1
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Yin Q, Xiang L, Han X, Zhang Y, Lyn R, Yuan L, Chen S. The evolutionary advantage of artemisinin production by Artemisia annua. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00239-5. [PMID: 39362811 DOI: 10.1016/j.tplants.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/27/2024] [Accepted: 09/12/2024] [Indexed: 10/05/2024]
Abstract
Artemisinin, a potent antimalarial compound, is predominantly derived from Artemisia annua. The uniqueness of artemisinin production in A. annua lies in its complex biochemical pathways and genetic composition, distinguishing it from other plant species, even within the Asteraceae family. In this review, we investigate the potential of A. annua for artemisinin production, drawing evidence from natural populations and mutants. Leveraging high-quality whole-genome sequence analyses, we offer insights into the evolution of artemisinin biosynthesis. We also highlight current understanding of the protective functions of artemisinin in A. annua in response to both biotic and abiotic stresses. In addition, we explore the mechanisms used by A. annua to mitigate the phytotoxicity generated by artemisinin catabolism.
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Affiliation(s)
- Qinggang Yin
- Artemisinin Research Center, Institute of Chinese Materia Medica, State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China; Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA; The Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Li Xiang
- Artemisinin Research Center, Institute of Chinese Materia Medica, State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaoyan Han
- China National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yujun Zhang
- Artemisinin Research Center, Institute of Chinese Materia Medica, State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruiqing Lyn
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA; The Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA; The Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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2
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Xie C, An N, Zhou L, Shen X, Wang J, Yan Y, Sun X, Yuan Q. Establishing a coumarin production platform by protein and metabolic engineering. Metab Eng 2024; 86:89-98. [PMID: 39313108 DOI: 10.1016/j.ymben.2024.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 09/21/2024] [Indexed: 09/25/2024]
Abstract
Coumarins are a vast family of natural products with diverse biological activities. Cinnamyl-CoA ortho-hydroxylases (CCHs) catalyze the gateway and rate-limiting step in coumarin biosynthesis. However, engineering CCHs is challenging due to the large size of the substrates and the vague structure-activity relationship. Herein, directed evolution and structure-guided engineering were performed to engineer a CCH (AtF6'H from Arabidopsis thaliana) using a fluorescence-based screening method, yielding the transplantable surface mutations and the substrate-specific pocket mutations with improved activity. Structural analysis and molecular dynamics simulations elucidated the conformational changes that led to increased catalytic efficiency. Applying appropriate variants with the optimized upstream biosynthetic pathways improved the titers of three simple coumarins by 5 to 22-fold. Further introducing glycosylation modules resulted in the production of four coumarin glucosides, among which the titer of aesculin was increased by 15.7-fold and reached 3 g/L in scale-up fermentation. This work unleashed the potential of CCHs and established an Escherichia coli platform for coumarins production.
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Affiliation(s)
- Chong Xie
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China
| | - Ning An
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China
| | - Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, United States
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, No.15, Beisanhuan East Road, Beijing, 100029, China.
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3
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He S, Gao J, Li B, Luo Z, Liu P, Xu X, Wu M, Yang J, He X, Wang Z. NtWIN1 regulates the biosynthesis of scopoletin and chlorogenic acid by targeting NtF6'H1 and NtCCoAMT genes in Nicotiana tabacum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108937. [PMID: 39018774 DOI: 10.1016/j.plaphy.2024.108937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Scopoletin and chlorogenic acid (CGA) are important polyphenols that regulate plant growth, development, and stress resistance. The ERF transcription factor WAX INDUCER1 (WIN1) promotes the biosynthesis of cutin, suberine, and wax. However, its full roles in regulating the accumulation of plant secondary metabolites still remain to be further clarified. In this study, NtWIN1 gene encoding a SHINE-type AP2/ERF transcription factor of the Va subgroup was identified from N. tabacum. NtWIN1 showed high expression levels in tobacco stems, sepals, and pistils. Overexpression (OE) and knock-out of NtWIN1 showed that it promoted the accumulation of total polyphenols and altered their composition. Compare to that of WT plants, the CGA contents significantly increased by 25%-50% in the leaves, flowers, and capsules of OE lines, while the scopoletin contents in the OE plants significantly decreased by 30%-67%. In contrast, the CGA contents in ntwin1 lines reduced by 23%-26%, and the scopoletin contents in ntwin1 increased by 38%-75% compare to that of WT plants. Chromatin immunoprecipitation and Dual-Luc transcription activation assays showed that NtWIN1 could bind to the promoters of NtF6'H1 and NtCCoAMT, thereby modulating their expression. The scopoletin content in ntwin1/ntf6'h1 double mutant was significantly lower than that in ntwin1 and WT plants, but showed no significant differences with that in ntf6'h1 mutant, further indicating that the inhibition of NtWIN1 on scopoletin accumulation depends on the activity of NtF6'H1. Our study illustrates the new roles of NtWIN1, and provides a possible target for regulating the synthesis of polyphenols in tobacco.
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Affiliation(s)
- Shun He
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Junping Gao
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, 410007, China
| | - Bingyu Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zhaopeng Luo
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Xin Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Xinxi He
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, 410007, China.
| | - Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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4
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Seligmann B, Liu S, Franke J. Chemical tools for unpicking plant specialised metabolic pathways. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102554. [PMID: 38820646 DOI: 10.1016/j.pbi.2024.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]
Abstract
Elucidating the biochemical pathways of specialised metabolites in plants is key to enable or improve their sustainable biotechnological production. Chemical tools can greatly facilitate the discovery of biosynthetic genes and enzymes. Here, we summarise transdisciplinary approaches where methods from chemistry and chemical biology helped to overcome key challenges of pathway elucidation. Based on recent examples, we describe how state-of-the-art isotope labelling experiments can guide the selection of biosynthetic gene candidates, how affinity-based probes enable the identification of novel enzymes, how semisynthesis can improve the availability of elusive pathway intermediates, and how biomimetic reactions provide a better understanding of inherent chemical reactivity. We anticipate that a wider application of such chemical methods will accelerate the pace of pathway elucidation in plants.
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Affiliation(s)
- Benedikt Seligmann
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Shenyu Liu
- Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany
| | - Jakob Franke
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany; Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
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Manoilenko S, Dippe M, Fuchs T, Eisenschmidt-Bönn D, Ziegler J, Bauer AK, Wessjohann LA. Enzymatic one-step synthesis of natural 2-pyrones and new-to-nature derivatives from coenzyme A esters. J Biotechnol 2024; 388:72-82. [PMID: 38616039 DOI: 10.1016/j.jbiotec.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
The 2-pyrone moiety is present in a wide range of structurally diverse natural products with various biological activities. The plant biosynthetic routes towards these compounds mainly depend on the activity of either type III polyketide synthase-like 2-pyrone synthases or hydroxylating 2-oxoglutarate dependent dioxygenases. In the present study, the substrate specificity of these enzymes is investigated by a systematic screening using both natural and artificial substrates with the aims of efficiently forming (new) products and understanding the underlying catalytic mechanisms. In this framework, we focused on the in vitro functional characterization of a 2-pyrone synthase Gh2PS2 from Gerbera x hybrida and two dioxygenases AtF6'H1 and AtF6'H2 from Arabidopsis thaliana using a set of twenty aromatic and aliphatic CoA esters as substrates. UHPLC-ESI-HRMSn based analyses of reaction intermediates and products revealed a broad substrate specificity of the enzymes, enabling the facile "green" synthesis of this important class of natural products and derivatives in a one-step/one-pot reaction in aqueous environment without the need for halogenated or metal reagents and protective groups. Using protein modeling and substrate docking we identified amino acid residues that seem to be important for the observed product scope.
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Affiliation(s)
- Svitlana Manoilenko
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Martin Dippe
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany.
| | - Tristan Fuchs
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Daniela Eisenschmidt-Bönn
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Anne-Katrin Bauer
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle 06120, Germany.
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Liu H, Wang Y, Chang Q, Li Q, Fang J, Cao N, Tong X, Jiang X, Yu X, Cheng Y. Combined metabolome and transcriptome reveal HmF6'H1 regulating simple coumarin accumulation against powdery mildew infection in Heracleum moellendorffii Hance. BMC PLANT BIOLOGY 2024; 24:507. [PMID: 38844853 PMCID: PMC11155083 DOI: 10.1186/s12870-024-05185-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Powdery mildew, caused by Eeysiphe heraclei, seriously threatens Heracleum moellendorffii Hance. Plant secondary metabolites are essential to many activities and are necessary for defense against biotic stress. In order to clarify the functions of these metabolites in response to the pathogen, our work concentrated on the variations in the accumulation of secondary metabolites in H. moellendorffii during E. heraclei infection. RESULTS Following E. heraclei infection, a significant upregulation of coumarin metabolites-particularly simple coumarins and associated genes was detected by RNA-seq and UPLC-MS/MS association analysis. Identifying HmF6'H1, a Feruloyl CoA 6'-hydroxylase pivotal in the biosynthesis of the coumarin basic skeleton through ortho-hydroxylation, was a significant outcome. The cytoplasmic HmF6'H1 protein was shown to be able to catalyze the ortho-hydroxylation of p-coumaroyl-CoA and caffeoyl-CoA, resulting in the formation of umbelliferone and esculetin, respectively. Over-expression of the HmF6'H1 gene resulted in increased levels of simple coumarins, inhibiting the biosynthesis of furanocoumarins and pyranocoumarins by suppressing PT gene expression, enhancing H. moellendorffii resistance to powdery mildew. CONCLUSIONS These results established HmF6'H1 as a resistance gene aiding H. moellendorffii in combatting E. heraclei infection, offering additional evidence of feruloyl-CoA 6'-hydroxylase role in catalyzing various types of simple coumarins. Therefore, this work contributes to our understanding of the function of simple coumarins in plants' defense against powdery mildew infection.
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Affiliation(s)
- Hanbing Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Yiran Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - QinZheng Chang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Qiubi Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Jiahui Fang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Ning Cao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Xuejiao Tong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Xinmei Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Xihong Yu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Yao Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China.
