1
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Li C, Jiang R, Wang X, Lv Z, Li W, Chen W. Feedback regulation of plant secondary metabolism: Applications and challenges. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111983. [PMID: 38211735 DOI: 10.1016/j.plantsci.2024.111983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/04/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
Plant secondary metabolites offer resistance to invasion by herbivorous organisms, and are also useful in the chemical, pharmaceutical, cosmetic, and fragrance industries. There are numerous approaches to enhancing secondary metabolite yields. However, a growing number of studies has indicated that feedback regulation may be critical in regulating secondary metabolite biosynthesis. Here, we review examples of feedback regulation in secondary metabolite biosynthesis pathways, phytohormone signal transduction, and complex deposition sites associated with secondary metabolite biosynthesis. We propose a new strategy to enhance secondary metabolite production based on plant feedback regulation. We also discuss challenges in feedback regulation that must be overcome before its application to enhancing secondary metabolite yields. This review discusses recent advances in the field and highlights a strategy to overcome feedback regulation-related obstacles and obtain high secondary metabolite yields.
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Affiliation(s)
- Chuhan Li
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Rui Jiang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xingxing Wang
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zongyou Lv
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Wankui Li
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
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2
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El-Azaz J, Moore B, Takeda-Kimura Y, Yokoyama R, Wijesingha Ahchige M, Chen X, Schneider M, Maeda HA. Coordinated regulation of the entry and exit steps of aromatic amino acid biosynthesis supports the dual lignin pathway in grasses. Nat Commun 2023; 14:7242. [PMID: 37945591 PMCID: PMC10636026 DOI: 10.1038/s41467-023-42587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023] Open
Abstract
Vascular plants direct large amounts of carbon to produce the aromatic amino acid phenylalanine to support the production of lignin and other phenylpropanoids. Uniquely, grasses, which include many major crops, can synthesize lignin and phenylpropanoids from both phenylalanine and tyrosine. However, how grasses regulate aromatic amino acid biosynthesis to feed this dual lignin pathway is unknown. Here we show, by stable-isotope labeling, that grasses produce tyrosine >10-times faster than Arabidopsis without compromising phenylalanine biosynthesis. Detailed in vitro enzyme characterization and combinatorial in planta expression uncovered that coordinated expression of specific enzyme isoforms at the entry and exit steps of the aromatic amino acid pathway enables grasses to maintain high production of both tyrosine and phenylalanine, the precursors of the dual lignin pathway. These findings highlight the complex regulation of plant aromatic amino acid biosynthesis and provide novel genetic tools to engineer the interface of primary and specialized metabolism in plants.
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Affiliation(s)
- Jorge El-Azaz
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Bethany Moore
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Yuri Takeda-Kimura
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Faculty of Agriculture, Yamagata University, Yamagata-shi, Japan
| | - Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Micha Wijesingha Ahchige
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Xuan Chen
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- International Institute of Tea Industry Innovation for "one Belt, one Road", Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Matthew Schneider
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Cell Culture Company, Minneapolis, MN, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Kumari A, Kumar V, Ovadia R, Oren-Shamir M. Phenylalanine in motion: A tale of an essential molecule with many faces. Biotechnol Adv 2023; 68:108246. [PMID: 37652145 DOI: 10.1016/j.biotechadv.2023.108246] [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: 05/23/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Phenylalanine has a unique role in plants as a source of a wide range of specialized metabolites, named phenylpropanoids that contribute to the adjustment of plants to changing developmental and environmental conditions. The profile of these metabolites differs between plants and plant organs. Some of the prominent phenylpropanoids include anthocyanins, phenolic acids, flavonoids, tannins, stilbenes, lignins, glucosinolates and benzenoid phenylpropanoid volatiles. Phenylalanine biosynthesis, leading to increased phenylpropanoid levels, is induced under stress. However, high availability of phenylalanine in plants under non-stressed conditions can be achieved either by genetically engineering plants to overproduce phenylalanine, or by external treatment of whole plants or detached plant organs with phenylalanine solutions. The objective of this review is to portray the many effects that increased phenylalanine availability has in plants under non-stressed conditions, focusing mainly on external applications. These applications include spraying and drenching whole plants with phenylalanine solutions, postharvest treatments by dipping fruit and cut flower stems, and addition of phenylalanine to cell suspensions. The results of these treatments include increased fragrance in flowers, increased aroma and pigmentation in fruit, increased production of health promoting metabolites in plant cell cultures, and increased resistance of plants, pre- and post-harvest, to a wide variety of pathogens. These effects suggest that plants can very efficiently uptake phenylalanine from their roots, leaves, flowers and fruits, translocate it from one organ to the other and between cell compartments, and metabolize it into phenylpropanoids. The mechanisms by which Phe treatment increases plant resistance to pathogens reveal new roles of phenylpropanoids in induction of genes related to the plant immune system. The simplicity of treatments with phenylalanine open many possibilities for industrial use. Many of the phenylalanine-treatment effects on increased resistance to plant pathogens have also been successful in commercial field trials.
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Affiliation(s)
- Anita Kumari
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel.
| | - Varun Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel.
| | - Rinat Ovadia
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel.
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel.
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4
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Wang R, Liu K, Tang B, Su D, He X, Deng H, Wu M, Bouzayen M, Grierson D, Liu M. The MADS-box protein SlTAGL1 regulates a ripening-associated SlDQD/SDH2 involved in flavonoid biosynthesis and resistance against Botrytis cinerea in post-harvest tomato fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1746-1757. [PMID: 37326247 DOI: 10.1111/tpj.16354] [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: 12/06/2022] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
3-Dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) is a key rate-limiting enzyme that catalyzes the synthesis of the shikimate, which is an important metabolic intermediate in plants and animals. However, the function of SlDQD/SDH family genes in tomato (Solanum lycopersicum) fruit metabolites is still unknown. In the present study, we identified a ripening-associated SlDQD/SDH member, SlDQD/SDH2, that plays a key role in shikimate and flavonoid metabolism. Overexpression of this gene resulted in an increased content of shikimate and flavonoids, while knockout of this gene by CRISPR/Cas9 mediated gene editing led to a significantly lower content of shikimate and flavonoids by downregulation of flavonoid biosynthesis-related genes. Moreover, we showed that SlDQD/SDH2 confers resistance against Botrytis cinerea attack in post-harvest tomato fruit. Dual-luciferase reporter and EMSA assays indicated that SlDQD/SDH2 is a direct target of the key ripening regulator SlTAGL1. In general, this study provided a new insight into the biosynthesis of flavonoid and B. cinerea resistance in fruit tomatoes.
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Affiliation(s)
- Ruochen Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Bei Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Dan Su
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xiaoqing He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Heng Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Mengbo Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Mondher Bouzayen
- GBF Laboratory, Université de Toulouse, INRA, Castanet-Tolosan, 31320, France
| | - Don Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
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5
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Lin CY, Tian Y, Nelson-Vasilchik K, Hague J, Kakumanu R, Lee MY, Pidatala VR, Trinh J, De Ben CM, Dalton J, Northen TR, Baidoo EEK, Simmons BA, Gladden JM, Scown CD, Putnam DH, Kausch AP, Scheller HV, Eudes A. Engineering sorghum for higher 4-hydroxybenzoic acid content. Metab Eng Commun 2022; 15:e00207. [PMID: 36188638 PMCID: PMC9519784 DOI: 10.1016/j.mec.2022.e00207] [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: 06/25/2022] [Revised: 07/25/2022] [Accepted: 09/19/2022] [Indexed: 11/01/2022] Open
Abstract
Engineering bioenergy crops to accumulate coproducts in planta can increase the value of lignocellulosic biomass and enable a sustainable bioeconomy. In this study, we engineered sorghum with a bacterial gene encoding a chorismate pyruvate-lyase (ubiC) to reroute the plastidial pool of chorismate from the shikimate pathway into the valuable compound 4-hydroxybenzoic acid (4-HBA). A gene encoding a feedback-resistant version of 3-deoxy-d-arabino-heptulonate-7-phosphate synthase (aroG) was also introduced in an attempt to increase the carbon flux through the shikimate pathway. At the full maturity and senesced stage, two independent lines that co-express ubiC and aroG produced 1.5 and 1.7 dw% of 4-HBA in biomass, which represents 36- and 40-fold increases compared to the titer measured in wildtype. The two transgenic lines showed no obvious phenotypes, growth defects, nor alteration of cell wall polysaccharide content when cultivated under controlled conditions. In the field, when harvested before grain maturity, transgenic lines contained 0.8 and 1.2 dw% of 4-HBA, which represent economically relevant titers based on recent technoeconomic analysis. Only a slight reduction (11-15%) in biomass yield was observed in transgenics grown under natural environment. This work provides the first metabolic engineering steps toward 4-HBA overproduction in the bioenergy crop sorghum to improve the economics of biorefineries by accumulating a value-added coproduct that can be recovered from biomass and provide an additional revenue stream.
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Affiliation(s)
- Chien-Yuan Lin
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yang Tian
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Joel Hague
- Department of Cell and Molecular Biology, University of Rhode Island, Rhode Island, RI, 02892, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mi Yeon Lee
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Venkataramana R Pidatala
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jessica Trinh
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher M De Ben
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Jutta Dalton
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Corinne D Scown
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Energy & Biosciences Institute, University of California-Berkeley, Berkeley, CA, 94720, USA.,Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel H Putnam
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Albert P Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, Rhode Island, RI, 02892, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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6
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Li Q, Fang X, Zhao Y, Cao R, Dong J, Ma P. The SmMYB36-SmERF6/SmERF115 module regulates the biosynthesis of tanshinones and phenolic acids in salvia miltiorrhiza hairy roots. HORTICULTURE RESEARCH 2022; 10:uhac238. [PMID: 36643739 PMCID: PMC9832864 DOI: 10.1093/hr/uhac238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/16/2022] [Indexed: 06/17/2023]
Abstract
Tanshinone and phenolic acids are the most important active substances of Salvia miltiorrhiza, and the insight into their transcriptional regulatory mechanisms is an essential process to increase their content in vivo. SmMYB36 has been found to have important regulatory functions in the synthesis of tanshinone and phenolic acid; paradoxically, its mechanism of action in S. miltiorrhiza is not clear. Here, we demonstrated that SmMYB36 functions as a promoter of tanshinones accumulation and a suppressor of phenolic acids through the generation of SmMYB36 overexpressed and chimeric SmMYB36-SRDX (EAR repressive domain) repressor hairy roots in combination with transcriptomic-metabolomic analysis. SmMYB36 directly down-regulate the key enzyme gene of primary metabolism, SmGAPC, up-regulate the tanshinones biosynthesis branch genes SmDXS2, SmGGPPS1, SmCPS1 and down-regulate the phenolic acids biosynthesis branch enzyme gene, SmRAS. Meanwhile, SmERF6, a positive regulator of tanshinone synthesis activating SmCPS1, was up-regulated and SmERF115, a positive regulator of phenolic acid biosynthesis activating SmRAS, was down-regulated. Furthermore, the seven acidic amino acids at the C-terminus of SmMYB36 are required for both self-activating domain and activation of target gene expression. As a consequence, this study contributes to reveal the potential relevance of transcription factors synergistically regulating the biosynthesis of tanshinone and phenolic acid.
