovered from tulip, catalyzes the conversion of major defensive secondary metabolites, tuliposides, to antimicrobial tulipalins. The TCEs belong to the carboxylesterase family in the α/β-hydrolase fold superfamily, and specifically catalyze intramolecular transesterification, but not hydrolysis. This non-ester-hydrolyzing carboxylesterase is an example of an enzyme showing catalytic properties that are unpredictable from its primary structure. This review describes the biochemical and physiological aspects of tulipalin biogenesis, and the diverse functions of plant carboxylesterases in the α/β-hydrolase fold superfamily.
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Affiliation(s)
- Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
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48
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O’Neill EC, Kelly S. Engineering biosynthesis of high-value compounds in photosynthetic organisms. Crit Rev Biotechnol 2016; 37:779-802. [DOI: 10.1080/07388551.2016.1237467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK
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49
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An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci. Sci Rep 2016; 6:30143. [PMID: 27440503 PMCID: PMC4954952 DOI: 10.1038/srep30143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/29/2016] [Indexed: 11/26/2022] Open
Abstract
Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.
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50
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Munakata R, Olry A, Karamat F, Courdavault V, Sugiyama A, Date Y, Krieger C, Silie P, Foureau E, Papon N, Grosjean J, Yazaki K, Bourgaud F, Hehn A. Molecular evolution of parsnip (Pastinaca sativa) membrane-bound prenyltransferases for linear and/or angular furanocoumarin biosynthesis. THE NEW PHYTOLOGIST 2016; 211:332-44. [PMID: 26918393 DOI: 10.1111/nph.13899] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/13/2016] [Indexed: 05/06/2023]
Abstract
In Apiaceae, furanocoumarins (FCs) are plant defence compounds that are present as linear or angular isomers. Angular isomers appeared during plant evolution as a protective response to herbivores that are resistant to linear molecules. Isomeric biosynthesis occurs through prenylation at the C6 or C8 position of umbelliferone. Here, we report cloning and functional characterization of two different prenyltransferases, Pastinaca sativa prenyltransferase 1 and 2 (PsPT1 and PsPT2), that are involved in these crucial reactions. Both enzymes are targeted to plastids and synthesize osthenol and demethylsuberosin (DMS) using exclusively umbelliferone and dimethylallylpyrophosphate (DMAPP) as substrates. Enzymatic characterization using heterologously expressed proteins demonstrated that PsPT1 is specialized for the synthesis of the linear form, demethylsuberosin, whereas PsPT2 more efficiently catalyses the synthesis of its angular counterpart, osthenol. These results are the first example of a complementary prenyltransferase pair from a single plant species that is involved in synthesizing defensive compounds. This study also provides a better understanding of the molecular mechanisms governing the angular FC biosynthetic pathway in apiaceous plants, which involves two paralogous enzymes that share the same phylogenetic origin.
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Affiliation(s)
- Ryosuke Munakata
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Alexandre Olry
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
| | - Fazeelat Karamat
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
| | - Vincent Courdavault
- EA2106 'Biomolécules et Biotechnologies Végétales', Université François-Rabelais de Tours, Tours, France
| | - Akifumi Sugiyama
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yoshiaki Date
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Célia Krieger
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
| | - Prisca Silie
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
| | - Emilien Foureau
- EA2106 'Biomolécules et Biotechnologies Végétales', Université François-Rabelais de Tours, Tours, France
| | - Nicolas Papon
- EA2106 'Biomolécules et Biotechnologies Végétales', Université François-Rabelais de Tours, Tours, France
| | - Jérémy Grosjean
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
| | - Kazufumi Yazaki
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Frédéric Bourgaud
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
| | - Alain Hehn
- Laboratoire Agronomie et Environnement, INRA UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR 1121, 2 avenue de la forêt de Haye TSA 40602 54518, Vandœuvre-lès-Nancy, France
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