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Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2024; 51:467-478. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
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Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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8
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Zeng J, Liu X, Dong Z, Zhang F, Qiu F, Zhong M, Zhao T, Yang C, Zeng L, Lan X, Zhang H, Zhou J, Chen M, Tang K, Liao Z. Discovering a mitochondrion-localized BAHD acyltransferase involved in calystegine biosynthesis and engineering the production of 3β-tigloyloxytropane. Nat Commun 2024; 15:3623. [PMID: 38684703 PMCID: PMC11058270 DOI: 10.1038/s41467-024-47968-0] [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: 11/16/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Solanaceous plants produce tropane alkaloids (TAs) via esterification of 3α- and 3β-tropanol. Although littorine synthase is revealed to be responsible for 3α-tropanol esterification that leads to hyoscyamine biosynthesis, the genes associated with 3β-tropanol esterification are unknown. Here, we report that a BAHD acyltransferase from Atropa belladonna, 3β-tigloyloxytropane synthase (TS), catalyzes 3β-tropanol and tigloyl-CoA to form 3β-tigloyloxytropane, the key intermediate in calystegine biosynthesis and a potential drug for treating neurodegenerative disease. Unlike other cytosolic-localized BAHD acyltransferases, TS is localized to mitochondria. The catalytic mechanism of TS is revealed through molecular docking and site-directed mutagenesis. Subsequently, 3β-tigloyloxytropane is synthesized in tobacco. A bacterial CoA ligase (PcICS) is found to synthesize tigloyl-CoA, an acyl donor for 3β-tigloyloxytropane biosynthesis. By expressing TS mutant and PcICS, engineered Escherichia coli synthesizes 3β-tigloyloxytropane from tiglic acid and 3β-tropanol. This study helps to characterize the enzymology and chemodiversity of TAs and provides an approach for producing 3β-tigloyloxytropane.
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Affiliation(s)
- Junlan Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaoqiang Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zhaoyue Dong
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Fangyuan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Fei Qiu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Mingyu Zhong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Tengfei Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chunxian Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lingjiang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Xizang Characteristic Agricultural and Animal Husbandry Resources, Xizang Agricultural and Animal Husbandry College, Nyingchi, 860000, China
| | - Hongbo Zhang
- Key Laboratory of Synthetic Biology of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Junhui Zhou
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Min Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Kexuan Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhihua Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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9
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Wang J, Chen P, Zhao T, Huang X, Zong J, Luo Q, Peng C, Wu X, Qiu F, Zhao D, Xiang L, Zhang Y, Yang C, Zhang F, Liao Z, Fu Y, Zeng J. Biosynthesis of Scopoletin in Sweet Potato Confers Resistance against Fusarium oxysporum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7749-7764. [PMID: 38537104 DOI: 10.1021/acs.jafc.3c09389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Fusarium wilt is a severe fungal disease caused by Fusarium oxysporum in sweet potato. We conducted transcriptome analysis to explore the resistance mechanism of sweet potato against F. oxysporum. Our findings highlighted the role of scopoletin, a hydroxycoumarin, in enhancing resistance. In vitro experiments confirmed that scopoletin and umbelliferone had inhibitory effects on the F. oxysporum growth. We identified hydroxycoumarin synthase genes IbF6'H2 and IbCOSY that are responsible for scopoletin production in sweet potatoes. The co-overexpression of IbF6'H2 and IbCOSY in tobacco plants produced the highest scopoletin levels and disease resistance. This study provides insights into the molecular basis of sweet potato defense against Fusarium wilt and identifies valuable genes for breeding wilt-resistant cultivars.
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Affiliation(s)
- Jing Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Peitao Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Tengfei Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xianhui Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jikai Zong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Qingqing Luo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Chao Peng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoyan Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fei Qiu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Dongchao Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Lien Xiang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Chunxian Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fangyuan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhihua Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yufan Fu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Junlan Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Engineering and Technology Research Center for Sweet potato of Chongqing, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
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10
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Paffrath V, Tandron Moya YA, Weber G, von Wirén N, Giehl RFH. A major role of coumarin-dependent ferric iron reduction in strategy I-type iron acquisition in Arabidopsis. THE PLANT CELL 2024; 36:642-664. [PMID: 38016103 PMCID: PMC10896297 DOI: 10.1093/plcell/koad279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/16/2023] [Indexed: 11/30/2023]
Abstract
Many non-graminaceous species release various coumarins in response to iron (Fe) deficiency. However, the physiological relevance of these coumarins remains poorly understood. Here, we show that the three enzymes leading to sideretin biosynthesis co-exist in Arabidopsis (Arabidopsis thaliana) epidermal and cortical cells and that the shift to fraxetin at alkaline pH depends on MYB72-mediated repression of CYTOCHROME P450, FAMILY 82, SUBFAMILY C, POLYPEPTIDE 4 (CYP82C4). In vitro, only fraxetin and sideretin can reduce part of the Fe(III) that they mobilize. We demonstrate that coumarin-mediated Fe(III) reduction is critical under acidic conditions, as fraxetin and sideretin can complement the Fe(III)-chelate reductase mutant ferric reduction oxidase 2 (fro2), and disruption of coumarin biosynthesis in fro2 plants impairs Fe acquisition similar to in the Fe(II) uptake-deficient mutant iron-regulated transporter 1 (irt1). Disruption of sideretin biosynthesis in a fro2 cyp82C4-1 double mutant revealed that sideretin is the dominant chemical reductant that functions with FRO2 to mediate Fe(II) formation for root uptake. At alkaline pH, Fe(III) reduction by coumarins becomes almost negligible but fraxetin still sustains high Fe(III) mobilization, suggesting that its main function is to provide chelated Fe(III) for FRO2. Our study indicates that strategy-I plants link sideretin and fraxetin biosynthesis and secretion to external pH to recruit distinct coumarin chemical activities to maximize Fe acquisition according to prevailing soil pH conditions.
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Affiliation(s)
- Vanessa Paffrath
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstr 3, 06466 Seeland, Germany
| | - Yudelsy A Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstr 3, 06466 Seeland, Germany
| | - Günther Weber
- Leibniz-Institut für Analytische Wissenschaften (ISAS) e.V., Bunsen-Kirchhoff-Str 11, 44139 Dortmund, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstr 3, 06466 Seeland, Germany
| | - Ricardo F H Giehl
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstr 3, 06466 Seeland, Germany
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11
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Liu BK, Xv BJ, Si CC, Shi WQ, Ding GZ, Tang LX, Xv M, Shi CY, Liu HJ. Effect of potassium fertilization on storage root number, yield, and appearance quality of sweet potato ( Ipomoea batatas L.). FRONTIERS IN PLANT SCIENCE 2024; 14:1298739. [PMID: 38455375 PMCID: PMC10917953 DOI: 10.3389/fpls.2023.1298739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024]
Abstract
Increasing storage root number is a pivotal approach to enhance both storage root (SR) yield and appearance quality of sweet potato. Here, 2-year field experiments were conducted to investigate the effect of 0 (K0), 120 (K1), 240 (K2), and 360 (K3) kg ha-1 potassium fertilizer (K2O) on lignin metabolism, root growth, storage root yield, and uniformity. The results demonstrated that potassium (K) application led to a decrease in the activities of key enzymes involved in lignin biosynthesis, including phenylalanine deaminase (PAL), 4-coumarate coenzyme A ligase (4-CL), cinnamic acid dehydrogenase (CAD), polyphenol oxidase (PPO), and peroxidase (POD). This resulted in a significant reduction in lignin and G-type lignin contents in potential SRs compared to K0 treatment within 10-30 days after planting (DAP). BJ553 exhibited a significant decrease in PAL activity, as well as lignin and G-type contents at 10 DAP, whereas YS25 showed delayed effects until 20 DAP. However, the number and distribution of secondary xylem conduits as well as the mid-column diameter area in roots were increased in K2 treatment. Interestingly, K2 treatment exhibited significantly larger potential SR diameter than other treatments at 15, 20, and 25 DAP. At harvest, K2 treatment increased the SR number, the single SR weight, and overall yield greatly compared with K0 treatment, with an average increase of 19.12%, 16.54%, and 16.92% respectively. The increase of SR number in BJ553 was higher than that of YS25. Furthermore, K2 treatment exhibited the lowest coefficient of variation for both SR length and diameter, indicating a higher yield of middle-sized SRs. In general, appropriate potassium application could effectively suppress lignin biosynthesis, leading to a reduction in the degree of pericycle lignification in potential SRs. This promotes an increase in the number of storage roots and ultimately enhances both yield and appearance quality of sweet potato. The effect of potassium fertilizer on lignin metabolism in BJ553 roots was earlier and resulted in a greater increase in the SR number compared to YS25.
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Affiliation(s)
- Ben-kui Liu
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Bing-jie Xv
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Cheng-cheng Si
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
| | - Wen-qing Shi
- Shandong Agricultural Technology Extension Center, Jinan, Shandong, China
| | - Guo-zheng Ding
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Li-xue Tang
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Ming Xv
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Chun-yv Shi
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hong-jvan Liu
- College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China
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12
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Zhu Z, Chen R, Zhang L. Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production. Nat Prod Rep 2024; 41:6-24. [PMID: 37807808 DOI: 10.1039/d3np00012e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Covering: 2000 to 2023Simple phenylpropanoids are a large group of natural products with primary C6-C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.
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Affiliation(s)
- Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China
- Innovative Drug R&D Centre, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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Bai M, Jiang S, Chu S, Yu Y, Shan D, Liu C, Zong L, Liu Q, Liu N, Xu W, Mei Z, Jian J, Zhang C, Zhao S, Chiu TY, Simonsen HT. The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis. Gigascience 2024; 13:giae025. [PMID: 38837945 PMCID: PMC11152176 DOI: 10.1093/gigascience/giae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/23/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A-E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and thus the development of better breeding strategies. RESULTS A telomere-to-telomere (T2T) genome was assembled for P. praeruptorum by combining PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes with genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced 2 whole-genome duplication events. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins. CONCLUSIONS A T2T genome for P. praeruptorum was obtained, providing molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.