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Affiliation(s)
| | | | | | - Ruizhi Cao
- College of Life Sciences, Northwest A&F University, Yangling 71210, China
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7
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Skaliter O, Livneh Y, Agron S, Shafir S, Vainstein A. A whiff of the future: functions of phenylalanine-derived aroma compounds and advances in their industrial production. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1651-1669. [PMID: 35638340 PMCID: PMC9398379 DOI: 10.1111/pbi.13863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 05/19/2023]
Abstract
Plants produce myriad aroma compounds-odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry ketone and vanillin. In the last decade, great strides have been made in elucidating this pathway with the identification of numerous aroma-related biosynthetic enzymes and factors regulating metabolic shunts. These scientific achievements, together with public acknowledgment of aroma compounds' medicinal benefits and growing consumer demand for natural products, are driving the development of novel biological sources for wide-scale, eco-friendly, and inexpensive production. Microbes and plants that are readily amenable to metabolic engineering are garnering attention as suitable platforms for achieving this goal. In this review, we discuss the importance of aroma compounds from the perspectives of humans, pollinators and plant-plant interactions. Focusing on vanillin and raspberry ketone, which are of high interest to the industry, we present key knowledge on the biosynthesis and regulation of phenylalanine-derived aroma compounds, describe advances in the adoption of microbes and plants as platforms for their production, and propose routes for improvement.
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Affiliation(s)
- Oded Skaliter
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Yarin Livneh
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Shani Agron
- Department of NeurobiologyThe Weizmann Institute of ScienceRehovotIsrael
| | - Sharoni Shafir
- B. Triwaks Bee Research Center, Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
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8
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Lou H, Yang Y, Zheng S, Ma Z, Chen W, Yu C, Song L, Wu J. Identification of key genes contributing to amino acid biosynthesis in Torreya grandis using transcriptome and metabolome analysis. Food Chem 2022; 379:132078. [PMID: 35063846 DOI: 10.1016/j.foodchem.2022.132078] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/29/2022]
Abstract
Torreya grandis has high economic and nutritional value due to the high nutrients in its kernels. The kernels of different development stages vary enormously in their amino acids content. However, the molecular basis and the regulatory mechanism of amino acid biosynthesis remain unclear. Here, transcriptome and metabolome analysis were performed. Correlation analysis result showed that 4 unigenes were significantly and positively correlated with at least 10 amino acids. The full length CDS of 2 unigenes (TgDAHP2 and TgASA1) were successfully cloned from the 4 unigenes for DAHP, ASA and CITS. Subcelluar localization analysis showed that both TgDAHP2 and TgASA1 were localized to the chloroplast. Overexpression of TgDAHP2 and TgASA1 in Arabidopsis can greatly increase the content of most amino acids. Moreover, 3 transcription factors were found to positively regulate the expression of TgASA1. This research contributes to understand the molecular regulatory mechanisms of amino acid biosynthesis in T. grandis.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yi Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhenmin Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
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9
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Yokoyama R, de Oliveira MVV, Takeda-Kimura Y, Ishihara H, Alseekh S, Arrivault S, Kukshal V, Jez JM, Stitt M, Fernie AR, Maeda HA. Point mutations that boost aromatic amino acid production and CO 2 assimilation in plants. SCIENCE ADVANCES 2022; 8:eabo3416. [PMID: 35675400 PMCID: PMC9176744 DOI: 10.1126/sciadv.abo3416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Aromatic compounds having unusual stability provide high-value chemicals and considerable promise for carbon storage. Terrestrial plants can convert atmospheric CO2 into diverse and abundant aromatic compounds. However, it is unclear how plants control the shikimate pathway that connects the photosynthetic carbon fixation with the biosynthesis of aromatic amino acids, the major precursors of plant aromatic natural products. This study identified suppressor of tyra2 (sota) mutations that deregulate the first step in the plant shikimate pathway by alleviating multiple effector-mediated feedback regulation in Arabidopsis thaliana. The sota mutant plants showed hyperaccumulation of aromatic amino acids accompanied by up to a 30% increase in net CO2 assimilation. The identified mutations can be used to enhance plant-based, sustainable conversion of atmospheric CO2 to high-energy and high-value aromatic compounds.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Hirofumi Ishihara
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Vandna Kukshal
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mark Stitt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Hiroshi A. Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
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10
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Yokoyama R, Kleven B, Gupta A, Wang Y, Maeda HA. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase as the gatekeeper of plant aromatic natural product biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102219. [PMID: 35550985 DOI: 10.1016/j.pbi.2022.102219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The shikimate pathway connects the central carbon metabolism with the biosynthesis of aromatic amino acids-l-tyrosine, l-phenylalanine, and l-tryptophan-which play indispensable roles as precursors of numerous aromatic phytochemicals. Despite the importance of the shikimate pathway-derived products for both plant physiology and human society, the regulatory mechanism of the shikimate pathway remains elusive. This review summarizes the recent progress and current understanding on the plant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHP synthase or DHS) enzymes that catalyze the committed reaction of the shikimate pathway. We particularly focus on how the DHS activity is regulated in plants in comparison to those of microbes and discuss potential roles of DHS as the critical gatekeeper for the production of plant aromatic compounds.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| | - Bailey Kleven
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Anika Gupta
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yuer Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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11
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Ghai D, Kaur A, Kahlon PS, Pawar SV, Sembi JK. A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:837563. [PMID: 35574139 PMCID: PMC9100589 DOI: 10.3389/fpls.2022.837563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.
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Affiliation(s)
- Devina Ghai
- Department of Botany, Panjab University, Chandigarh, India
| | - Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, India
| | - Parvinderdeep S. Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sandip V. Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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12
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Fiesel PD, Parks HM, Last RL, Barry CS. Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae. Nat Prod Rep 2022; 39:1438-1464. [PMID: 35332352 DOI: 10.1039/d2np00003b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary metabolites, are conserved across the plant kingdom and are required for processes essential to growth and development. These include amino acids, sugars, lipids, and organic acids. In contrast, specialized metabolites, historically termed secondary metabolites, are structurally diverse, exhibit lineage-specific distribution and provide selective advantage to host species to facilitate reproduction and environmental adaptation. Due to their potent bioactivities, plant specialized metabolites attract considerable attention for use as flavorings, fragrances, pharmaceuticals, and bio-pesticides. The Solanaceae (Nightshade family) consists of approximately 2700 species and includes crops of significant economic, cultural, and scientific importance: these include potato, tomato, pepper, eggplant, tobacco, and petunia. The Solanaceae has emerged as a model family for studying the biochemical evolution of plant specialized metabolism and multiple examples exist of lineage-specific metabolites that influence the senses and physiology of commensal and harmful organisms, including humans. These include, alcohols, phenylpropanoids, and carotenoids that contribute to fruit aroma and color in tomato (fruity), glandular trichome-derived terpenoids and acylsugars that contribute to plant defense (stinky & sticky, respectively), capsaicinoids in chilli-peppers that influence seed dispersal (spicy), and steroidal glycoalkaloids (bitter) from Solanum, nicotine (addictive) from tobacco, as well as tropane alkaloids (deadly) from Deadly Nightshade that deter herbivory. Advances in genomics and metabolomics, coupled with the adoption of comparative phylogenetic approaches, resulted in deeper knowledge of the biosynthesis and evolution of these metabolites. This review highlights recent progress in this area and outlines opportunities for - and challenges of-developing a more comprehensive understanding of Solanaceae metabolism.
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Affiliation(s)
- Paul D Fiesel
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Hannah M Parks
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L Last
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
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13
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Xu Q, Niu SC, Li KL, Zheng PJ, Zhang XJ, Jia Y, Liu Y, Niu YX, Yu LH, Chen DF, Zhang GQ. Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium. Front Genet 2022; 13:844622. [PMID: 35299950 PMCID: PMC8921531 DOI: 10.3389/fgene.2022.844622] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 01/07/2023] Open
Abstract
Orchids constitute approximately 10% of flowering plant species. However, only about 10 orchid genomes have been published. Metabolites are the main way through which orchids respond to their environment. Dendrobium nobile, belonging to Dendrobium, the second largest genus in Orchidaceae, has high ornamental, medicinal, and ecological value. D. nobile is the source of many popular horticultural varieties. Among the Dendrobium species, D. nobile has the highest amount of dendrobine, which is regarded as one of the criteria for evaluating medicinal quality. Due to lack of data and analysis at the genomic level, the biosynthesis pathways of dendrobine and other related medicinal ingredients in D. nobile are unknown. In this paper, we report a chromosome-scale reference genome of D. nobile to facilitate the investigation of its genomic characteristics for comparison with other Dendrobium species. The assembled genome size of D. nobile was 1.19 Gb. Of the sequences, 99.45% were anchored to 19 chromosomes. Furthermore, we identified differences in gene number and gene expression patterns compared with two other Dendrobium species by integrating whole-genome sequencing and transcriptomic analysis [e.g., genes in the polysaccharide biosynthesis pathway and upstream of the alkaloid (dendrobine) biosynthesis pathway]. Differences in the TPS and CYP450 gene families were also found among orchid species. All the above differences might contribute to the species-specific medicinal ingredient biosynthesis pathways. The metabolic pathway-related analysis will provide further insight into orchid responses to the environment. Additionally, the reference genome will provide important insights for further molecular elucidation of the medicinal active ingredients of Dendrobium and enhance the understanding of orchid evolution.
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Affiliation(s)
- Qing Xu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| | - Shan-Ce Niu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Kang-Li Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Pei-Ji Zheng
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Jing Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yin Jia
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yang Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yun-Xia Niu
- School of Vocational Education, Tianjin University of Technology and Education, Tianjin, China
| | - Li-Hong Yu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Duan-Fen Chen
- College of Horticulture, Hebei Agricultural University, Baoding, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| | - Guo-Qiang Zhang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- Laboratory for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, The National Orchid Conservation Center of China, Shenzhen, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
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14
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Kanaris M, Poulin J, Shahinas D, Johnson D, Crowley VM, Fucile G, Provart N, Christendat D. Elevated tyrosine results in the cytosolic retention of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:789-803. [PMID: 34797933 DOI: 10.1111/tpj.15590] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
The shikimate pathway plays a central role in the biosynthesis of aromatic amino acids and specialized metabolites in plants. The first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) serves as a key regulatory point for the pathway in various organisms. These enzymes are important in regulating the shikimate pathway in multiple microbial systems. The mechanism of regulation of DAHPS is poorly understood in plants, and the role of tyrosine (Tyr) with respect to the three DAHPS isozymes from Arabidopsis thaliana was investigated. In vitro enzymatic analyses established that Tyr does not function as an allosteric regulator for the A. thaliana DAHPS isozymes. In contrast, Arabidopsis T-DNA insertional mutants for the DAHPS1 locus, dahps1, are hypersensitive to elevated Tyr. Tyr hypersensitivity can be reversed with tryptophan and phenylalanine supplementation, indicating that Tyr is affecting the shikimate pathway flux in the dahps1 mutant. Tyr treatment of Arabidopsis seedlings showed reduced accumulation of overexpressed DAHPS2 in the chloroplast. Further, bimolecular fluorescence complementation studies revealed that DAHPS2 interacts with a 14-3-3 protein in the cytosol, and this interaction is enhanced with Tyr treatment. This interaction with 14-3-3 may retain DAHPS2 in the cytosol, which prevents its ability to function in the chloroplast with elevated Tyr.
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Affiliation(s)
- Michael Kanaris
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Jimmy Poulin
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Dea Shahinas
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Daniel Johnson
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Valerie M Crowley
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Geoffrey Fucile
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
- Center for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
- Center for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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15
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Gámez-Arcas S, Baroja-Fernández E, García-Gómez P, Muñoz FJ, Almagro G, Bahaji A, Sánchez-López ÁM, Pozueta-Romero J. Action mechanisms of small microbial volatile compounds in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:498-510. [PMID: 34687197 DOI: 10.1093/jxb/erab463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/21/2021] [Indexed: 05/22/2023]
Abstract
Microorganisms communicate with plants by exchanging chemical signals throughout the phytosphere. Before direct contact with plants occurs, beneficial microorganisms emit a plethora of volatile compounds that promote plant growth and photosynthesis as well as developmental, metabolic, transcriptional, and proteomic changes in plants. These compounds can also induce systemic drought tolerance and improve water and nutrient acquisition. Recent studies have shown that this capacity is not restricted to beneficial microbes; it also extends to phytopathogens. Plant responses to microbial volatile compounds have frequently been associated with volatile organic compounds with molecular masses ranging between ~ 45Da and 300Da. However, microorganisms also release a limited number of volatile compounds with molecular masses of less than ~45Da that react with proteins and/or act as signaling molecules. Some of these compounds promote photosynthesis and growth when exogenously applied in low concentrations. Recently, evidence has shown that small volatile compounds are important determinants of plant responses to microbial volatile emissions. However, the regulatory mechanisms involved in these responses remain poorly understood. This review summarizes current knowledge of biochemical and molecular mechanisms involved in plant growth, development, and metabolic responses to small microbial volatile compounds.
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Affiliation(s)
- Samuel Gámez-Arcas
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Iruñako etorbidea 123, 31192 Mutiloabeti, Nafarroa, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Iruñako etorbidea 123, 31192 Mutiloabeti, Nafarroa, Spain
| | - Pablo García-Gómez
- Plant Nutrition Department, Centro de Edafología y Biología Aplicada (CEBAS-CSIC), Campus Universitario de Espinardo, Espinardo, 30100 Murcia, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Iruñako etorbidea 123, 31192 Mutiloabeti, Nafarroa, Spain
| | - Goizeder Almagro
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Iruñako etorbidea 123, 31192 Mutiloabeti, Nafarroa, Spain
| | - Abdellatif Bahaji
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Iruñako etorbidea 123, 31192 Mutiloabeti, Nafarroa, Spain
| | - Ángela María Sánchez-López
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Iruñako etorbidea 123, 31192 Mutiloabeti, Nafarroa, Spain
| | - Javier Pozueta-Romero
- Institute for Mediterranean and Subtropical Horticulture 'La Mayora' (IHSM-UMA-CSIC), Campus de Teatinos, Avda. Louis Pasteur, 49, 29010 Málaga, Spain
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16
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Yoo H, Shrivastava S, Lynch JH, Huang XQ, Widhalm JR, Guo L, Carter BC, Qian Y, Maeda HA, Ogas JP, Morgan JA, Marshall-Colón A, Dudareva N. Overexpression of arogenate dehydratase reveals an upstream point of metabolic control in phenylalanine biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:737-751. [PMID: 34403557 DOI: 10.1111/tpj.15467] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Out of the three aromatic amino acids, the highest flux in plants is directed towards phenylalanine, which is utilized to synthesize proteins and thousands of phenolic metabolites contributing to plant fitness. Phenylalanine is produced predominantly in plastids via the shikimate pathway and subsequent arogenate pathway, both of which are subject to complex transcriptional and post-transcriptional regulation. Previously, it was shown that allosteric feedback inhibition of arogenate dehydratase (ADT), which catalyzes the final step of the arogenate pathway, restricts flux through phenylalanine biosynthesis. Here, we show that in petunia (Petunia hybrida) flowers, which typically produce high phenylalanine levels, ADT regulation is relaxed, but not eliminated. Moderate expression of a feedback-insensitive ADT increased flux towards phenylalanine, while high overexpression paradoxically reduced phenylalanine formation. This reduction could be partially, but not fully, recovered by bypassing other known metabolic flux control points in the aromatic amino acid network. Using comparative transcriptomics, reverse genetics, and metabolic flux analysis, we discovered that transcriptional regulation of the d-ribulose-5-phosphate 3-epimerase gene in the pentose phosphate pathway controls flux into the shikimate pathway. Taken together, our findings reveal that regulation within and upstream of the shikimate pathway shares control over phenylalanine biosynthesis in the plant cell.
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Affiliation(s)
- Heejin Yoo
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Stuti Shrivastava
- Department of Plant Biology, University of Illinois Urbana-Champaign, 265 Morrill Hall, MC-116, Urbana, IL, 61801, USA
| | - Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Xing-Qi Huang
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Benjamin C Carter
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Yichun Qian
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI, 53706, USA
| | - Joseph P Ogas
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - John A Morgan
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., West Lafayette, IN, 47907-2100, USA
| | - Amy Marshall-Colón
- Department of Plant Biology, University of Illinois Urbana-Champaign, 265 Morrill Hall, MC-116, Urbana, IL, 61801, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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17
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Jin H, Wang Y, Zhao P, Wang L, Zhang S, Meng D, Yang Q, Cheong LZ, Bi Y, Fu Y. Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12385-12401. [PMID: 34649432 DOI: 10.1021/acs.jafc.1c04632] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Numerous plant secondary metabolites have remarkable impacts on both food supplements and pharmaceuticals for human health improvement. However, higher plants can only generate small amounts of these chemicals with specific temporal and spatial arrangements, which are unable to satisfy the expanding market demands. Cyanobacteria can directly utilize CO2, light energy, and inorganic nutrients to synthesize versatile plant-specific photosynthetic intermediates and organic compounds in large-scale photobioreactors with outstanding economic merit. Thus, they have been rapidly developed as a "green" chassis for the synthesis of bioproducts. Flavonoids, chemical compounds based on aromatic amino acids, are considered to be indispensable components in a variety of nutraceutical, pharmaceutical, and cosmetic applications. In contrast to heterotrophic metabolic engineering pioneers, such as yeast and Escherichia coli, information about the biosynthesis flavonoids and their derivatives is less comprehensive than that of their photosynthetic counterparts. Here, we review both benefits and challenges to promote cyanobacterial cell factories for flavonoid biosynthesis. With increasing concerns about global environmental issues and food security, we are confident that energy self-supporting cyanobacteria will attract increasing attention for the generation of different kinds of bioproducts. We hope that the work presented here will serve as an index and encourage more scientists to join in the relevant research area.
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Affiliation(s)
- Haojie Jin
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yan Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Pengquan Zhao
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Litao Wang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Su Zhang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Dong Meng
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Qing Yang
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
| | - Ling-Zhi Cheong
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Yonghong Bi
- State Key Laboratory of Fresh Water Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, P.R. China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing 100083, P.R. China
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18
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Wang R, Lenka SK, Kumar V, Sikron-Persi N, Dynkin I, Weiss D, Perl A, Fait A, Oren-Shamir M. A Synchronized Increase of Stilbenes and Flavonoids in Metabolically Engineered Vitis vinifera cv. Gamay Red Cell Culture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7922-7931. [PMID: 34236173 DOI: 10.1021/acs.jafc.1c02119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Stilbenes and flavonoids are two major health-promoting phenylpropanoid groups in grapes. Attempts to promote the accumulation of one group usually resulted in a decrease in the other. This study presents a unique strategy for simultaneously increasing metabolites in both groups in V. vinifera cv. Gamay Red grape cell culture, by overexpression of flavonol synthase (FLS) and increasing Phe availability. Increased Phe availability was achieved by transforming the cell culture with a second gene, the feedback-insensitive E. coli DAHP synthase (AroG*), and feeding them with Phe. A combined metabolomic and transcriptomic analysis reveals that the increase in both phenylpropanoid groups is accompanied by an induction of many of the flavonoid biosynthetic genes and no change in the expression levels of stilbene synthase. Furthermore, FLS overexpression with increased Phe availability resulted in higher anthocyanin levels, mainly those derived from delphinidin, due to the induction of F3'5'H. These insights may contribute to the development of grape berries with increased health benefits.
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Affiliation(s)
- Ru Wang
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159 Rishon LeZion 7505101, Israel
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Sangram Keshari Lenka
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159 Rishon LeZion 7505101, Israel
| | - Varun Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159 Rishon LeZion 7505101, Israel
| | - Noga Sikron-Persi
- French Associates Institute for Agriculture & Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 849900, Israel
| | - Irena Dynkin
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159 Rishon LeZion 7505101, Israel
| | - David Weiss
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Avichai Perl
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159 Rishon LeZion 7505101, Israel
| | - Aaron Fait
- French Associates Institute for Agriculture & Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 849900, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159 Rishon LeZion 7505101, Israel
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19
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Yokoyama R, de Oliveira MVV, Kleven B, Maeda HA. The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation. THE PLANT CELL 2021; 33:671-696. [PMID: 33955484 PMCID: PMC8136874 DOI: 10.1093/plcell/koaa042] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/19/2020] [Indexed: 05/22/2023]
Abstract
The plant shikimate pathway directs bulk carbon flow toward biosynthesis of aromatic amino acids (AAAs, i.e. tyrosine, phenylalanine, and tryptophan) and numerous aromatic phytochemicals. The microbial shikimate pathway is feedback inhibited by AAAs at the first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DHS). However, AAAs generally do not inhibit DHS activities from plant extracts and how plants regulate the shikimate pathway remains elusive. Here, we characterized recombinant Arabidopsis thaliana DHSs (AthDHSs) and found that tyrosine and tryptophan inhibit AthDHS2, but not AthDHS1 or AthDHS3. Mixing AthDHS2 with AthDHS1 or 3 attenuated its inhibition. The AAA and phenylpropanoid pathway intermediates chorismate and caffeate, respectively, strongly inhibited all AthDHSs, while the arogenate intermediate counteracted the AthDHS1 or 3 inhibition by chorismate. AAAs inhibited DHS activity in young seedlings, where AthDHS2 is highly expressed, but not in mature leaves, where AthDHS1 is predominantly expressed. Arabidopsis dhs1 and dhs3 knockout mutants were hypersensitive to tyrosine and tryptophan, respectively, while dhs2 was resistant to tyrosine-mediated growth inhibition. dhs1 and dhs3 also had reduced anthocyanin accumulation under high light stress. These findings reveal the highly complex regulation of the entry reaction of the plant shikimate pathway and lay the foundation for efforts to control the production of AAAs and diverse aromatic natural products in plants.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Marcos V V de Oliveira
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Bailey Kleven
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
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20
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Fang F, Oliva M, Ovadia R, Bar E, Nissim-Levi A, Kumar V, Wang R, Neeman A, Zaccai M, Lewinsohn E, Oren-Shamir M. Increased substrate availability reveals the potential of scentless lisianthus flowers in producing fragrant benzenoid-phenylpropanoids. PHYSIOLOGIA PLANTARUM 2021; 172:19-28. [PMID: 33161590 DOI: 10.1111/ppl.13264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
Lisianthus (Eustoma grandiflorum), a leading plant in the cut flower industry, is scentless. Here we show that lisianthus flowers have potential to produce several fragrant benzenoid-phenylpropanoids when substrate availability is not limited. To enable hyperaccumulation of substrates for the production of volatile benzenoid-phenylpropanoids, lisianthus commercial hybrid "Excalibur Pink" was transformed via floral dipping with a feedback-insensitive Escherichia coli DAHP synthase (AroG*) and Clarkia breweri benzyl alcohol acetyltransferase (BEAT), under constitutive promoters. The T1 progeny of "Excalibur Pink" plants segregated into four visual phenotypes, with pink or white colored petals and multiple or single petal layers. Interestingly, transformation with AroG* and BEAT caused no significant effect in the pigment composition among phenotypes, but did increase the levels of down-stream fragrant volatile benzenoids. All the transgenic lines exclusively accumulated methyl benzoate, a fragrant benzenoid, either in their petals or leaves. Furthermore, feeding with benzyl alcohol resulted in the accumulation of two novel benzenoids, benzyl acetate (the product of BEAT) and benzoate, as well as a dramatic increase in the concentrations of additional benzenoid-phenylpropanoid volatiles. Presumably, the degree of benzaldehyde overproduction after benzyl alcohol feeding in both leaves and flowers revealed their reverse conversion in lisianthus plants. These findings demonstrate the concealed capability of lisianthus plants to produce a wide array of fragrant benzenoid-phenylpropanoids, given high substrate concentrations, which could in turn open opportunities for future scent engineering.