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Affiliation(s)
- Mingzhou Bai
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Sanjie Jiang
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Shanshan Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230000, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei 230000, China
| | - Yangyang Yu
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Dai Shan
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Chun Liu
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Liang Zong
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan 430000, China
| | - Qun Liu
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan 430000, China
| | - Nana Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310000, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou 310000, China
| | - Weisong Xu
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Zhanlong Mei
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Jianbo Jian
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Chi Zhang
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Shancen Zhao
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
| | - Tsan-Yu Chiu
- BGI-Genomics, BGI-Shenzhen, Shenzhen 518000, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou 310000, China
| | - Henrik Toft Simonsen
- Laboratoire Biotechnologies Végétales Plantes aromatiques et médicinales, Université Jean Monnet, St. Étienne 42023, France
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14
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Song C, Zhang Y, Manzoor MA, Wei P, Yi S, Chu S, Tong Z, Song X, Xu T, Wang F, Peng H, Chen C, Han B. A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis. Int J Biol Macromol 2024; 255:128218. [PMID: 37992933 DOI: 10.1016/j.ijbiomac.2023.128218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
Peucedanum praeruptorum Dunn, a traditional Chinese medicine rich in coumarin, belongs to the Apiaceae family. A high-quality assembled genome of P. praeruptorum is lacking, which has posed obstacles to functional identification and molecular evolution studies of genes associated with coumarin production. Here, a chromosome-scale reference genome of P. praeruptorum, an important medicinal and aromatic plant, was first sequenced and assembled using Oxford Nanopore Technologies and Hi-C sequencing. The final assembled genome size was 1.83 Gb, with a contig N50 of 11.12 Mb. The entire BUSCO evaluation and second-generation read comparability rates were 96.0 % and 99.31 %, respectively. Furthermore, 99.91 % of the genome was anchored to 11 pseudochromosomes. The comparative genomic study revealed the presence of 18,593 orthogroups, which included 476 species-specific orthogroups and 1211 expanded gene families. Two whole-genome duplication (WGD) events and one whole-genome triplication (WGT) event occurred in P. praeruptorum. In addition to the γ-WGT shared by core eudicots or most eudicots, the first WGD was shared by Apiales, while the most recent WGD was unique to Apiaceae. Our study demonstrated that WGD events that occurred in Apioideae highlighted the important role of tandem duplication in the biosynthesis of coumarins and terpenes in P. praeruptorum. Additionally, the expansion of the cytochrome P450 monooxygenase, O-methyltransferase, ATP-binding cassette (ABC) transporter, and terpene synthase families may be associated with the abundance of coumarins and terpenoids. Moreover, we identified >170 UDP-glucosyltransferase members that may be involved in the glycosylation post-modification of coumarins. Significant gene expansion was observed in the ABCG, ABCB, and ABCC subgroups of the ABC transporter family, potentially facilitating the transmembrane transport of coumarins after bolting. The P. praeruptorum genome provides valuable insights into the machinery of coumarin biosynthesis and enhances our understanding of Apiaceae evolution.
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Affiliation(s)
- Cheng Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 201109, China
| | - Peipei Wei
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Shanyong Yi
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Shanshan Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Zhenzhen Tong
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiangwen Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Tao Xu
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Fang Wang
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Huasheng Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cunwu Chen
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China.
| | - Bangxing Han
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China.
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15
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Wu B, Shi S, Zhang H, Lu B, Nan P, A Y. Anabolic metabolism of autotoxic substance coumarins in plants. PeerJ 2023; 11:e16508. [PMID: 38077428 PMCID: PMC10710134 DOI: 10.7717/peerj.16508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
Background Autotoxicity is an intraspecific manifestation of allelopathy in plant species. The specialized metabolites and their derivatives that cause intraspecific allelopathic inhibition in the plant are known as autotoxic substances. Consequently, autotoxic substances production seriously affects the renewal and stability of ecological communities. Methods This article systematically summarizes the types of autotoxic substances present in different plants. They mainly include phenolic compounds, terpenoids, and nitrogenous organic compounds. Phenolic coumarins are the main autotoxic substances in many plants. Therefore, we also discuss differences in coumarin types and content among plant varieties, developmental stages, and tissue parts, as well as their mechanisms of autotoxicity. In addition, we review the metabolic pathways involved in coumarin biosynthesis, the key enzymes, genes, and transcription factors, as well as factors affecting coumarin biosynthesis. Results Coumarin biosynthesis involves three stages: (1) the formation of the coumarin nucleus; (2) acylation, hydroxylation, and cyclization; (3) structural modification. The key enzymes involved in the coumarin nuclear formation stage include PAL, C4H, 4CL, HCT, CAOMT, COSY, F6'H, and CCoAOMT1, and the key genes involved include BGA, CYP450 and MDR, among others. Ortho-hydroxylation is a key step in coumarin biosynthesis and PS, COSY and S8H are the key enzymes involved in this process. Finally, UGTs are responsible for the glycosylation modification of coumarins, and the MaUGT gene may therefore be involved in coumarin biosynthesis. Conclusion It is important to elucidate the autotoxicity and anabolic mechanisms of coumarins to create new germplasms that produce fewer autotoxic substances.
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Affiliation(s)
- Bei Wu
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shangli Shi
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Huihui Zhang
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Baofu Lu
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Pan Nan
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yun A
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural University, Lanzhou, Gansu, China
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16
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Beesley A, Beyer SF, Wanders V, Levecque S, Bredenbruch S, Habash SS, Schleker ASS, Gätgens J, Oldiges M, Schultheiss H, Conrath U, Langenbach CJG. Engineered coumarin accumulation reduces mycotoxin-induced oxidative stress and disease susceptibility. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2490-2506. [PMID: 37578146 PMCID: PMC10651151 DOI: 10.1111/pbi.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/23/2023] [Accepted: 07/23/2023] [Indexed: 08/15/2023]
Abstract
Coumarins can fight pathogens and are thus promising for crop protection. Their biosynthesis, however, has not yet been engineered in crops. We tailored the constitutive accumulation of coumarins in transgenic Nicotiana benthamiana, Glycine max and Arabidopsis thaliana plants, as well as in Nicotiana tabacum BY-2 suspension cells. We did so by overexpressing A. thaliana feruloyl-CoA 6-hydroxylase 1 (AtF6'H1), encoding the key enzyme of scopoletin biosynthesis. Besides scopoletin and its glucoside scopolin, esculin at low level was the only other coumarin detected in transgenic cells. Mechanical damage of scopolin-accumulating tissue led to a swift release of scopoletin, presumably from the scopolin pool. High scopolin levels in A. thaliana roots coincided with reduced susceptibility to the root-parasitic nematode Heterodera schachtii. In addition, transgenic soybean plants were more tolerant to the soil-borne pathogenic fungus Fusarium virguliforme. Because mycotoxin-induced accumulation of reactive oxygen species and cell death were reduced in the AtF6'H1-overexpressors, the weaker sensitivity to F. virguliforme may be caused by attenuated oxidative damage of coumarin-hyperaccumulating cells. Together, engineered coumarin accumulation is promising for enhanced disease resilience of crops.
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Affiliation(s)
| | - Sebastian F. Beyer
- Department of Plant PhysiologyRWTH Aachen UniversityAachenGermany
- Present address:
BASF SE, Agricultural CenterLimburgerhofGermany
| | - Verena Wanders
- Department of Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Sophie Levecque
- Department of Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | | | - Samer S. Habash
- Department of Molecular PhytomedicineUniversity of BonnBonnGermany
- Present address:
BASF Vegetable SeedsNunhemNetherlands
| | | | - Jochem Gätgens
- Department of Bioprocesses and BioanalyticsResearch Center Jülich GmbHJülichGermany
| | - Marco Oldiges
- Department of Bioprocesses and BioanalyticsResearch Center Jülich GmbHJülichGermany
| | | | - Uwe Conrath
- Department of Plant PhysiologyRWTH Aachen UniversityAachenGermany
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17
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Wang Z, Zhou Y, Wang Y, Yan X. Reconstitution and Optimization of the Marmesin Biosynthetic Pathway in Yeast. ACS Synth Biol 2023; 12:2922-2933. [PMID: 37767718 DOI: 10.1021/acssynbio.3c00267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Marmesin is essential in plant defense systems and exhibits various biological activities. In this study, we reconstituted the marmesin biosynthetic pathway in the Saccharomyces cerevisiae BY4741 chassis. We engineered the aromatic amino acid (AAA) biosynthetic pathways by introducing Escherichia coli-derived ppsA to improve the availability of the AAA precursor phosphoenolpyruvate, overexpressing the feedback inhibition resistance genes ARO4K229L and ARO7G141S to direct the metabolic flux toward the tyrosine branch, and deleting ARO10, PDC5, and PDC6 to reduce the byproducts from the Ehrlich pathway. The umbelliferone 6-dimethylallyltransferase (U6DT) and marmesin synthase (MS) involved in marmesin synthesis were optimized to increase marmesin production. Marmesin production was improved by truncating the transmembrane domains of PcU6DT, FcMS, and AtCPR1 and increasing the copy numbers of the genes encoding the truncated enzymes. Finally, a marmesin titer of 27.7 mg/L was obtained in shake flasks using the engineered yeast strain MU5. The constructed marmesin-producing strain provides the foundation for the green and large-scale production of pharmaceutically important furanocoumarins.