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Affiliation(s)
- Fang Fang
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
| | - Moran Oliva
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rinat Ovadia
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
| | - Einat Bar
- Department of Vegetable Crops, Agriculture Research Organization, Newe Ya'ar Research Center, Volcani Center, Ramat Yishay, Israel
| | - Ada Nissim-Levi
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
| | - Varun Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
| | - Ru Wang
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
| | - Agmon Neeman
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
| | - Michele Zaccai
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Efraim Lewinsohn
- Department of Vegetable Crops, Agriculture Research Organization, Newe Ya'ar Research Center, Volcani Center, Ramat Yishay, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Rishon LeZion, Israel
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21
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In-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-product. Metab Eng 2021; 66:148-156. [PMID: 33895365 DOI: 10.1016/j.ymben.2021.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/18/2021] [Indexed: 02/07/2023]
Abstract
2-Pyrone-4,6-dicarboxylic acid (PDC), a chemically stable intermediate that naturally occurs during microbial degradation of lignin by bacteria, represents a promising building block for diverse biomaterials and polyesters such as biodegradable plastics. The lack of a chemical synthesis method has hindered large-scale utilization of PDC and metabolic engineering approaches for its biosynthesis have recently emerged. In this study, we demonstrate a strategy for the production of PDC via manipulation of the shikimate pathway using plants as green factories. In tobacco leaves, we first showed that transient expression of bacterial feedback-resistant 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (AroG) and 3-dehydroshikimate dehydratase (QsuB) produced high titers of protocatechuate (PCA), which was in turn efficiently converted into PDC upon co-expression of PCA 4,5-dioxygenase (PmdAB) and 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (PmdC) derived from Comamonas testosteroni. We validated that stable expression of AroG in Arabidopsis in a genetic background containing the QsuB gene enhanced PCA content in plant biomass, presumably via an increase of the carbon flux through the shikimate pathway. Further, introducing AroG and the PDC biosynthetic genes (PmdA, PmdB, and PmdC) into the Arabidopsis QsuB background, or introducing the five genes (AroG, QsuB, PmdA, PmdB, and PmdC) stacked on a single construct into wild-type plants, resulted in PDC titers of ~1% and ~3% dry weight in plant biomass, respectively. Consistent with previous studies of plants expressing QsuB, all PDC producing lines showed strong reduction in lignin content in stems. This low lignin trait was accompanied with improvements of biomass saccharification efficiency due to reduced cell wall recalcitrance to enzymatic degradation. Importantly, most transgenic lines showed no reduction in biomass yields. Therefore, we conclude that engineering plants with the proposed de-novo PDC pathway provides an avenue to enrich biomass with a value-added co-product while simultaneously improving biomass quality for the supply of fermentable sugars. Implementing this strategy into bioenergy crops has the potential to support existing microbial fermentation approaches that exploit lignocellulosic biomass feedstocks for PDC production.
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22
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Engineering insect resistance using plant specialized metabolites. Curr Opin Biotechnol 2021; 70:115-121. [PMID: 33866214 DOI: 10.1016/j.copbio.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
Plants in nature are protected against insect herbivory by a wide variety of specialized metabolites. Although insect herbivores generally tolerate the defensive metabolites of their preferred host plants, the presence of additional chemical defenses in otherwise closely related plant species can nevertheless provide resistance. This chemical resistance to insect herbivory can be enhanced by genetic engineering to increase the production of endogenous defensive metabolites, modify existing biochemical pathways, or move the biosynthesis of entirely new classes of specialized metabolites into recipient plants. However, current plant genetic engineering strategies are limited by insufficient knowledge of the biosynthetic pathways of plant specialized metabolism, unintended side-effects that result from redirecting plant metabolism, inadequate transgene construction and delivery methods, and requirements for tissue-specific production of defensive metabolites to enhance herbivore resistance.
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23
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Wang R, Lenka SK, Kumar V, Gashu K, Sikron-Persi N, Dynkin I, Weiss D, Perl A, Fait A, Oren-Shamir M. Metabolic Engineering Strategy Enables a Hundred-Fold Increase in Viniferin Levels in Vitis vinifera cv. Gamay Red Cell Culture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3124-3133. [PMID: 33683879 DOI: 10.1021/acs.jafc.0c08086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Stilbenes are phytoalexins with health-promoting benefits for humans. Here, we boost stilbenes' production, and in particular the resveratrol dehydrodimer viniferin, with significant pharmacological properties, by overexpressing stilbene synthase (STS) under unlimited phenylalanine (Phe) supply. Vitis vinifera cell cultures were co-transformed with a feedback-insensitive E. coli DAHP synthase (AroG*) and STS genes, under constitutive promoters. All transgenic lines had increased levels of Phe and stilbenes (74-fold higher viniferin reaching 0.74 mg/g DW). External Phe feeding of AroG* + STS lines caused a synergistic effect on resveratrol and viniferin accumulation, achieving a 26-fold (1.33 mg/g DW) increase in resveratrol and a 620-fold increase (6.2 mg/g DW) in viniferin, which to date is the highest viniferin accumulation reported in plant cultures. We suggest that this strategy of combining higher Phe availability and STS expression generates grape cell cultures as potential factories for sustainable production of stilbenes with a minor effect on the levels of flavonoids.
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Affiliation(s)
- Ru Wang
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Sangram Keshari Lenka
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Varun Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Kelem Gashu
- Ben-Gurion University of the Negev, Jacob Blaustein Insts. for Desert Research, French Associates Institute for Agriculture & Biotechnology of Drylands, Midreshet Ben-Gurion 849900, Israel
| | - Noga Sikron-Persi
- Ben-Gurion University of the Negev, Jacob Blaustein Insts. for Desert Research, French Associates Institute for Agriculture & Biotechnology of Drylands, Midreshet Ben-Gurion 849900, Israel
| | - Irena Dynkin
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - David Weiss
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Avichai Perl
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Aaron Fait
- Ben-Gurion University of the Negev, Jacob Blaustein Insts. for Desert Research, French Associates Institute for Agriculture & Biotechnology of Drylands, Midreshet Ben-Gurion 849900, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
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24
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Jin L, Wang D, Mu Y, Guo Y, Lin Y, Qiu L, Pan Y. Proteomics analysis reveals that foreign cp4-epsps gene regulates the levels of shikimate and branched pathways in genetically modified soybean line H06-698. GM CROPS & FOOD 2021; 12:497-508. [PMID: 34984949 PMCID: PMC9208623 DOI: 10.1080/21645698.2021.2000320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022]
Abstract
Although genetically modified (GM) glyphosate-resistant soybeans with cp4-epsps gene have been widely planted all over the world, their proteomic characteristics are not very clear. In this study, the soybean seeds of a GM soybean line H06-698 (H) with cp4-epsps gene and its non-transgenic counterpart Mengdou12 (M), which were collected from two experiment fields in two years and used as 4 sample groups, were analyzed with label-free proteomics technique. A total of 1706 proteins were identified quantitatively by label-free quantification, and a total of 293 proteins were detected as common differential abundance proteins (DAPs, FC is not less than 1.5) both in two groups or more. Functional enrichment analysis of common DAPs identified from four groups, shows that most up-regulated proteins were clustered into stress response, carbon and energy metabolism, and genetic information processing. Further documentary analysis shows that 15 proteins play important roles in shikimate pathways, reactive oxygen species (ROS) and stress response. These results indicated that the change of protein abundance in different samples were affected by various factors, but except shikimate and branched pathways related proteins, only ROS and stress-related proteins were found to be stably regulated by cp4-epsps gene, and no unexpected and safety-related proteins such as antinutritional factors, allergenic proteins, and toxic proteins were found as DAPs. The influence of foreign genes in genetically modified plants is worthy of attention and this work provides new clues for exploring the regulated proteins and pathways in GM plants.
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Affiliation(s)
- Longguo Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daoping Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongying Mu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangjie Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinghong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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25
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Ameztoy K, Sánchez-López ÁM, Muñoz FJ, Bahaji A, Almagro G, Baroja-Fernández E, Gámez-Arcas S, De Diego N, Doležal K, Novák O, Pěnčík A, Alpízar A, Rodríguez-Concepción M, Pozueta-Romero J. Proteostatic Regulation of MEP and Shikimate Pathways by Redox-Activated Photosynthesis Signaling in Plants Exposed to Small Fungal Volatiles. FRONTIERS IN PLANT SCIENCE 2021; 12:637976. [PMID: 33747018 PMCID: PMC7973468 DOI: 10.3389/fpls.2021.637976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 05/07/2023]
Abstract
Microorganisms produce volatile compounds (VCs) with molecular masses of less than 300 Da that promote plant growth and photosynthesis. Recently, we have shown that small VCs of less than 45 Da other than CO2 are major determinants of plant responses to fungal volatile emissions. However, the regulatory mechanisms involved in the plants' responses to small microbial VCs remain unclear. In Arabidopsis thaliana plants exposed to small fungal VCs, growth promotion is accompanied by reduction of the thiol redox of Calvin-Benson cycle (CBC) enzymes and changes in the levels of shikimate and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway-related compounds. We hypothesized that plants' responses to small microbial VCs involve post-translational modulation of enzymes of the MEP and shikimate pathways via mechanisms involving redox-activated photosynthesis signaling. To test this hypothesis, we compared the responses of wild-type (WT) plants and a cfbp1 mutant defective in a redox-regulated isoform of the CBC enzyme fructose-1,6-bisphosphatase to small VCs emitted by the fungal phytopathogen Alternaria alternata. Fungal VC-promoted growth and photosynthesis, as well as metabolic and proteomic changes, were substantially weaker in cfbp1 plants than in WT plants. In WT plants, but not in cfbp1 plants, small fungal VCs reduced the levels of both transcripts and proteins of the stromal Clp protease system and enhanced those of plastidial chaperonins and co-chaperonins. Consistently, small fungal VCs promoted the accumulation of putative Clp protease clients including MEP and shikimate pathway enzymes. clpr1-2 and clpc1 mutants with disrupted plastidial protein homeostasis responded weakly to small fungal VCs, strongly indicating that plant responses to microbial volatile emissions require a finely regulated plastidial protein quality control system. Our findings provide strong evidence that plant responses to fungal VCs involve chloroplast-to-nucleus retrograde signaling of redox-activated photosynthesis leading to proteostatic regulation of the MEP and shikimate pathways.
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Affiliation(s)
- Kinia Ameztoy
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Ángela María Sánchez-López
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Abdellatif Bahaji
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Goizeder Almagro
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Samuel Gámez-Arcas
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Karel Doležal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science of Palackı University and Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palackı University and Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ales Pěnčík
- Laboratory of Growth Regulators, Faculty of Science of Palackı University and Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Adán Alpízar
- Unidad de Proteómica Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC) Campus de Teatinos, Málaga, Spain
- *Correspondence: Javier Pozueta-Romero,
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26
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Chen J, Zhu M, Liu R, Zhang M, Lv Y, Liu Y, Xiao X, Yuan J, Cai H. BIOMASS YIELD 1 regulates sorghum biomass and grain yield via the shikimate pathway. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5506-5520. [PMID: 32497182 PMCID: PMC7501818 DOI: 10.1093/jxb/eraa275] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/28/2020] [Indexed: 05/26/2023]
Abstract
Biomass and grain yield are key agronomic traits in sorghum (Sorghum bicolor); however, the molecular mechanisms that regulate these traits are not well understood. Here, we characterized the biomass yield 1 (by1) mutant, which displays a dramatically altered phenotype that includes reduced plant height, narrow stems, erect and narrow leaves, and abnormal floral organs. Histological analysis suggested that these phenotypic defects are mainly caused by inhibited cell elongation and abnormal floral organ development. Map-based cloning revealed that BY1 encodes a 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) that catalyses the first step of the shikimate pathway. BY1 was localized in chloroplasts and was ubiquitously distributed in the organs examined, particularly in the roots, stems, leaves, and panicles, which was consistent with its role in biomass production and grain yield. Transcriptome analysis and metabolic profiling revealed that BY1 was involved in primary metabolism and that it affected the biosynthesis of various secondary metabolites, especially flavonoids. Taken together, these findings demonstrate that BY1 affects biomass and grain yield in sorghum by regulating primary and secondary metabolism via the shikimate pathway. Moreover, our results provide important insights into the relationship between plant development and metabolism.
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Affiliation(s)
- Jun Chen
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing, China
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE; Beijing China
| | - Mengjiao Zhu
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE; Beijing China
| | - Ruixiang Liu
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing, China
| | - Meijing Zhang
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing, China
| | - Ya Lv
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE; Beijing China
| | - Yishan Liu
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE; Beijing China
| | - Xin Xiao
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE; Beijing China
| | - Jianhua Yuan
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing, China
| | - Hongwei Cai
- Department of Plant Genetics, Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE; Beijing China
- College of Grassland Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed Association, 388-5 Higashiakada, Nasushiobara, Tochigi, Japan
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27
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Kumar V, Hatan E, Bar E, Davidovich-Rikanati R, Doron-Faigenboim A, Spitzer-Rimon B, Elad Y, Alkan N, Lewinsohn E, Oren-Shamir M. Phenylalanine increases chrysanthemum flower immunity against Botrytis cinerea attack. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:226-240. [PMID: 32645754 DOI: 10.1111/tpj.14919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 05/28/2023]
Abstract
Flowers are the most vulnerable plant organ to infection by the necrotrophic fungus Botrytis cinerea. Here we show that pre-treatment of chrysanthemum (Chrysanthemum morifolium) flowers with phenylalanine (Phe) significantly reduces their susceptibility to B. cinerea. To comprehend how Phe treatment induces resistance, we monitored the dynamics of metabolites (by GC/LC-MS) and transcriptomes (by RNAseq) in flowers after Phe treatment and B. cinerea infection. Phe treatment resulted in accumulation of 3-phenyllactate and benzaldehyde, and in particular induced the expression of genes related to Ca2+ signaling and receptor kinases, implicating an induction of the defense response. Interestingly, the main effects of Phe treatment were observed in flowers exposed to B. cinerea infection, stabilizing the global fluctuations in the levels of metabolites and transcripts while reducing susceptibility to the fungus. We suggest that Phe-induced resistance is associated to cell priming, enabling rapid and targeted reprogramming of cellular defense responses to resist disease development. After Phe pre-treatment, the levels of the anti-fungal volatiles phenylacetaldehyde and eugenol were maintained and the level of coniferin, a plausible monolignol precursor in cell wall lignification, was strongly increased. In addition, Phe pre-treatment reduced ROS generation, prevented ethylene emission, and caused changes in the expression of a minor number of genes related to cell wall biogenesis, encoding the RLK THESEUS1, or involved in Ca2+ and hormonal signaling processes. Our findings point to Phe pre-treatment as a potential orchestrator of a broad-spectrum defense response which may not only provide an ecologically friendly pest control strategy but also offers a promising way of priming plants to induce defense responses against B. cinerea.
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Affiliation(s)
- Varun Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
| | - Erel Hatan
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
| | - Einat Bar
- Department of Vegetable Crops, Agriculture Research Organization, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Rachel Davidovich-Rikanati
- Department of Vegetable Crops, Agriculture Research Organization, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crops, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
| | - Ben Spitzer-Rimon
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
| | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
| | - Efraim Lewinsohn
- Department of Vegetable Crops, Agriculture Research Organization, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, Rishon LeZion, P.O.B 15159, Israel
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28
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Lynch JH, Dudareva N. Aromatic Amino Acids: A Complex Network Ripe for Future Exploration. TRENDS IN PLANT SCIENCE 2020; 25:670-681. [PMID: 32526172 DOI: 10.1016/j.tplants.2020.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 05/28/2023]
Abstract
In plants, high carbon flux is committed to the biosynthesis of phenylalanine, tyrosine, and tryptophan, owing to their roles not only in the production of proteins, but also as precursors to thousands of primary and specialized metabolites. The core plastidial pathways that supply the majority of aromatic amino acids (AAAs) have previously been described in detail. More recently, the discovery of cytosolic enzymes contributing to overall AAA biosynthesis, as well as the identification of intracellular transporters and the continuing elucidation of transcriptional and post-transcriptional regulatory mechanisms, have revealed the complexity of this intercompartmental metabolic network. Here, we review the latest breakthroughs in AAA production and use the newest findings to highlight both longstanding and newly developed questions.
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Affiliation(s)
- Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN 47907-2063, USA
| | - Natalia Dudareva
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
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29
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Weiss R, Guebitz GM, Pellis A, Nyanhongo GS. Harnessing the Power of Enzymes for Tailoring and Valorizing Lignin. Trends Biotechnol 2020; 38:1215-1231. [PMID: 32423726 DOI: 10.1016/j.tibtech.2020.03.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Lignin, a structural component of lignocellulosic plants, is an alternative raw material with enormous potential to replace diminishing fossil-based resources for the sustainable production of many chemicals and materials. Unfortunately, lignin's heterogeneity, low reactivity, and strong intra- and intermolecular hydrogen interactions and modifications introduced during the pulping process present significant technical challenges. However, the increasing ability to tailor lignin biosynthesis pathways by targeting enzymes and the continued discovery of more robust biocatalysts are enabling the synthesis of novel valuable products. This review summarizes how enzymes involved in lignin biosynthesis pathways and microbial enzymes are being harnessed to produce chemicals and materials and to upgrade lignin properties for the synthesis of a variety of value-added lignin industrial products.
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Affiliation(s)
- Renate Weiss
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Georg M Guebitz
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria; Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
| | - Alessandro Pellis
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Gibson S Nyanhongo
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria; Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria.
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30
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Zulet-González A, Barco-Antoñanzas M, Gil-Monreal M, Royuela M, Zabalza A. Increased Glyphosate-Induced Gene Expression in the Shikimate Pathway Is Abolished in the Presence of Aromatic Amino Acids and Mimicked by Shikimate. FRONTIERS IN PLANT SCIENCE 2020; 11:459. [PMID: 32411158 PMCID: PMC7202288 DOI: 10.3389/fpls.2020.00459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/27/2020] [Indexed: 05/19/2023]
Abstract
The herbicide glyphosate inhibits the plant enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the aromatic amino acid (AAA) biosynthetic pathway, also known as the shikimate pathway. Amaranthus palmeri is a fast-growing weed, and several populations have evolved resistance to glyphosate through increased EPSPS gene copy number. The main objective of this study was to elucidate the regulation of the shikimate pathway and determine whether the regulatory mechanisms of glyphosate-sensitive and glyphosate-resistant plants were different. Leaf disks of sensitive and resistant (due to EPSPS gene amplification) A. palmeri plants were incubated for 24 h with glyphosate, AAA, glyphosate + AAA, or several intermediates of the pathway: shikimate, quinate, chorismate and anthranilate. In the sensitive population, glyphosate induced shikimate accumulation and induced the gene expression of the shikimate pathway. While AAA alone did not elicit any change, AAA applied with glyphosate abolished the effects of the herbicide on gene expression. It was not possible to fully mimic the effect of glyphosate by incubation with any of the intermediates, but shikimate was the intermediate that induced the highest increase (three-fold) in the expression level of the genes of the shikimate pathway of the sensitive population. These results suggest that, in this population, the lack of end products (AAA) of the shikimate pathway and shikimate accumulation would be the signals inducing gene expression in the AAA pathway after glyphosate application. In general, the effects on gene expression detected after the application of the intermediates were more severe in the sensitive population than in the resistant population. These results suggest that when EPSPS is overexpressed, as in the resistant population, the regulatory mechanisms of the AAA pathway are disrupted or buffered. The mechanisms underlying this behavior remain to be elucidated.
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Affiliation(s)
| | | | | | | | - Ana Zabalza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona, Spain
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Jacobowitz JR, Weng JK. Exploring Uncharted Territories of Plant Specialized Metabolism in the Postgenomic Era. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:631-658. [PMID: 32176525 DOI: 10.1146/annurev-arplant-081519-035634] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
For millennia, humans have used plants for food, raw materials, and medicines, but only within the past two centuries have we begun to connect particular plant metabolites with specific properties and utilities. Since the utility of classical molecular genetics beyond model species is limited, the vast specialized metabolic systems present in the Earth's flora remain largely unstudied. With an explosion in genomics resources and a rapidly expanding toolbox over the past decade, exploration of plant specialized metabolism in nonmodel species is becoming more feasible than ever before. We review the state-of-the-art tools that have enabled this rapid progress. We present recent examples of de novo biosynthetic pathway discovery that employ various innovative approaches. We also draw attention to the higher-order organization of plant specialized metabolism at subcellular, cellular, tissue, interorgan, and interspecies levels, which will have important implications for the future design of comprehensive metabolic engineering strategies.