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Affiliation(s)
- Zhaoxin Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ying Zhou
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuefei Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Xiaohui Yan
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
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18
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Wang P, Fan Z, Wei W, Yang C, Wang Y, Shen X, Yan X, Zhou Z. Biosynthesis of the Plant Coumarin Osthole by Engineered Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:2455-2462. [PMID: 37450901 DOI: 10.1021/acssynbio.3c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Osthole is a coumarin compound found in the traditional Chinese medicine Cnidium monnieri. Extensive studies have shown that osthole exhibits many medicinal properties, and recently, researchers have found that it possesses potent airway-relaxation activity by inhibiting phosphodiesterase 4D activity, making it a potential novel bronchodilator that does not target β2-adrenoceptors for asthma treatment. Here, we report the complete biosynthesis of osthole in engineered yeast. We created an umbelliferone (UMB)-producing strain by reconstituting the complete UMB pathway in yeast. We found that coumarin synthase (COSY) is essential for the conversion of 2',4'-dihydroxycinnamoyl-CoA into UMB in yeast; this conversion has been treated as a spontaneous step in previously reported UMB-producing microbials. By introducing downstream prenyltransferase and methyltransferase genes and addressing problems such as protein expression and cofactor supply to fulfill the downstream steps, complete biosynthesis of osthole was achieved. Finally, through metabolic engineering, to ensure precursor supply, and the debugging of rate-limited steps, the osthole titer reached 108.10 mg/L in shake flasks and 255.1 mg/L in fed-batch fermentation. Our study is the first to produce osthole using engineered microbes, providing a blueprint for the supply of plant-derived osthole via microbial fermentation, which will remove the barriers of resource limitations for osthole-based drug development.
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Affiliation(s)
- Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenjun Fan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenping Wei
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengshuai Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao Shen
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Yin Q, Wu T, Gao R, Wu L, Shi Y, Wang X, Wang M, Xu Z, Zhao Y, Su X, Su Y, Han X, Yuan L, Xiang L, Chen S. Multi-omics reveal key enzymes involved in the formation of phenylpropanoid glucosides in Artemisia annua. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107795. [PMID: 37301186 DOI: 10.1016/j.plaphy.2023.107795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Although mainly known for producing artemisinin, Artemisia annua is enriched in phenylpropanoid glucosides (PGs) with significant bioactivities. However, the biosynthesis of A. annua PGs is insufficiently investigated. Different A. annua ecotypes from distinct growing environments accumulate varying amounts of metabolites, including artemisinin and PGs such as scopolin. UDP-glucose:phenylpropanoid glucosyltransferases (UGTs) transfers glucose from UDP-glucose in PG biosynthesis. Here, we found that the low-artemisinin ecotype GS produces a higher amount of scopolin, compared to the high-artemisinin ecotype HN. By combining transcriptome and proteome analyses, we selected 28 candidate AaUGTs from 177 annotated AaUGTs. Using AlphaFold structural prediction and molecular docking, we determined the binding affinities of 16 AaUGTs. Seven of the AaUGTs enzymatically glycosylated phenylpropanoids. AaUGT25 converted scopoletin to scopolin and esculetin to esculin. The lack of accumulation of esculin in the leaf and the high catalytic efficiency of AaUGT25 on esculetin suggest that esculetin is methylated to scopoletin, the precursor of scopolin. We also discovered that AaOMT1, a previously uncharacterized O-methyltransferase, converts esculetin to scopoletin, suggesting an alternative route for producing scopoletin, which contributes to the high-level accumulation of scopolin in A. annua leaves. AaUGT1 and AaUGT25 responded to induction of stress-related phytohormones, implying the involvement of PGs in stress responses.
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Affiliation(s)
- Qinggang Yin
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Tianze Wu
- School of Chemistry Chemical Engineering and Life Sciences, Wuhan University of Technology, No. 122, Lo Lion Road, Wuhan, Hubei, 430070, China
| | - Ranran Gao
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Lan Wu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yuhua Shi
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xingwen Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mengyue Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhichao Xu
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, 150006, China
| | - Yueliang Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaojia Su
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453000, China
| | - Yanyan Su
- Amway(China) Botanical R&D Center, Wuxi, 214115, China
| | - Xiaoyan Han
- China National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA; Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546-0236, USA
| | - Li Xiang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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20
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Mai HJ, Baby D, Bauer P. Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1204723. [PMID: 37554559 PMCID: PMC10406446 DOI: 10.3389/fpls.2023.1204723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/04/2023] [Indexed: 08/10/2023]
Abstract
Cellular homeostasis of the micronutrient iron is highly regulated in plants and responsive to nutrition, stress, and developmental signals. Genes for iron management encode metal and other transporters, enzymes synthesizing chelators and reducing substances, transcription factors, and several types of regulators. In transcriptome or proteome datasets, such iron homeostasis-related genes are frequently found to be differentially regulated. A common method to detect whether a specific cellular pathway is affected in the transcriptome data set is to perform Gene Ontology (GO) enrichment analysis. Hence, the GO database is a widely used resource for annotating genes and identifying enriched biological pathways in Arabidopsis thaliana. However, iron homeostasis-related GO terms do not consistently reflect gene associations and levels of evidence in iron homeostasis. Some genes in the existing iron homeostasis GO terms lack direct evidence of involvement in iron homeostasis. In other aspects, the existing GO terms for iron homeostasis are incomplete and do not reflect the known biological functions associated with iron homeostasis. This can lead to potential errors in the automatic annotation and interpretation of GO term enrichment analyses. We suggest that applicable evidence codes be used to add missing genes and their respective ortholog/paralog groups to make the iron homeostasis-related GO terms more complete and reliable. There is a high likelihood of finding new iron homeostasis-relevant members in gene groups and families like the ZIP, ZIF, ZIFL, MTP, OPT, MATE, ABCG, PDR, HMA, and HMP. Hence, we compiled comprehensive lists of genes involved in iron homeostasis that can be used for custom enrichment analysis in transcriptomic or proteomic studies, including genes with direct experimental evidence, those regulated by central transcription factors, and missing members of small gene families or ortholog/paralog groups. As we provide gene annotation and literature alongside, the gene lists can serve multiple computational approaches. In summary, these gene lists provide a valuable resource for researchers studying iron homeostasis in A. thaliana, while they also emphasize the importance of improving the accuracy and comprehensiveness of the Gene Ontology.
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Affiliation(s)
- Hans-Jörg Mai
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Dibin Baby
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
- Heinrich Heine University, Center of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
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21
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Zhang Y, Fernie AR. Leveraging glycoside-targeted metabolomics to gain insight into biological function. TRENDS IN PLANT SCIENCE 2023; 28:737-739. [PMID: 37076401 DOI: 10.1016/j.tplants.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
In plants, uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs) catalyze glycosylation of secondary metabolites, but assigning physiological functions to UGTs is still a daunting task. The recent study of Wu et al. presents a useful method to resolve this problem by elegantly combining modification-specific metabolomics with isotope tracing.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
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22
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Mankotia S, Singh D, Monika K, Kalra M, Meena H, Meena V, Yadav RK, Pandey AK, Satbhai SB. ELONGATED HYPOCOTYL 5 regulates BRUTUS and affects iron acquisition and homeostasis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1267-1284. [PMID: 36920240 DOI: 10.1111/tpj.16191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 06/17/2023]
Abstract
Iron (Fe) is an essential micronutrient for both plants and animals. Fe-limitation significantly reduces crop yield and adversely impacts on human nutrition. Owing to limited bioavailability of Fe in soil, plants have adapted different strategies that not only regulate Fe-uptake and homeostasis but also bring modifications in root system architecture to enhance survival. Understanding the molecular mechanism underlying the root growth responses will have critical implications for plant breeding. Fe-uptake is regulated by a cascade of basic helix-loop-helix (bHLH) transcription factors (TFs) in plants. In this study, we report that HY5 (Elongated Hypocotyl 5), a member of the basic leucine zipper (bZIP) family of TFs, plays an important role in the Fe-deficiency signaling pathway in Arabidopsis thaliana. The hy5 mutant failed to mount optimum Fe-deficiency responses, and displayed root growth defects under Fe-limitation. Our analysis revealed that the induction of the genes involved in Fe-uptake pathway (FIT-FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR, FRO2-FERRIC REDUCTION OXIDASE 2 and IRT1-IRON-REGULATED TRANSPORTER1) is reduced in the hy5 mutant as compared with the wild-type plants under Fe-deficiency. Moreover, we also found that the expression of coumarin biosynthesis genes is affected in the hy5 mutant under Fe-deficiency. Our results also showed that HY5 negatively regulates BRUTUS (BTS) and POPEYE (PYE). Chromatin immunoprecipitation followed by quantitative polymerase chain reaction revealed direct binding of HY5 to the promoters of BTS, FRO2 and PYE. Altogether, our results showed that HY5 plays an important role in the regulation of Fe-deficiency responses in Arabidopsis.
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Affiliation(s)
- Samriti Mankotia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
| | - Dhriti Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
| | - Kumari Monika
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
| | - Muskan Kalra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
| | - Himani Meena
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
| | - Varsha Meena
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar, 140306, India
| | - Ram Kishor Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar, 140306, India
| | - Santosh B Satbhai
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Mohali, Punjab, 140306, India
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23
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Chuang L, Liu S, Franke J. Post-Cyclization Skeletal Rearrangements in Plant Triterpenoid Biosynthesis by a Pair of Branchpoint Isomerases. J Am Chem Soc 2023; 145:5083-5091. [PMID: 36821810 PMCID: PMC9999417 DOI: 10.1021/jacs.2c10838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Triterpenoids possess potent biological activities, but their polycyclic skeletons are challenging to synthesize. The skeletal diversity of triterpenoids in plants is generated by oxidosqualene cyclases based on epoxide-triggered cationic rearrangement cascades. Normally, triterpenoid skeletons then remain unaltered during subsequent tailoring steps. In contrast, the highly modified triterpenoids found in Sapindales plants imply the existence of post-cyclization skeletal rearrangement enzymes that have not yet been found. We report here a biosynthetic pathway in Sapindales plants for the modification of already cyclized tirucallane triterpenoids, controlling the pathway bifurcation between different plant triterpenoid classes. Using a combination of bioinformatics, heterologous expression in plants and chemical analyses, we identified a cytochrome P450 monooxygenase and two isomerases which harness the epoxidation-rearrangement biosynthetic logic of triterpene cyclizations for modifying the tirucallane scaffold. The two isomerases share the same epoxide substrate made by the cytochrome P450 monooxygenase CYP88A154, but generate two different rearrangement products, one containing a cyclopropane ring. Our findings reveal a process for skeletal rearrangements of triterpenoids in nature that expands their scaffold diversity after the initial cyclization. In addition, the enzymes described here are crucial for the biotechnological production of limonoid, quassinoid, apoprotolimonoid, and glabretane triterpenoids.