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Affiliation(s)
- Joseph R Jacobowitz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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32
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Zeng L, Wang X, Tan H, Liao Y, Xu P, Kang M, Dong F, Yang Z. Alternative Pathway to the Formation of trans-Cinnamic Acid Derived from l-Phenylalanine in Tea ( Camellia sinensis) Plants and Other Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3415-3424. [PMID: 32078319 DOI: 10.1021/acs.jafc.9b07467] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
trans-Cinnamic acid (CA) is a precursor of many phenylpropanoid compounds, including catechins and aroma compounds, in tea (Camellia sinensis) leaves and is derived from l-phenylalanine (l-Phe) deamination. We have discovered an alternative CA formation pathway from l-Phe via phenylpyruvic acid (PPA) and phenyllactic acid (PAA) in tea leaves through stable isotope-labeled precursor tracing and enzyme reaction evidence. Both PPA reductase genes (CsPPARs) involved in the PPA-to-PAA pathway were isolated from tea leaves and functionally characterized in vitro and in vivo. CsPPAR1 and CsPPAR2 transformed PPA into PAA and were both localized in the leaf cell cytoplasm. Rosa hybrida flowers (economic crop flower), Lycopersicon esculentum Mill. fruits (economic crop fruit), and Arabidopsis thaliana leaves (leaf model plant) also contained this alternative CA formation pathway, suggesting that it occurred in most plants, regardless of different tissues and species. These results improve our understanding of CA biosynthesis in tea plants and other plants.
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Affiliation(s)
- Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
| | - Xiaoqin Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
| | - Haibo Tan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
| | - Yinyin Liao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Ping Xu
- Department of Tea Science, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Ming Kang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
| | - Fang Dong
- Guangdong Food and Drug Vocational College, 321 Longdongbei Road, Tianhe District, Guangzhou, Guangdong 510520, People's Republic of China
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou, Guangdong 510650, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
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Ying S, Su M, Wu Y, Zhou L, Fu R, Li Y, Guo H, Luo J, Wang S, Zhang Y. Trichome regulator SlMIXTA-like directly manipulates primary metabolism in tomato fruit. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:354-363. [PMID: 31254436 PMCID: PMC6953195 DOI: 10.1111/pbi.13202] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Trichomes are storage compartments for specialized metabolites in many plant species. In trichome, plant primary metabolism is significantly changed, providing substrates for downstream secondary metabolism. However, little is known of how plants coordinate trichome formation and primary metabolism regulation. In this report, tomato (Solanum lycopersicum) trichome regulator SlMIXTA-like is indicated as a metabolic regulation gene by mGWAS analysis. Overexpression of SlMIXTA-like in tomato fruit enhances trichome formation. In addition, SlMIXTA-like can directly bind to the promoter region of gene encoding 3-deoxy-7-phosphoheptulonate synthase (SlDAHPS) to activate its expression. Induction of SlDAHPS expression enhances shikimate pathway activities and provides substrates for downstream secondary metabolism. Our data provide direct evidence that trichome regulator can directly manipulate primary metabolism, in which way plants can coordinate metabolic regulation and the formation of storage compartments for specialized metabolites. The newly identified SlMIXTA-like can be used for future metabolic engineering.
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Affiliation(s)
- Shiyu Ying
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Min Su
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Yu Wu
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Lu Zhou
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Rao Fu
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Yan Li
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Hao Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hainan Key Laboratory for Sustainable Utilisation of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikouChina
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilisation of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikouChina
| | - Yang Zhang
- Key Laboratory of Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
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Oliva M, Guy A, Galili G, Dor E, Schweitzer R, Amir R, Hacham Y. Enhanced Production of Aromatic Amino Acids in Tobacco Plants Leads to Increased Phenylpropanoid Metabolites and Tolerance to Stresses. FRONTIERS IN PLANT SCIENCE 2020; 11:604349. [PMID: 33510749 PMCID: PMC7835393 DOI: 10.3389/fpls.2020.604349] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/03/2020] [Indexed: 05/20/2023]
Abstract
Aromatic amino acids (AAAs) synthesized in plants via the shikimate pathway can serve as precursors for a wide range of secondary metabolites that are important for plant defense. The goals of the current study were to test the effect of increased AAAs on primary and secondary metabolic profiles and to reveal whether these plants are more tolerant to abiotic stresses (oxidative, drought and salt) and to Phelipanche egyptiaca (Egyptian broomrape), an obligate parasitic plant. To this end, tobacco (Nicotiana tabacum) plants were transformed with a bacterial gene (AroG) encode to feedback-insensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, the first enzyme of the shikimate pathway. Two sets of transgenic plants were obtained: the first had low expression of the AroG protein, a normal phenotype and minor metabolic changes; the second had high accumulation of the AroG protein with normal, or deleterious morphological changes having a dramatic shift in plant metabolism. Metabolic profiling analysis revealed that the leaves of the transgenic plants had increased levels of phenylalanine (up to 43-fold), tyrosine (up to 24-fold) and tryptophan (up to 10-fold) compared to control plants having an empty vector (EV) and wild type (WT) plants. The significant increase in phenylalanine was accompanied by higher levels of metabolites that belong to the phenylpropanoid pathway. AroG plants showed improved tolerance to salt stress but not to oxidative or drought stress. The most significant improved tolerance was to P. aegyptiaca. Unlike WT/EV plants that were heavily infected by the parasite, the transgenic AroG plants strongly inhibited P. aegyptiaca development, and only a few stems of the parasite appeared above the soil. This delayed development of P. aegyptiaca could be the result of higher accumulation of several phenylpropanoids in the transgenic AroG plants and in P. aegyptiaca, that apparently affected its growth. These findings indicate that high levels of AAAs and their related metabolites have the potential of controlling the development of parasitic plants.
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Affiliation(s)
- Moran Oliva
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Aviv Guy
- Laboratory of Plant Science, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
| | - Gad Galili
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Evgenia Dor
- Department of Weed Research, Agriculture Research Organization, Newe Ya’ar Research Center, The Volcani Center, Ramat Yishay, Israel
| | | | - Rachel Amir
- Laboratory of Plant Science, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
- *Correspondence: Rachel Amir,
| | - Yael Hacham
- Laboratory of Plant Science, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
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Oliva M, Hatan E, Kumar V, Galsurker O, Nisim-Levi A, Ovadia R, Galili G, Lewinsohn E, Elad Y, Alkan N, Oren-Shamir M. Increased phenylalanine levels in plant leaves reduces susceptibility to Botrytis cinerea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110289. [PMID: 31779900 DOI: 10.1016/j.plantsci.2019.110289] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 05/26/2023]
Abstract
Botrytis cinerea is a major plant pathogen, causing losses in crops during growth and storage. Here we show that increased accumulation of phenylalanine (Phe) and Phe-derived metabolites in plant leaves significantly reduces their susceptibility to B. cinerea. Arabidopsis, petunia and tomato plants were enriched with Phe by either overexpressing a feedback-insensitive E.coli DAHP synthase (AroG*), or by spraying or drenching detached leaves or whole plants with external Phe, prior to infection with B. cinerea. Metabolic analysis of Arabidopsis and petunia plants overexpressing AroG* as well as wt petunia plants treated externally with Phe, revealed an increase in Phe-derived phenylpropanoids accumulated in their leaves, and specifically in those inhibiting B. cinerea germination and growth, suggesting that different compounds reduce susceptibility to B. cinerea in different plants. Phe itself had no inhibitory effect on germination or growth of B. cinerea, and inhibition of Phe metabolism in petunia plants treated with external Phe prevented decreased susceptibility to the fungus. Thus, Phe metabolism into an array of metabolites, unique to each plant and plant organ, is the most probable cause for increased resistance to Botrytis. This mechanism may provide a basis for ecologically friendly control of a wide range of plant pathogens.
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Affiliation(s)
- Moran Oliva
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Erel Hatan
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Varun Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Ortal Galsurker
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Ada Nisim-Levi
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Rinat Ovadia
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Gad Galili
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efraim Lewinsohn
- Department of Vegetable Crops, Agriculture Research Organization, Newe Ya'ar Research Center, Volcani Center, Ramat Yishay, 30095, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Noam Alkan
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel.
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Lin CY, Eudes A. Strategies for the production of biochemicals in bioenergy crops. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:71. [PMID: 32318116 PMCID: PMC7158082 DOI: 10.1186/s13068-020-01707-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/02/2020] [Indexed: 05/12/2023]
Abstract
Industrial crops are grown to produce goods for manufacturing. Rather than food and feed, they supply raw materials for making biofuels, pharmaceuticals, and specialty chemicals, as well as feedstocks for fabricating fiber, biopolymer, and construction materials. Therefore, such crops offer the potential to reduce our dependency on petrochemicals that currently serve as building blocks for manufacturing the majority of our industrial and consumer products. In this review, we are providing examples of metabolites synthesized in plants that can be used as bio-based platform chemicals for partial replacement of their petroleum-derived counterparts. Plant metabolic engineering approaches aiming at increasing the content of these metabolites in biomass are presented. In particular, we emphasize on recent advances in the manipulation of the shikimate and isoprenoid biosynthetic pathways, both of which being the source of multiple valuable compounds. Implementing and optimizing engineered metabolic pathways for accumulation of coproducts in bioenergy crops may represent a valuable option for enhancing the commercial value of biomass and attaining sustainable lignocellulosic biorefineries.
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Affiliation(s)
- Chien-Yuan Lin
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Zeng L, Tan H, Liao Y, Jian G, Kang M, Dong F, Watanabe N, Yang Z. Increasing Temperature Changes Flux into Multiple Biosynthetic Pathways for 2-Phenylethanol in Model Systems of Tea ( Camellia sinensis) and Other Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10145-10154. [PMID: 31418564 DOI: 10.1021/acs.jafc.9b03749] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
2-Phenylethanol (2PE) is a representative aromatic aroma compound in tea (Camellia sinensis) leaves. However, its formation in tea remains unexplored. In our study, feeding experiments of [2H8]L-phenylalanine (Phe), [2H5]phenylpyruvic acid (PPA), or (E/Z)-phenylacetaldoxime (PAOx) showed that three biosynthesis pathways for 2PE derived from L-Phe occurred in tea leaves, namely, pathway I (via phenylacetaldehyde (PAld)), pathway II (via PPA and PAld), and pathway III (via (E/Z)-PAOx and PAld). Furthermore, increasing temperature resulted in increased flux into the pathway for 2PE from L-Phe via PPA and PAld. In addition, tomato fruits and petunia flowers also contained the 2PE biosynthetic pathway from L-Phe via PPA and PAld and increasing temperatures led to increased flux into this pathway, suggesting that such a phenomenon might be common among most plants containing 2PE. This represents a characteristic example of changes in flux into the biosynthesis pathways of volatile compounds in plants in response to stresses.
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Affiliation(s)
- Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany , South China Botanical Garden, Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
- Center of Economic Botany, Core Botanical Gardens , Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
| | - Haibo Tan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany , South China Botanical Garden, Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
- Center of Economic Botany, Core Botanical Gardens , Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
| | - Yinyin Liao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany , South China Botanical Garden, Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
- University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Guotai Jian
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany , South China Botanical Garden, Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
- University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
| | - Ming Kang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany , South China Botanical Garden, Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
| | - Fang Dong
- Guangdong Food and Drug Vocational College , No. 321 Longdongbei Road , Tianhe District , Guangzhou 510520 , China
| | - Naoharu Watanabe
- Graduate School of Science and Technology, Shizuoka University , No. 3-5-1 Johoku , Naka-ku, Hamamatsu 432-8561 , Japan
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany , South China Botanical Garden, Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
- Center of Economic Botany, Core Botanical Gardens , Chinese Academy of Sciences , No. 723 Xingke Road , Tianhe District , Guangzhou 510650 , China
- University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , China
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Eguchi R, Ono N, Hirai Morita A, Katsuragi T, Nakamura S, Huang M, Altaf-Ul-Amin M, Kanaya S. Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks. BMC Bioinformatics 2019; 20:380. [PMID: 31288752 PMCID: PMC6617615 DOI: 10.1186/s12859-019-2963-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousands of compounds in this class, few of their biosynthesis pathways are fully identified. In this study, we constructed a model to predict their precursors based on a novel kind of neural network called the molecular graph convolutional neural network. Molecular similarity is a crucial metric in the analysis of qualitative structure-activity relationships. However, it is sometimes difficult for current fingerprint representations to emphasize specific features for the target problems efficiently. It is advantageous to allow the model to select the appropriate features according to data-driven decisions for extracting more useful information, which influences a classification or regression problem substantially. RESULTS In this study, we applied a neural network architecture for undirected graph representation of molecules. By encoding a molecule as an abstract graph and applying "convolution" on the graph and training the weight of the neural network framework, the neural network can optimize feature selection for the training problem. By incorporating the effects from adjacent atoms recursively, graph convolutional neural networks can extract the features of latent atoms that represent chemical features of a molecule efficiently. In order to investigate alkaloid biosynthesis, we trained the network to distinguish the precursors of 566 alkaloids, which are almost all of the alkaloids whose biosynthesis pathways are known, and showed that the model could predict starting substances with an averaged accuracy of 97.5%. CONCLUSION We have showed that our model can predict more accurately compared to the random forest and general neural network when the variables and fingerprints are not selected, while the performance is comparable when we carefully select 507 variables from 18000 dimensions of descriptors. The prediction of pathways contributes to understanding of alkaloid synthesis mechanisms and the application of graph based neural network models to similar problems in bioinformatics would therefore be beneficial. We applied our model to evaluate the precursors of biosynthesis of 12000 alkaloids found in various organisms and found power-low-like distribution.
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Affiliation(s)
- Ryohei Eguchi
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Naoaki Ono
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan. .,Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Aki Hirai Morita
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tetsuo Katsuragi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Satoshi Nakamura
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Ming Huang
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Md Altaf-Ul-Amin
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Shigehiko Kanaya
- Division of Science and Technology, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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Pott DM, Osorio S, Vallarino JG. From Central to Specialized Metabolism: An Overview of Some Secondary Compounds Derived From the Primary Metabolism for Their Role in Conferring Nutritional and Organoleptic Characteristics to Fruit. FRONTIERS IN PLANT SCIENCE 2019; 10:835. [PMID: 31316537 PMCID: PMC6609884 DOI: 10.3389/fpls.2019.00835] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/11/2019] [Indexed: 05/23/2023]
Abstract
Fruit flavor and nutritional characteristics are key quality traits and ones of the main factors influencing consumer preference. Central carbon metabolism, also known as primary metabolism, contributes to the synthesis of intermediate compounds that act as precursors for plant secondary metabolism. Specific and specialized metabolic pathways that evolved from primary metabolism play a key role in the plant's interaction with its environment. In particular, secondary metabolites present in the fruit serve to increase its attractiveness to seed dispersers and to protect it against biotic and abiotic stresses. As a consequence, several important organoleptic characteristics, such as aroma, color, and fruit nutritional value, rely upon secondary metabolite content. Phenolic and terpenoid compounds are large and diverse classes of secondary metabolites that contribute to fruit quality and have their origin in primary metabolic pathways, while the delicate aroma of ripe fruits is formed by a unique combination of hundreds of volatiles that are derived from primary metabolites. In this review, we show that the manipulation of primary metabolism is a powerful tool to engineer quality traits in fruits, such as the phenolic, terpenoid, and volatile content. The enzymatic reactions responsible for the accumulation of primary precursors are bottlenecks in the transfer of metabolic flux from central to specialized metabolism and should be taken into account to increase the yield of the final products of the biosynthetic pathways. In addition, understanding the connection and regulation of the carbon flow between primary and secondary metabolism is a key factor for the development of fruit cultivars with enhanced organoleptic and nutritional traits.
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Affiliation(s)
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - José G. Vallarino
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
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40
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Cui D, Deng A, Bai H, Yang Z, Liang Y, Liu Z, Qiu Q, Wang L, Liu S, Zhang Y, Shi Y, Qi J, Wen T. Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. J Struct Biol 2019; 206:322-334. [DOI: 10.1016/j.jsb.2019.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/08/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
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41
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Holt S, Miks MH, de Carvalho BT, Foulquié-Moreno MR, Thevelein JM. The molecular biology of fruity and floral aromas in beer and other alcoholic beverages. FEMS Microbiol Rev 2019; 43:193-222. [PMID: 30445501 PMCID: PMC6524682 DOI: 10.1093/femsre/fuy041] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: (1) higher alcohols and esters, (2) polyfunctional thiols, (3) lactones and furanones, and (4) terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.
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Affiliation(s)
- Sylvester Holt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marta H Miks
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10–726 Olsztyn, Poland
| | - Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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42
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Yuan Y, Yu M, Jia Z, Song X, Liang Y, Zhang J. Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. BMC Genomics 2018. [PMID: 30594136 DOI: 10.1186/s12864-018-5305-6/1471-2164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a traditional Chinese herbal medicine with high medicinal value in China. Polysaccharides and alkaloids are its main active ingredients. To understand the difference of main active ingredients in different tissues, we determined the contents of polysaccharides and alkaloids in the roots, stems and leaves of D. huoshanense. In order to explore the reasons for the differences of active ingredients at the level of transcription, we selected roots, stems and leaves of D. huoshanenese for transcriptome sequencing and pathway mining. RESULTS The contents of polysaccharides and alkaloids of D. huoshanense were determined and it was found that there were significant differences in different tissues. A total of 716,634,006 clean reads were obtained and 478,361 unigenes were assembled by the Illumina platform sequencing. We identified 1407 carbohydrate-active related unigenes against CAZy database including 447 glycosyltransferase genes (GTs), 818 glycoside hydrolases (GHs), 60 carbohydrate esterases (CEs), 62 carbohydrate-binding modules (CBMs), and 20 polysaccharide lyases (PLs). In the glycosyltransferases (GTs) family, 315 differential expression genes (DEGs) were identified. In total, 124 and 58 DEGs were associated with the biosynthesis of alkaloids in Dh_L vs. Dh_S and Dh_R vs. Dh_L, respectively. A total of 62 DEGs associated with the terpenoid pathway were identified between Dh_R and Dh_S. Five key enzyme genes involved in the terpenoids pathway were identified, and their expression patterns in different tissues was validated using quantitative real-time PCR. CONCLUSIONS In summary, our study presents a transcriptome profile of D. huoshanense. These data contribute to our deeper relevant researches on active ingredients and provide useful insights into the molecular mechanisms regulating polysaccharides and alkaloids in Dendrobium.
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Affiliation(s)
- Yingdan Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037, China
| | - Maoyun Yu
- Anhui Tongjisheng Biotechnology Co., Ltd, Lu'an, 237000, China.
- Cultivation and Industrialization Center of Rare Medicinal Plants in Ta-pieh Mountains, West Anhui University, Lu'an, 23700, China.
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037, China
| | - Xue'er Song
- Institute of Pathology and Southwest Cancer Center, The First Affiliated Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Yingquan Liang
- Anhui Tongjisheng Biotechnology Co., Ltd, Lu'an, 237000, China
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037, China.
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43
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Yuan Y, Yu M, Jia Z, Song X, Liang Y, Zhang J. Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. BMC Genomics 2018; 19:978. [PMID: 30594136 PMCID: PMC6310986 DOI: 10.1186/s12864-018-5305-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 11/23/2018] [Indexed: 02/01/2023] Open
Abstract
Background Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a traditional Chinese herbal medicine with high medicinal value in China. Polysaccharides and alkaloids are its main active ingredients. To understand the difference of main active ingredients in different tissues, we determined the contents of polysaccharides and alkaloids in the roots, stems and leaves of D. huoshanense. In order to explore the reasons for the differences of active ingredients at the level of transcription, we selected roots, stems and leaves of D. huoshanenese for transcriptome sequencing and pathway mining. Results The contents of polysaccharides and alkaloids of D. huoshanense were determined and it was found that there were significant differences in different tissues. A total of 716,634,006 clean reads were obtained and 478,361 unigenes were assembled by the Illumina platform sequencing. We identified 1407 carbohydrate-active related unigenes against CAZy database including 447 glycosyltransferase genes (GTs), 818 glycoside hydrolases (GHs), 60 carbohydrate esterases (CEs), 62 carbohydrate-binding modules (CBMs), and 20 polysaccharide lyases (PLs). In the glycosyltransferases (GTs) family, 315 differential expression genes (DEGs) were identified. In total, 124 and 58 DEGs were associated with the biosynthesis of alkaloids in Dh_L vs. Dh_S and Dh_R vs. Dh_L, respectively. A total of 62 DEGs associated with the terpenoid pathway were identified between Dh_R and Dh_S. Five key enzyme genes involved in the terpenoids pathway were identified, and their expression patterns in different tissues was validated using quantitative real-time PCR. Conclusions In summary, our study presents a transcriptome profile of D. huoshanense. These data contribute to our deeper relevant researches on active ingredients and provide useful insights into the molecular mechanisms regulating polysaccharides and alkaloids in Dendrobium. Electronic supplementary material The online version of this article (10.1186/s12864-018-5305-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingdan Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037, China
| | - Maoyun Yu
- Anhui Tongjisheng Biotechnology Co., Ltd, Lu'an, 237000, China. .,Cultivation and Industrialization Center of Rare Medicinal Plants in Ta-pieh Mountains, West Anhui University, Lu'an, 23700, China.
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037, China
| | - Xue'er Song
- Institute of Pathology and Southwest Cancer Center, The First Affiliated Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Yingquan Liang
- Anhui Tongjisheng Biotechnology Co., Ltd, Lu'an, 237000, China
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China. .,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037, China.
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44
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Petersen A, Wang C, Crocoll C, Halkier BA. Biotechnological approaches in glucosinolate production. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1231-1248. [PMID: 30080309 PMCID: PMC6585788 DOI: 10.1111/jipb.12705] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Glucosinolates (GLSs) are sulfur-rich, amino acid-derived defense compounds characteristic of the Brassicales order. In the past, GLSs were mostly known as anti-nutritional factors in fodder, biopesticides in agriculture, and flavors in condiments such as mustard. However, in recent times, GLSs have received increased attention as promoters of human health. This has spurred intensive research towards generating rich sources of health-promoting GLSs. We provide a comprehensive overview of the biotechnological approaches applied to reach this goal. This includes optimization of GLS production and composition in native, GLS-producing plants, including hairy root and cell cultures thereof, as well as synthetic biology approaches in heterologous hosts, such as tobacco and the microbial organisms Escherichia coli and Saccharomyces cerevisiae. The progress using these different approaches is discussed.