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Affiliation(s)
- Ling Chuang
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Shenyu Liu
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Jakob Franke
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany.,Institute of Botany, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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24
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Tao M, Liu S, Li Y, Liu A, Tian J, Liu Y, Fu H, Zhu W. Molecular characterization of a feruloyl-CoA 6'-hydroxylase involved in coumarin biosynthesis in Clematis terniflora DC. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:162-170. [PMID: 36709578 DOI: 10.1016/j.plaphy.2023.01.046] [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: 08/12/2022] [Revised: 01/05/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Coumarin is an important secondary metabolite that affects plant physiology. It is a lactone of cis-o-hydroxycinnamic acid and widely exists in medicinal plants. Clematis terniflora DC. is a plant belonging to Ranunculaceae and is rich in variety of coumarins. Feruloyl-CoA 6'-hydroxylase has been reported as a key enzyme in the formation of coumarin basic skeleton only in some common plants, however, its evidence in other species is still lacking especially for the biosynthesis of coumarins in C. terniflora. In the present study, we identified a feruloyl-CoA 6'-hydroxylase CtF6'H in C. terniflora, and functional characterization indicated that CtF6'H could hydroxylate feruloyl-CoA to 6-hydroxyferuloyl-CoA. Furthermore, the expression level of CtF6'H was differed among different tissues in C. terniflora, while under UV-B radiation, the level of CtF6'H was increased in the leaves. Biochemical characteristics and subcellular location showed that CtF6'H was mainly present in the cytosol. The crystal structure of CtF6'H was simulated by homology modeling to predict the potential residues affecting enzyme activity. This study provides the additional evidence of feruloyl-CoA 6'-hydroxylase in different plant species and enriches our understanding of biosynthetic mechanism of coumarin in C. terniflora.
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Affiliation(s)
- Minglei Tao
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China; College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, China
| | - Yaohan Li
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yuchang Liu
- International Center of Zhejiang Fuyang High School, Hangzhou, 311400, China
| | - Hongwei Fu
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
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25
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Kim CY, Mitchell AJ, Kastner DW, Albright CE, Gutierrez MA, Glinkerman CM, Kulik HJ, Weng JK. Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY. Nat Commun 2023; 14:597. [PMID: 36737607 PMCID: PMC9898226 DOI: 10.1038/s41467-023-36299-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Plants contain rapidly evolving specialized enzymes that support the biosynthesis of functionally diverse natural products. In coumarin biosynthesis, a BAHD acyltransferase-family enzyme COSY was recently discovered to accelerate coumarin formation as the only known BAHD enzyme to catalyze an intramolecular acyl transfer reaction. Here we investigate the structural and mechanistic basis for COSY's coumarin synthase activity. Our structural analyses reveal an unconventional active-site configuration adapted to COSY's specialized activity. Through mutagenesis studies and deuterium exchange experiments, we identify a unique proton exchange mechanism at the α-carbon of the o-hydroxylated trans-hydroxycinnamoyl-CoA substrates during the catalytic cycle of COSY. Quantum mechanical cluster modeling and molecular dynamics further support this key mechanism for lowering the activation energy of the rate-limiting trans-to-cis isomerization step in coumarin production. This study unveils an unconventional catalytic mechanism mediated by a BAHD-family enzyme, and sheds light on COSY's evolutionary origin and its recruitment to coumarin biosynthesis in eudicots.
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Affiliation(s)
- Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Andrew J Mitchell
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - David W Kastner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Claire E Albright
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | | | | | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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26
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Robe K, Conjero G, Dubos C. The Use of Spectral Imaging to Follow the Iron and pH-Dependent Accumulation of Fluorescent Coumarins. Methods Mol Biol 2023; 2665:23-30. [PMID: 37166589 DOI: 10.1007/978-1-0716-3183-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plants challenged with iron deficiency produce in their roots and secrete into the rhizosphere several small molecules named coumarins that derive from the phenylpropanoid pathway. Coumarins are biosynthesized in different root cell types and transported to the root epidermis prior to their secretion in the surrounding media. Taking advantage of the natural fluorescence of most coumarins glycosides when exposed to UV light, we developed a method to uncover their individual cellular localization and accumulation. This approach couples spectral imaging acquisition and linear unmixing analysis. In this protocol, we describe guidelines, experimental setup, and conditions for the analysis of coumarins localization and accumulation in Arabidopsis thaliana root seedlings grown in control and iron deficiency conditions, at both acidic and alkaline pH.
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Affiliation(s)
- Kevin Robe
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Geneviève Conjero
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Christian Dubos
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
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27
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Mokshina N, Panina A, Galinousky D, Sautkina O, Mikshina P. Transcriptome profiling of celery petiole tissues reveals peculiarities of the collenchyma cell wall formation. PLANTA 2022; 257:18. [PMID: 36538078 DOI: 10.1007/s00425-022-04042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome and biochemical analyses are applied to individual plant cell types to reveal potential players involved in the molecular machinery of cell wall formation in specialized cells such as collenchyma. Plant collenchyma is a mechanical tissue characterized by an irregular, thickened cell wall and the ability to support cell elongation. The composition of the collenchyma cell wall resembles that of the primary cell wall and includes cellulose, xyloglucan, and pectin; lignin is absent. Thus, the processes associated with the formation of the primary cell wall in the collenchyma can be more pronounced compared to other tissues due to its thickening. Primary cell walls intrinsic to different tissues may differ in structure and composition, which should be reflected at the transcriptomic level. For the first time, we conducted transcriptome profiling of collenchyma strands isolated from young celery petioles and compared them with other tissues, such as parenchyma and vascular bundles. Genes encoding proteins involved in the primary cell wall formation during cell elongation, such as xyloglucan endotransglucosylase/hydrolases, expansins, and leucine-rich repeat proteins, were significantly activated in the collenchyma. As the key players in the transcriptome orchestra of collenchyma, xyloglucan endotransglucosylase/hydrolase transcripts were characterized in more detail, including phylogeny and expression patterns. The comprehensive approach that included transcriptome and biochemical analyses allowed us to reveal peculiarities of collenchyma cell wall formation and modification, matching the abundance of upregulated transcripts and their potential substrates for revealed gene products. As a result, specific isoforms of multigene families were determined for further functional investigation.
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Affiliation(s)
- Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia.
| | - Anastasia Panina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Dmitry Galinousky
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, CNRS, Université de Lille, 59655, Villeneuve d'Ascq, France
| | - Olga Sautkina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Polina Mikshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
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28
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Liu ZH, Li BZ, Yuan JS, Yuan YJ. Creative biological lignin conversion routes toward lignin valorization. Trends Biotechnol 2022; 40:1550-1566. [PMID: 36270902 DOI: 10.1016/j.tibtech.2022.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
Abstract
Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a 'biological funnel' offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy.
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Affiliation(s)
- Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Joshua S Yuan
- Department of Energy, Environmental, and Chemical Engineering, The McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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29
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Han X, Li C, Sun S, Ji J, Nie B, Maker G, Ren Y, Wang L. The chromosome-level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1224-1237. [PMID: 36259135 DOI: 10.1111/tpj.16007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Coumarins are natural products with important medicinal values, and include simple coumarins, furanocoumarins and pyranocoumarins. Female ginseng (Angelica sinensis) is a renowned herb with abundant coumarins, originated in China and known for the treatment of female ailments for thousands of years. The molecular basis of simple coumarin biosynthesis in A. sinensis and the evolutionary history of the genes involved in furanocoumarin biosynthesis are largely unknown. Here, we generated the first chromosome-scale genome of A. sinensis. It has a genome size of 2.37 Gb, which was generated by combining PacBio and Hi-C sequencing technologies. The genome was predicted to contain 43 202 protein-coding genes dispersed mainly on 11 pseudochromosomes. We not only provided evidence for whole-genome duplication (WGD) specifically occurring in the Apioideae subfamily, but also demonstrated the vital role of tandem duplication for phenylpropanoid biosynthesis in A. sinensis. Combined analyses of transcriptomic and metabolomic data revealed key genes and candidate transcription factors regulating simple coumarin biosynthesis. Furthermore, phylogenomic synteny network analyses suggested prenyltransferase genes involved in furanocoumarin biosynthesis evolved independently in the Moraceae, Fabaceae, Rutaceae and Apiaceae after ζ and ε WGD. Our work sheds light on coumarin biosynthesis, and provides a benchmark for accelerating genetic research and molecular breeding in A. sinensis.
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Affiliation(s)
- Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
- College of Science, Health, Engineering and Education, Murdoch University, 6150, Western Australia, Murdoch, 90 South Street, Australia
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Garth Maker
- College of Science, Health, Engineering and Education, Murdoch University, 6150, Western Australia, Murdoch, 90 South Street, Australia
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, 6150, Western Australia, Murdoch, 90 South Street, Australia
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, 528200, Foshan, China
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30
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Wu J, Zhu W, Shan X, Liu J, Zhao L, Zhao Q. Glycoside-specific metabolomics combined with precursor isotopic labeling for characterizing plant glycosyltransferases. MOLECULAR PLANT 2022; 15:1517-1532. [PMID: 35996753 DOI: 10.1016/j.molp.2022.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/19/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Glycosylation by uridine diphosphate-dependent glycosyltransferases (UGTs) in plants contributes to the complexity and diversity of secondary metabolites. UGTs are generally promiscuous in their use of acceptors, making it challenging to reveal the function of UGTs in vivo. Here, we described an approach that combined glycoside-specific metabolomics and precursor isotopic labeling analysis to characterize UGTs in Arabidopsis. We revisited the UGT72E cluster, which has been reported to catalyze the glycosylation of monolignols. Glycoside-specific metabolomics analysis reduced the number of differentially accumulated metabolites in the ugt72e1e2e3 mutant by at least 90% compared with that from traditional untargeted metabolomics analysis. In addition to the two previously reported monolignol glycosides, a total of 62 glycosides showed reduced accumulation in the ugt72e1e2e3 mutant, 22 of which were phenylalanine-derived glycosides, including 5-OH coniferyl alcohol-derived and lignan-derived glycosides, as confirmed by isotopic tracing of [13C6]-phenylalanine precursor. Our method revealed that UGT72Es could use coumarins as substrates, and genetic evidence showed that UGT72Es endowed plants with enhanced tolerance to low iron availability under alkaline conditions. Using the newly developed method, the function of UGT78D2 was also evaluated. These case studies suggest that this method can substantially contribute to the characterization of UGTs and efficiently investigate glycosylation processes, the complexity of which have been highly underestimated.