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Affiliation(s)
- Annette Petersen
- DynaMo CenterCopenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 401871 Frederiksberg CDenmark
| | - Cuiwei Wang
- DynaMo CenterCopenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 401871 Frederiksberg CDenmark
| | - Christoph Crocoll
- DynaMo CenterCopenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 401871 Frederiksberg CDenmark
| | - Barbara Ann Halkier
- DynaMo CenterCopenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 401871 Frederiksberg CDenmark
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45
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Fang F, Oliva M, Ehi-Eromosele S, Zaccai M, Arazi T, Oren-Shamir M. Successful floral-dipping transformation of post-anthesis lisianthus (Eustoma grandiflorum) flowers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:869-879. [PMID: 30156348 DOI: 10.1111/tpj.14076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
The adaptation of the Agrobacterium-mediated floral-dipping technique is limited, to date, to a small number of plants. In this paper, we present the efficient transformation of one of the leading plants in the cut flower industry, lisianthus (Eustoma grandiflorum). This method is approximately 18 months shorter than the known tissue culture-based transformation. The Excalibur Pink cultivar and two additional breeding lines, X-1042 and X-2541, were transformed using three different marker genes (benzyl alcohol acetyltransferase (BEAT) originating from Clarkia breweri, the feedback-insensitive bacterial gene AroG*, and the empty pART27 vector expressing a kanamycin-resistance cassette (nptII)). Genomic transformation was successful in all tested cases with transformation efficiency ranked from 0.2 to 2.9%, which is well in the range of results from Arabidopsis studies. Unlike Arabidopsis, in which floral-dipping transformation was efficient only at a pre-anthesis stage before ovary sealing, lisianthus flowers were transformed when dipping occurred 4 days pre-anthesis or 3-5 days post-anthesis with 1.5 and 3.7% efficiencies, respectively. Post-anthesis transformation occurred when the flower ovaries were sealed. Flower dipping of Excalibur Pink flowers with fluorescent Agrobacterium containing a GFP marker gene demonstrated Agrobacterium entrance into the sealed flower ovary through the open stigma and style tube. In this study, we demonstrated floral-dipping transformation of a commercial plant, lisianthus Excalibur Pink, occurring after sealing of the ovaries, probably via the stigma and wide open style tunnel.
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Affiliation(s)
- Fang Fang
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159, Rishon LeZion, Israel
| | - Moran Oliva
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159, Rishon LeZion, Israel
| | - Sonia Ehi-Eromosele
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159, Rishon LeZion, Israel
| | - Michele Zaccai
- Department of Life Sciences, Ben Gurion University of the Negev, PO Box 653, Beersheva, Israel
| | - Tzahi Arazi
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159, Rishon LeZion, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, PO Box 15159, Rishon LeZion, Israel
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46
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Holland CK, Jez JM. Arabidopsis: the original plant chassis organism. PLANT CELL REPORTS 2018; 37:1359-1366. [PMID: 29663032 DOI: 10.1007/s00299-018-2286-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/11/2018] [Indexed: 05/20/2023]
Abstract
Arabidopsis thaliana (thale cress) has a past, current, and future role in the era of synthetic biology. Arabidopsis is one of the most well-studied plants with a wealth of genomics, genetics, and biochemical resources available for the metabolic engineer and synthetic biologist. Here we discuss the tools and resources that enable the identification of target genes and pathways in Arabidopsis and heterologous expression in this model plant. While there are numerous examples of engineering Arabidopsis for decreased lignin, increased seed oil, increased vitamins, and environmental remediation, this plant has provided biochemical tools for introducing Arabidopsis genes, pathways, and/or regulatory elements into other plants and microorganisms. Arabidopsis is not a vegetative or oilseed crop, but it is as an excellent model chassis for proof-of-concept metabolic engineering and synthetic biology experiments in plants.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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47
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Fan R, Chen Y, Ye X, Wu J, Lin B, Zhong H. Transcriptome analysis of Polianthes tuberosa during floral scent formation. PLoS One 2018; 13:e0199261. [PMID: 30183703 PMCID: PMC6124719 DOI: 10.1371/journal.pone.0199261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/04/2018] [Indexed: 12/30/2022] Open
Abstract
Polianthes tuberosa is a popular ornamental plant. Its floral scent volatiles mainly consist of terpenes and benzenoids that emit a charming fragrance. However, our understanding of the molecular mechanism responsible for the floral scent of P. tuberosa is limited. Using transcriptome sequencing and de novo assembly, a total of 228,706,703 high-quality reads were obtained, which resulted in the identification of 96,906 unigenes (SRA Accession Number SRP126470, TSA Acc. No. GGEA00000000). Approximately 41.85% of the unigenes were functionally annotated using public databases. A total of 4,694 differentially expressed genes (DEGs)were discovered during flowering. Gas chromatography-mass spectrometry analysis revealed that the majority of the volatiles comprised benzenoids and small amounts of terpenes. Homology analysis identified 13 and 17 candidate genes associated with terpene and benzenoid biosynthesis, respectively. Among these, PtTPS1, PtDAHPSs, PtPAL1, and PtBCMT2 might play important roles in regulating the formation of floral volatiles. The data generated by transcriptome sequencing provide a critical resource for exploring concrete characteristics as well as for supporting functional genomics studies. The results of the present study also lay the foundation for the elucidation of the molecular mechanism underlying the regulation of floral scents in monocots.
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Affiliation(s)
- Ronghui Fan
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Flowers Research Center, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Characteristic Floriculture, Fuzhou, Fujian, China
| | - Yiquan Chen
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Xiuxian Ye
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Flowers Research Center, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Characteristic Floriculture, Fuzhou, Fujian, China
| | - Jianshe Wu
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Flowers Research Center, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Characteristic Floriculture, Fuzhou, Fujian, China
| | - Bing Lin
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Flowers Research Center, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Characteristic Floriculture, Fuzhou, Fujian, China
| | - Huaiqin Zhong
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Flowers Research Center, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Characteristic Floriculture, Fuzhou, Fujian, China
- * E-mail:
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48
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Eudes A, Berthomieu R, Hao Z, Zhao N, Benites VT, Baidoo EEK, Loqué D. Production of muconic acid in plants. Metab Eng 2018; 46:13-19. [PMID: 29474840 DOI: 10.1016/j.ymben.2018.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/06/2018] [Accepted: 02/13/2018] [Indexed: 12/16/2022]
Abstract
Muconic acid (MA) is a dicarboxylic acid used for the production of industrially relevant chemicals such as adipic acid, terephthalic acid, and caprolactam. Because the synthesis of these polymer precursors generates toxic intermediates by utilizing petroleum-derived chemicals and corrosive catalysts, the development of alternative strategies for the bio-based production of MA has garnered significant interest. Plants produce organic carbon skeletons by harvesting carbon dioxide and energy from the sun, and therefore represent advantageous hosts for engineered metabolic pathways towards the manufacturing of chemicals. In this work, we engineered Arabidopsis to demonstrate that plants can serve as green factories for the bio-manufacturing of MA. In particular, dual expression of plastid-targeted bacterial salicylate hydroxylase (NahG) and catechol 1,2-dioxygenase (CatA) resulted in the conversion of the endogenous salicylic acid (SA) pool into MA via catechol. Sequential increase of SA derived from the shikimate pathway was achieved by expressing plastid-targeted versions of bacterial salicylate synthase (Irp9) and feedback-resistant 3-deoxy-D-arabino-heptulosonate synthase (AroG). Introducing this SA over-producing strategy into engineered plants that co-express NahG and CatA resulted in a 50-fold increase in MA titers. Considering that MA was easily recovered from senesced plant biomass after harvest, we envision the phytoproduction of MA as a beneficial option to add value to bioenergy crops.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Roland Berthomieu
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Ecole Polytechnique, Université Paris-Saclay, Palaiseau 91120, France
| | - Zhangying Hao
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nanxia Zhao
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France.
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Jun D, Minic Z, Bhat SV, Vanderlinde EM, Yost CK, Babu M, Dahms TES. Metabolic Adaptation of a C-Terminal Protease A-Deficient Rhizobium leguminosarum in Response to Loss of Nutrient Transport. Front Microbiol 2018; 8:2617. [PMID: 29354107 PMCID: PMC5758756 DOI: 10.3389/fmicb.2017.02617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Post-translational modification expands the functionality of the proteome beyond genetic encoding, impacting many cellular processes. Cleavage of the carboxyl terminus is one of the many different ways proteins can be modified for functionality. Gel-electrophoresis and mass spectrometric-based techniques were used to identify proteins impacted by deficiency of a C-terminal protease, CtpA, in Rhizobium leguminosarum bv. viciae 3841. Predicted CtpA substrates from 2D silver stained gels were predominantly outer membrane and transport proteins. Proteins with altered abundance in the wild type and ctpA (RL4692) mutant, separated by 2D difference gel electrophoresis, were selected for analysis by mass spectrometry. Of those identified, 9 were the periplasmic solute-binding components of ABC transporters, 5 were amino acid metabolic enzymes, 2 were proteins involved in sulfur metabolism, and 1 each was related to carbon metabolism, protein folding and signal transduction. Alterations to ABC-binding-cassette transporters, nutrient uptake efficiency and to amino acid metabolism indicated an impact on amino acid metabolism and transport for the ctpA mutant, which was validated by measured amino acid levels.
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Affiliation(s)
- Dong Jun
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Zoran Minic
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Supriya V. Bhat
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Elizabeth M. Vanderlinde
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
- Department of Biology, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Chris K. Yost
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Tanya E. S. Dahms
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
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Deng X, Zhao L, Fang T, Xiong Y, Ogutu C, Yang D, Vimolmangkang S, Liu Y, Han Y. Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus. HORTICULTURE RESEARCH 2018; 5:29. [PMID: 29872534 PMCID: PMC5981371 DOI: 10.1038/s41438-018-0035-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 05/10/2023]
Abstract
Lotus predominantly accumulates benzylisoquinoline alkaloids (BIAs), but their biosynthesis and regulation remain unclear. Here, we investigated structural and regulatory genes involved in BIA accumulation in lotus. Two clustered CYP80 genes were identified to be responsible for the biosynthesis of bis-BIAs and aporphine-type BIAs, respectively, and their tissue-specific expression causes divergence in alkaloid component between leaf and embryo. In contrast with the common (S)-reticuline precursor for most BIAs, aporphine alkaloids in lotus leaf may result from the (S)-N-methylcoclaurine precursor. Structural diversity of BIA alkaloids in the leaf is attributed to enzymatic modifications, including intramolecular C-C phenol coupling on ring A and methylation and demethylation at certain positions. Additionally, most BIA biosynthetic pathway genes show higher levels of expression in the leaf of high-BIA cultivar compared with low-BIA cultivar, suggesting transcriptional regulation of BIA accumulation in lotus. Five transcription factors, including three MYBs, one ethylene-responsive factor, and one basic helix-loop-helix (bHLH), were identified to be candidate regulators of BIA biosynthesis in lotus. Our study reveals a BIA biosynthetic pathway and its transcriptional regulation in lotus, which will enable a deeper understanding of BIA biosynthesis in plants.
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Affiliation(s)
- Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Li Zhao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Yaqian Xiong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Collins Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Sornkanok Vimolmangkang
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Yanling Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
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