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Affiliation(s)
- Jie Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wentao Zhu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiaotong Shan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jinyue Liu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingling Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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31
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Liang G. Iron uptake, signaling, and sensing in plants. PLANT COMMUNICATIONS 2022; 3:100349. [PMID: 35706354 PMCID: PMC9483112 DOI: 10.1016/j.xplc.2022.100349] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 05/10/2023]
Abstract
Iron (Fe) is an essential micronutrient that affects the growth and development of plants because it participates as a cofactor in numerous physiological and biochemical reactions. As a transition metal, Fe is redox active. Fe often exists in soil in the form of insoluble ferric hydroxides that are not bioavailable to plants. Plants have developed sophisticated mechanisms to ensure an adequate supply of Fe in a fluctuating environment. Plants can sense Fe status and modulate the transcription of Fe uptake-associated genes, finally controlling Fe uptake from soil to root. There is a critical need to understand the molecular mechanisms by which plants maintain Fe homeostasis in response to Fe fluctuations. This review focuses on recent advances in elucidating the functions of Fe signaling components. Taking Arabidopsis thaliana and Oryza sativa as examples, this review begins by discussing the Fe acquisition systems that control Fe uptake from soil, the major components that regulate Fe uptake systems, and the perception of Fe status. Future explorations of Fe signal transduction will pave the way for understanding the regulatory mechanisms that underlie the maintenance of plant Fe homeostasis.
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Affiliation(s)
- Gang Liang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Kunming, Yunnan 650223, China.
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32
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He BT, Liu ZH, Li BZ, Yuan YJ. Advances in biosynthesis of scopoletin. Microb Cell Fact 2022; 21:152. [PMID: 35918699 PMCID: PMC9344664 DOI: 10.1186/s12934-022-01865-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/28/2022] [Indexed: 11/21/2022] Open
Abstract
Scopoletin is a typical example of coumarins, which can be produced in plants. Scopoletin acts as a precursor for pharmaceutical and health care products, and also possesses promising biological properties, including antibacterial, anti-tubercular, anti-hypertensive, anti-inflammatory, anti-diabetic, and anti-hyperuricemic activity. Despite the potential benefits, the production of scopoletin using traditional extraction processes from plants is unsatisfactory. In recent years, synthetic biology has developed rapidly and enabled the effective construction of microbial cell factories for production of high value-added chemicals. Herein, this review summarizes the progress of scopoletin biosynthesis in artificial microbial cell factories. The two main pathways of scopoletin biosynthesis are summarized firstly. Then, synthetic microbial cell factories are reviewed as an attractive improvement strategy for biosynthesis. Emerging techniques in synthetic biology and metabolic engineering are introduced as innovative tools for the efficient synthesis of scopoletin. This review showcases the potential of biosynthesis of scopoletin in artificial microbial cell factories.
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Affiliation(s)
- Bo-Tao He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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33
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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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Hoengenaert L, Wouters M, Kim H, De Meester B, Morreel K, Vandersyppe S, Pollier J, Desmet S, Goeminne G, Ralph J, Boerjan W, Vanholme R. Overexpression of the scopoletin biosynthetic pathway enhances lignocellulosic biomass processing. SCIENCE ADVANCES 2022; 8:eabo5738. [PMID: 35857515 PMCID: PMC9278857 DOI: 10.1126/sciadv.abo5738] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Lignin is the main factor limiting the enzymatic conversion of lignocellulosic biomass into fermentable sugars. To reduce the recalcitrance engendered by the lignin polymer, the coumarin scopoletin was incorporated into the lignin polymer through the simultaneous expression of FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) and COUMARIN SYNTHASE (COSY) in lignifying cells in Arabidopsis. The transgenic lines overproduced scopoletin and incorporated it into the lignin polymer, without adversely affecting plant growth. About 3.3% of the lignin units in the transgenic lines were derived from scopoletin, thereby exceeding the levels of the traditional p-hydroxyphenyl units. Saccharification efficiency of alkali-pretreated scopoletin-overproducing lines was 40% higher than for wild type.
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Affiliation(s)
- Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Marlies Wouters
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hoon Kim
- Department of Biochemistry and U.S. Department of Energy’s Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steven Vandersyppe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - John Ralph
- Department of Biochemistry and U.S. Department of Energy’s Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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Njiru C, Xue W, De Rouck S, Alba JM, Kant MR, Chruszcz M, Vanholme B, Dermauw W, Wybouw N, Van Leeuwen T. Intradiol ring cleavage dioxygenases from herbivorous spider mites as a new detoxification enzyme family in animals. BMC Biol 2022; 20:131. [PMID: 35658860 PMCID: PMC9167512 DOI: 10.1186/s12915-022-01323-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/09/2022] [Indexed: 12/13/2022] Open
Abstract
Background Generalist herbivores such as the two-spotted spider mite Tetranychus urticae thrive on a wide variety of plants and can rapidly adapt to novel hosts. What traits enable polyphagous herbivores to cope with the diversity of secondary metabolites in their variable plant diet is unclear. Genome sequencing of T. urticae revealed the presence of 17 genes that code for secreted proteins with strong homology to “intradiol ring cleavage dioxygenases (DOGs)” from bacteria and fungi, and phylogenetic analyses show that they have been acquired by horizontal gene transfer from fungi. In bacteria and fungi, DOGs have been well characterized and cleave aromatic rings in catecholic compounds between adjacent hydroxyl groups. Such compounds are found in high amounts in solanaceous plants like tomato, where they protect against herbivory. To better understand the role of this gene family in spider mites, we used a multi-disciplinary approach to functionally characterize the various T. urticae DOG genes. Results We confirmed that DOG genes were present in the T. urticae genome and performed a phylogenetic reconstruction using transcriptomic and genomic data to advance our understanding of the evolutionary history of spider mite DOG genes. We found that DOG expression differed between mites from different plant hosts and was induced in response to jasmonic acid defense signaling. In consonance with a presumed role in detoxification, expression was localized in the mite’s gut region. Silencing selected DOGs expression by dsRNA injection reduced the mites’ survival rate on tomato, further supporting a role in mitigating the plant defense response. Recombinant purified DOGs displayed a broad substrate promiscuity, cleaving a surprisingly wide array of aromatic plant metabolites, greatly exceeding the metabolic capacity of previously characterized microbial DOGs. Conclusion Our findings suggest that the laterally acquired spider mite DOGs function as detoxification enzymes in the gut, disarming plant metabolites before they reach toxic levels. We provide experimental evidence to support the hypothesis that this proliferated gene family in T. urticae is causally linked to its ability to feed on an extremely wide range of host plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01323-1.
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Liu S, Zhong Z, Sun Z, Tian J, Sulaiman K, Shawky E, Fu H, Zhu W. De novo Transcriptome Analysis Revealed the Putative Pathway Genes Involved in Biosynthesis of Moracins in Morus alba L. ACS OMEGA 2022; 7:11343-11352. [PMID: 35415355 PMCID: PMC8992258 DOI: 10.1021/acsomega.2c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Moracins, a kind of 2-phenyl-benzofuran compound from Moraceae, serve as phytoalexins with antimicrobial, anti-inflammatory, antitumor, and antidiabetes activities and respond to biotic and abiotic stresses, while their biosynthetic pathway and regulatory mechanism remain unclear. Here, we report a de novo transcriptome sequencing for different tissues of seedlings, as well as leaves under different stresses, in M. alba L. A total of 88 282 unigenes were assembled with an average length of 937 bp, and 82.2% of them were annotated. On the basis of the differential expression analysis and enzymatic activity assays in vitro, moracins were traced to the phenylpropanoid pathway, and a putative biosynthetic pathway of moracins was proposed. Unigenes coding key enzymes in the pathway were identified and their expression levels were verified by real-time quantitative reverse transcription PCR (qRT-PCR). Particularly, a p-coumaroyl CoA 2'-hydroxylase was presumed to be involved in the biosynthesis of stilbenes and deoxychalcones in mulberry. Additionally, the transcription factors that might participate in the regulation of moracin biosynthesis were obtained by coexpression analysis. These results shed light on the putative biosynthetic pathway of moracins, providing a basis for further investigation in functional characterization and transcriptional regulation of moracin biosynthesis in mulberry.
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Affiliation(s)
- Shengzhi Liu
- College
of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Zhuoheng Zhong
- College
of Life Sciences and Medicine, Zhejiang
Sci-Tech University, Hangzhou 310018, China
| | - Zijian Sun
- College
of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jingkui Tian
- The
Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang
Cancer Hospital), Institute of Basic Medicine
and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
| | - Kaisa Sulaiman
- The
Xinjiang Uygur Autonomous Region National Institute of Traditional
Chinese Medicine, Urumchi, Xinjiang 830092, China
| | - Eman Shawky
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, Alexandria 21521, Egypt
| | - Hongwei Fu
- College
of Life Sciences and Medicine, Zhejiang
Sci-Tech University, Hangzhou 310018, China
| | - Wei Zhu
- The
Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang
Cancer Hospital), Institute of Basic Medicine
and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
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37
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Lešková A, Javot H, Giehl RFH. Metal crossroads in plants: modulation of nutrient acquisition and root development by essential trace metals. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1751-1765. [PMID: 34791130 DOI: 10.1093/jxb/erab483] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The metals iron, zinc, manganese, copper, molybdenum, and nickel are essential for the growth and development of virtually all plant species. Although these elements are required at relatively low amounts, natural factors and anthropogenic activities can significantly affect their availability in soils, inducing deficiencies or toxicities in plants. Because essential trace metals can shape root systems and interfere with the uptake and signaling mechanisms of other nutrients, the non-optimal availability of any of them can induce multi-element changes in plants. Interference by one essential trace metal with the acquisition of another metal or a non-metal nutrient can occur prior to or during root uptake. Essential trace metals can also indirectly impact the plant's ability to capture soil nutrients by targeting distinct root developmental programs and hormone-related processes, consequently inducing largely metal-specific changes in root systems. The presence of metal binding domains in many regulatory proteins also enables essential trace metals to coordinate nutrient uptake by acting at high levels in hierarchical signaling cascades. Here, we summarize the known molecular and cellular mechanisms underlying trace metal-dependent modulation of nutrient acquisition and root development, and highlight the importance of considering multi-element interactions to breed crops better adapted to non-optimal trace metal availabilities.
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Affiliation(s)
- Alexandra Lešková
- Aix Marseille Univ, CEA, CNRS, Bioscience and Biotechnology Institut of Aix-Marseille (BIAM), SAVE, Saint Paul-Lez-Durance, F-13108, France
| | - Hélène Javot
- Aix Marseille Univ, CEA, CNRS, Bioscience and Biotechnology Institut of Aix-Marseille (BIAM), SAVE, Saint Paul-Lez-Durance, F-13108, France
| | - Ricardo F H Giehl
- Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
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38
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Wu F, Duan Z, Xu P, Yan Q, Meng M, Cao M, Jones CS, Zong X, Zhou P, Wang Y, Luo K, Wang S, Yan Z, Wang P, Di H, Ouyang Z, Wang Y, Zhang J. Genome and systems biology of Melilotus albus provides insights into coumarins biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:592-609. [PMID: 34717292 PMCID: PMC8882801 DOI: 10.1111/pbi.13742] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 05/08/2023]
Abstract
Melilotus species are used as green manure and rotation crops worldwide and contain abundant pharmacologically active coumarins. However, there is a paucity of information on its genome and coumarin production and function. Here, we reported a chromosome-scale assembly of Melilotus albus genome with 1.04 Gb in eight chromosomes, containing 71.42% repetitive elements. Long terminal repeat retrotransposon bursts coincided with declining of population sizes during the Quaternary glaciation. Resequencing of 94 accessions enabled insights into genetic diversity, population structure, and introgression. Melilotus officinalis had relatively larger genetic diversity than that of M. albus. The introgression existed between M. officinalis group and M. albus group, and gene flows was from M. albus to M. officinalis. Selection sweep analysis identified candidate genes associated with flower colour and coumarin biosynthesis. Combining genomics, BSA, transcriptomics, metabolomics, and biochemistry, we identified a β-glucosidase (BGLU) gene cluster contributing to coumarin biosynthesis. MaBGLU1 function was verified by overexpression in M. albus, heterologous expression in Escherichia coli, and substrate feeding, revealing its role in scopoletin (coumarin derivative) production and showing that nonsynonymous variation drives BGLU enzyme activity divergence in Melilotus. Our work will accelerate the understanding of biologically active coumarins and their biosynthetic pathways, and contribute to genomics-enabled Melilotus breeding.
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Affiliation(s)
- Fan Wu
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zhen Duan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pan Xu
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Qi Yan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Minghui Meng
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Mingshu Cao
- Grasslands Research CentreAgResearch LimitedPalmerston NorthNew Zealand
| | - Chris S. Jones
- Feed and Forage DevelopmentInternational Livestock Research InstituteNairobiKenya
| | - Xifang Zong
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pei Zhou
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Yimeng Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Kai Luo
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Shengsheng Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Penglei Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Hongyan Di
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zifeng Ouyang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
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Yang B, Liu SH, He Y, Li Y, Feng L, Zhang M, Zhao J, Zhang Y, Yu X, Chen H, Hou D, Zhao J, Yu M. Integration of transcriptomics and metabolomics to identify key coumarin biosynthetic genes in Bupleurum chinense. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2023327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Bin Yang
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Shi-Hang Liu
- Department of Genetic Resources, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yilian He
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Yuchan Li
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Liang Feng
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Meng Zhang
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Jun Zhao
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Yiguan Zhang
- Department of Genetic Resources, Sichuan Institute for Translational Chinese Medicine, Chengdu, Sichuan, PR China
| | - Xia Yu
- Department of Genetic, Genetic Research Institute, Yongchuan Hospital of Chongqing Medical University, Yongchuan, Chongqing, PR China
| | - Hua Chen
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Dabin Hou
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Junning Zhao
- Department of Genetic Resources, Sichuan Institute for Translational Chinese Medicine, Chengdu, Sichuan, PR China
| | - Ma Yu
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
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Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis. Int J Mol Sci 2021; 22:ijms222212319. [PMID: 34830202 PMCID: PMC8618292 DOI: 10.3390/ijms222212319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/23/2022] Open
Abstract
Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a trans-differentiation step characterized by the proliferation of a mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. Therefore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals for pharmacological, nutraceutical and cosmeceutical use. Thus, it is of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, a time point at which a well-visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies characterizing each of the four time points investigated (0, 1, 10 and 34 days). The results show that, while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to the immune response and cell wall loosening, respectively.
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Desmet S, Morreel K, Dauwe R. Origin and Function of Structural Diversity in the Plant Specialized Metabolome. PLANTS (BASEL, SWITZERLAND) 2021; 10:2393. [PMID: 34834756 PMCID: PMC8621143 DOI: 10.3390/plants10112393] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 05/07/2023]
Abstract
The plant specialized metabolome consists of a multitude of structurally and functionally diverse metabolites, variable from species to species. The specialized metabolites play roles in the response to environmental changes and abiotic or biotic stresses, as well as in plant growth and development. At its basis, the specialized metabolism is built of four major pathways, each starting from a few distinct primary metabolism precursors, and leading to distinct basic carbon skeleton core structures: polyketides and fatty acid derivatives, terpenoids, alkaloids, and phenolics. Structural diversity in specialized metabolism, however, expands exponentially with each subsequent modification. We review here the major sources of structural variety and question if a specific role can be attributed to each distinct structure. We focus on the influences that various core structures and modifications have on flavonoid antioxidant activity and on the diversity generated by oxidative coupling reactions. We suggest that many oxidative coupling products, triggered by initial radical scavenging, may not have a function in se, but could potentially be enzymatically recycled to effective antioxidants. We further discuss the wide structural variety created by multiple decorations (glycosylations, acylations, prenylations), the formation of high-molecular weight conjugates and polyesters, and the plasticity of the specialized metabolism. We draw attention to the need for untargeted methods to identify the complex, multiply decorated and conjugated compounds, in order to study the functioning of the plant specialized metabolome.
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Affiliation(s)
- Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (S.D.); (K.M.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (S.D.); (K.M.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Rebecca Dauwe
- Unité de Recherche Biologie des Plantes et Innovation (BIOPI), UMR Transfrontalière BioEcoAgro, Université de Picardie Jules Verne, 80000 Amiens, France
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Gautam CK, Tsai HH, Schmidt W. IRONMAN tunes responses to iron deficiency in concert with environmental pH. PLANT PHYSIOLOGY 2021; 187:1728-1745. [PMID: 34618058 PMCID: PMC8566206 DOI: 10.1093/plphys/kiab329] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 05/16/2023]
Abstract
Iron (Fe) is an essential mineral element that governs the composition of natural plant communities and limits crop yield in agricultural ecosystems due to its extremely low availability in most soils, particularly at alkaline pH. To extract sufficient Fe from the soil under such conditions, some plants, including Arabidopsis (Arabidopsis thaliana), secrete Fe-mobilizing phenylpropanoids, which mobilize sparingly soluble Fe hydroxides by reduction and chelation. We show here that ectopic expression of the peptides IRONMAN (IMA1) and IMA2 improves growth on calcareous soil by inducing biosynthesis and secretion of the catecholic coumarin 7,8-dihydroxy-6-methoxycoumarin (fraxetin) via increased expression of MYB72 and SCOPOLETIN 8-HYDROXYLASE, a response that is strictly dependent on elevated environmental pH (pHe). By contrast, transcription of the cytochrome P450 family protein CYP82C4, catalyzing the subsequent hydroxylation of fraxetin to sideretin, which forms less stable complexes with iron, was strongly repressed under such conditions. We concluded that IMA peptides regulate processes supporting Fe uptake at both acidic and elevated pH by controlling gene expression upstream of or in concert with a putative pHe signal, adapting the plant to prevailing edaphic conditions. This regulatory pattern confers tolerance to calcareous soils by extending the pH range in which Fe can be efficiently absorbed from the soil. Our results further suggest that pHe calibrates the activities of components of the Fe deficiency response, accentuating processes that are most efficient under the prevailing conditions. Altering the expression of IMA peptides provides a route for generating plants adapted to calcareous soils.
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Affiliation(s)
- Chandan Kumar Gautam
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Huei-Hsuan Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei 11529, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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Perkowska I, Potrykus M, Siwinska J, Siudem D, Lojkowska E, Ihnatowicz A. Interplay between Coumarin Accumulation, Iron Deficiency and Plant Resistance to Dickeya spp. Int J Mol Sci 2021; 22:ijms22126449. [PMID: 34208600 PMCID: PMC8235353 DOI: 10.3390/ijms22126449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/17/2023] Open
Abstract
Coumarins belong to a group of secondary metabolites well known for their high biological activities including antibacterial and antifungal properties. Recently, an important role of coumarins in plant resistance to pathogens and their release into the rhizosphere upon pathogen infection was discovered. It is also well documented that coumarins play a crucial role in the Arabidopsis thaliana growth under Fe-limited conditions. However, the mechanisms underlying interplay between plant resistance, accumulation of coumarins and Fe status, remain largely unknown. In this work, we investigated the effect of both mentioned factors on the disease severity using the model system of Arabidopsis/Dickeya spp. molecular interactions. We evaluated the disease symptoms in Arabidopsis plants, wild-type Col-0 and its mutants defective in coumarin accumulation, grown in hydroponic cultures with contrasting Fe regimes and in soil mixes. Under all tested conditions, Arabidopsis plants inoculated with Dickeya solani IFB0099 strain developed more severe disease symptoms compared to lines inoculated with Dickeya dadantii 3937. We also showed that the expression of genes encoding plant stress markers were strongly affected by D. solani IFB0099 infection. Interestingly, the response of plants to D. dadantii 3937 infection was genotype-dependent in Fe-deficient hydroponic solution.
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Affiliation(s)
- Izabela Perkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Marta Potrykus
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
- Department of Environmental Toxicology, Faculty of Health Sciences with Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Debowa 23 A, 80-204 Gdansk, Poland
| | - Joanna Siwinska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Dominika Siudem
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Ewa Lojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
| | - Anna Ihnatowicz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (I.P.); (M.P.); (J.S.); (D.S.); (E.L.)
- Correspondence: ; Tel.: +48-58-5236330
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El Houari I, Van Beirs C, Arents HE, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. THE NEW PHYTOLOGIST 2021; 230:2275-2291. [PMID: 33728703 DOI: 10.1111/nph.17349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/06/2021] [Indexed: 05/20/2023]
Abstract
The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored. We use complementary pharmacological and genetic approaches to block CINNAMATE-4-HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes. Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in AUX transport. The upstream accumulation in cis-cinnamic acid was found to be likely to cause polar AUX transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem-mediated AUX transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, AUX homeostasis. Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of AUX distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development.
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Affiliation(s)
- Ilias El Houari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Caroline Van Beirs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Helena E Arents
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Huibin Han
- Institute of Science and Technology (IST) Austria, Klosterneuburg, 3400, Austria
| | - Alexandra Chanoca
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Davy Opdenacker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Metabolomics Core, Ghent, 9052, Belgium
| | - Véronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Ward Steenackers
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, Klosterneuburg, 3400, Austria
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
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Two chemically distinct root lignin barriers control solute and water balance. Nat Commun 2021; 12:2320. [PMID: 33875659 PMCID: PMC8055973 DOI: 10.1038/s41467-021-22550-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/11/2021] [Indexed: 02/02/2023] Open
Abstract
Lignin is a complex polymer deposited in the cell wall of specialised plant cells, where it provides essential cellular functions. Plants coordinate timing, location, abundance and composition of lignin deposition in response to endogenous and exogenous cues. In roots, a fine band of lignin, the Casparian strip encircles endodermal cells. This forms an extracellular barrier to solutes and water and plays a critical role in maintaining nutrient homeostasis. A signalling pathway senses the integrity of this diffusion barrier and can induce over-lignification to compensate for barrier defects. Here, we report that activation of this endodermal sensing mechanism triggers a transcriptional reprogramming strongly inducing the phenylpropanoid pathway and immune signaling. This leads to deposition of compensatory lignin that is chemically distinct from Casparian strip lignin. We also report that a complete loss of endodermal lignification drastically impacts mineral nutrients homeostasis and plant growth.
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Schnabel A, Athmer B, Manke K, Schumacher F, Cotinguiba F, Vogt T. Identification and characterization of piperine synthase from black pepper, Piper nigrum L. Commun Biol 2021; 4:445. [PMID: 33833371 PMCID: PMC8032705 DOI: 10.1038/s42003-021-01967-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/03/2021] [Indexed: 01/19/2023] Open
Abstract
Black pepper (Piper nigrum L.) is the world's most popular spice and is also used as an ingredient in traditional medicine. Its pungent perception is due to the interaction of its major compound, piperine (1-piperoyl-piperidine) with the human TRPV-1 or vanilloid receptor. We now identify the hitherto concealed enzymatic formation of piperine from piperoyl coenzyme A and piperidine based on a differential RNA-Seq approach from developing black pepper fruits. This enzyme is described as piperine synthase (piperoyl-CoA:piperidine piperoyl transferase) and is a member of the BAHD-type of acyltransferases encoded by a gene that is preferentially expressed in immature fruits. A second BAHD-type enzyme, also highly expressed in immature black pepper fruits, has a rather promiscuous substrate specificity, combining diverse CoA-esters with aliphatic and aromatic amines with similar efficiencies, and was termed piperamide synthase. Recombinant piperine and piperamide synthases are members of a small gene family in black pepper. They can be used to facilitate the microbial production of a broad range of medicinally relevant aliphatic and aromatic piperamides based on a wide array of CoA-donors and amine-derived acceptors, offering widespread applications.
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Affiliation(s)
- Arianne Schnabel
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany
| | - Benedikt Athmer
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany
| | - Kerstin Manke
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany
| | | | - Fernando Cotinguiba
- Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro/RJ, Brasil
| | - Thomas Vogt
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Halle (Saale), Germany.
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Yu K, Stringlis IA, van Bentum S, de Jonge R, Snoek BL, Pieterse CMJ, Bakker PAHM, Berendsen RL. Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis-Mutualist Communication. Microorganisms 2021; 9:microorganisms9030575. [PMID: 33799825 PMCID: PMC8000642 DOI: 10.3390/microorganisms9030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas simiae WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of Arabidopsis roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic Arabidopsis-WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Arabidopsis Col-0 and the coumarin-biosynthesis mutant f6′h1. We found that coumarins in F6′H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6′H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins’ function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.
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Affiliation(s)
- Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China
| | - Ioannis A. Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Sietske van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Basten L. Snoek
- Theoretical Biology & Bioinformatics, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Roeland L. Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
- Correspondence: ; Tel.: +31-3025-36860
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Robe K, Izquierdo E, Vignols F, Rouached H, Dubos C. The Coumarins: Secondary Metabolites Playing a Primary Role in Plant Nutrition and Health. TRENDS IN PLANT SCIENCE 2021; 26:248-259. [PMID: 33246890 DOI: 10.1016/j.tplants.2020.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 05/16/2023]
Abstract
Although abundant in soils, iron (Fe) is poorly bioavailable for plants. Improving Fe uptake in crops, enabling them to grow in Fe-depleted soils, has become a major focal interest. The secretion of Fe-mobilizing coumarins by plant roots recently emerged as an important factor allowing nongrass species to cope with low Fe bioavailability. The main molecular actors involved in the biosynthesis and secretion of coumarins have been identified, but the precise regulatory mechanisms that tune their production remain poorly understood. Here, we review the recent progress in coumarin synthesis and transport in plants and future research directions to gain knowledge of these mechanisms, which will offer novel opportunities for improving plant growth and health and for generating Fe-fortified crops.
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Affiliation(s)
- Kevin Robe
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Esther Izquierdo
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Florence Vignols
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Hatem Rouached
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Christian Dubos
- BPMP, Université de Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France.
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Robe K, Conejero G, Gao F, Lefebvre-Legendre L, Sylvestre-Gonon E, Rofidal V, Hem S, Rouhier N, Barberon M, Hecker A, Gaymard F, Izquierdo E, Dubos C. Coumarin accumulation and trafficking in Arabidopsis thaliana: a complex and dynamic process. THE NEW PHYTOLOGIST 2021; 229:2062-2079. [PMID: 33205512 DOI: 10.1111/nph.17090] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/22/2020] [Indexed: 05/26/2023]
Abstract
Iron (Fe) is a major micronutrient and is required for plant growth and development. Nongrass species have evolved a reduction-based strategy to solubilize and take up Fe. The secretion of Fe-mobilizing coumarins (e.g. fraxetin, esculetin and sideretin) by plant roots plays an important role in this process. Although the biochemical mechanisms leading to their biosynthesis have been well described, very little is known about their cellular and subcellular localization or their mobility within plant tissues. Spectral imaging was used to monitor, in Arabidopsis thaliana, the in planta localization of Fe-mobilizing coumarins and scopolin. Molecular, genetic and biochemical approaches were also used to investigate the dynamics of coumarin accumulation in roots. These approaches showed that root hairs play a major role in scopoletin secretion, whereas fraxetin and esculetin secretion occurs through all epidermis cells. The findings of this study also showed that the transport of coumarins from the cortex to the rhizosphere relies on the PDR9 transporter under Fe-deficient conditions. Additional experiments support the idea that coumarins move throughout the plant body via the xylem sap and that several plant species can take up coumarins present in the surrounding media. Altogether, the data presented here demonstrate that coumarin storage and accumulation in roots is a highly complex and dynamic process.
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Affiliation(s)
- Kevin Robe
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Geneviève Conejero
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Fei Gao
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Linnka Lefebvre-Legendre
- Department of Botany and Plant Biology, University of Geneva, 30 Quai Ernest Ansermet, Geneva, 1211, Switzerland
| | | | - Valérie Rofidal
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Sonia Hem
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | | | - Marie Barberon
- Department of Botany and Plant Biology, University of Geneva, 30 Quai Ernest Ansermet, Geneva, 1211, Switzerland
| | - Arnaud Hecker
- INRAE, IAM, Université de Lorraine, Nancy, F-54000, France
| | - Frédéric Gaymard
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Esther Izquierdo
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Christian Dubos
- BPMP, CNRS, INRAE, Institut Agro, University of Montpellier, Montpellier, France
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50
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Stassen MJJ, Hsu SH, Pieterse CMJ, Stringlis IA. Coumarin Communication Along the Microbiome-Root-Shoot Axis. TRENDS IN PLANT SCIENCE 2021; 26:169-183. [PMID: 33023832 DOI: 10.1016/j.tplants.2020.09.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 05/06/2023]
Abstract
Plants shape their rhizosphere microbiome by secreting root exudates into the soil environment. Recently, root-exuded coumarins were identified as novel players in plant-microbiome communication. Beneficial members of the root-associated microbiome stimulate coumarin biosynthesis in roots and their excretion into the rhizosphere. The iron-mobilizing activity of coumarins facilitates iron uptake from the soil environment, while their selective antimicrobial activity shapes the root microbiome, resulting in promotion of plant growth and health. Evidence is accumulating that, in analogy to strigolactones and flavonoids, coumarins may act in microbiome-to-root-to-shoot signaling events. Here, we review this multifaceted role of coumarins in bidirectional chemical communication along the microbiome-root-shoot axis.
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Affiliation(s)
- Max J J Stassen
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Shu-Hua Hsu
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands; Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, 10617, Taipei, Taiwan
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
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