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Rao X, Barros J. Modeling lignin biosynthesis: a pathway to renewable chemicals. TRENDS IN PLANT SCIENCE 2024; 29:546-559. [PMID: 37802691 DOI: 10.1016/j.tplants.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Plant biomass contains lignin that can be converted into high-value-added chemicals, fuels, and materials. The precise genetic manipulation of lignin content and composition in plant cells offers substantial environmental and economic benefits. However, the intricate regulatory mechanisms governing lignin formation challenge the development of crops with specific lignin profiles. Mathematical models and computational simulations have recently been employed to gain fundamental understanding of the metabolism of lignin and related phenolic compounds. This review article discusses the strategies used for modeling plant metabolic networks, focusing on the application of mathematical modeling for flux network analysis in monolignol biosynthesis. Furthermore, we highlight how current challenges might be overcome to optimize the use of metabolic modeling approaches for developing lignin-engineered plants.
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Affiliation(s)
- Xiaolan Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
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2
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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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3
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Habib MA, Islam MM, Islam MM, Hasan MM, Baek KH. Current Status and De Novo Synthesis of Anti-Tumor Alkaloids in Nicotiana. Metabolites 2023; 13:metabo13050623. [PMID: 37233664 DOI: 10.3390/metabo13050623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Alkaloids are the most diversified nitrogen-containing secondary metabolites, having antioxidant and antimicrobial properties, and are extensively used in pharmaceuticals to treat different types of cancer. Nicotiana serves as a reservoir of anti-cancer alkaloids and is also used as a model plant for the de novo synthesis of various anti-cancer molecules through genetic engineering. Up to 4% of the total dry weight of Nicotiana was found to be composed of alkaloids, where nicotine, nornicotine, anatabine, and anabasine are reported as the dominant alkaloids. Additionally, among the alkaloids present in Nicotiana, β-carboline (Harmane and Norharmane) and Kynurenines are found to show anti-tumor effects, especially in the cases of colon and breast cancers. Creating new or shunting of existing biosynthesis pathways in different species of Nicotiana resulted in de novo or increased synthesis of different anti-tumor molecules or their derivatives or precursors including Taxadiane (~22.5 µg/g), Artemisinin (~120 μg/g), Parthenolide (~2.05 ng/g), Costunolide (~60 ng/g), Etoposide (~1 mg/g), Crocin (~400 µg/g), Catharanthine (~60 ng/g), Tabersonine (~10 ng/g), Strictosidine (~0.23 mg/g), etc. Enriching the precursor pool, especially Dimethylallyl Diphosphate (DMAPP), down-regulating other bi-product pathways, compartmentalization or metabolic shunting, or organelle-specific reconstitution of the precursor pool, might trigger the enhanced accumulation of the targeted anti-cancer alkaloid in Nicotiana.
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Affiliation(s)
- Md Ahsan Habib
- Department of Plant Pathology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md Mobinul Islam
- Department of Plant Pathology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md Mukul Islam
- Department of Plant Pathology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md Mohidul Hasan
- Department of Plant Pathology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
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4
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Chen X, Wu Z, Yin Z, Zhang Y, Rui C, Wang J, Malik WA, Lu X, Wang D, Wang J, Guo L, Wang S, Zhao L, Zebinisso Qaraevna B, Chen C, Wang X, Ye W. Comprehensive genomic characterization of cotton cationic amino acid transporter genes reveals that GhCAT10D regulates salt tolerance. BMC PLANT BIOLOGY 2022; 22:441. [PMID: 36109698 PMCID: PMC9476346 DOI: 10.1186/s12870-022-03829-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/06/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND The cationic amino acid transporters (CAT) play indispensable roles in maintaining metabolic functions, such as synthesis of proteins and nitric oxide (NO), biosynthesis of polyamine, and flow of amino acids, by mediating the bidirectional transport of cationic amino acids in plant cells. RESULTS In this study, we performed a genome-wide and comprehensive study of 79 CAT genes in four species of cotton. Localization of genes revealed that CAT genes reside on the plasma membrane. Seventy-nine CAT genes were grouped into 7 subfamilies by phylogenetic analysis. Structure analysis of genes showed that CAT genes from the same subgroup have similar genetic structure and exon number. RNA-seq and real-time PCR indicated that the expression of most GhCAT genes were induced by salt, drought, cold and heat stresses. Cis-elements analysis of GhCAT promoters showed that the GhCAT genes promoters mainly contained plant hormones responsive elements and abiotic stress elements, which indicated that GhCAT genes may play key roles in response to abiotic stress. Moreover, we also conducted gene interaction network of the GhCAT proteins. Silencing GhCAT10D expression decreased the resistance of cotton to salt stress because of a decrease in the accumulation of NO and proline. CONCLUSION Our results indicated that CAT genes might be related with salt tolerance in cotton and lay a foundation for further study on the regulation mechanism of CAT genes in cationic amino acids transporting and distribution responsing to abiotic stress.
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Affiliation(s)
- Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Zhe Wu
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan, 063299, Hebei, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Cun Rui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Jing Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Waqar Afzal Malik
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Bobokhonova Zebinisso Qaraevna
- Department of Cotton Growing, Genetics, Breeding and Seed, Tajik Agrarian University Named Shirinsho Shotemur Dushanbe, Dushanbe, Republic of Tajikistan
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xiuping Wang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan, 063299, Hebei, China.
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China.
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5
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Tong Y, Yi SC, Liu SY, Xu L, Qiu ZX, Zeng DQ, Tang WW. Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113943. [PMID: 35999761 DOI: 10.1016/j.ecoenv.2022.113943] [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: 12/24/2021] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.
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Affiliation(s)
- Yao Tong
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Shan-Chi Yi
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Shu-Yu Liu
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Lin Xu
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Zhuo-Xun Qiu
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Dong-Qiang Zeng
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Wen-Wei Tang
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China.
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6
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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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7
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Bergman ME, Evans SE, Davis B, Hamid R, Bajwa I, Jayathilake A, Chahal AK, Phillips MA. An Arabidopsis GCMS chemical ionization technique to quantify adaptive responses in central metabolism. PLANT PHYSIOLOGY 2022; 189:2072-2090. [PMID: 35512197 PMCID: PMC9342981 DOI: 10.1093/plphys/kiac207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 05/06/2023]
Abstract
We present a methodology to survey central metabolism in 13CO2-labeled Arabidopsis (Arabidopsis thaliana) rosettes by ammonia positive chemical ionization-gas chromatography-mass spectrometry. This technique preserves the molecular ion cluster of methyloxime/trimethylsilyl-derivatized analytes up to 1 kDa, providing unambiguous nominal mass assignment of >200 central metabolites and 13C incorporation rates into a subset of 111 from the tricarboxylic acid (TCA) cycle, photorespiratory pathway, amino acid metabolism, shikimate pathway, and lipid and sugar metabolism. In short-term labeling assays, we observed plateau labeling of ∼35% for intermediates of the photorespiratory cycle except for glyoxylate, which reached only ∼4% labeling and was also present at molar concentrations several fold lower than other photorespiratory intermediates. This suggests photorespiratory flux may involve alternate intermediate pools besides the generally accepted route through glyoxylate. Untargeted scans showed that in illuminated leaves, noncyclic TCA cycle flux and citrate export to the cytosol revert to a cyclic flux mode following methyl jasmonate (MJ) treatment. MJ also caused a block in the photorespiratory transamination of glyoxylate to glycine. Salicylic acid treatment induced the opposite effects in both cases, indicating the antagonistic relationship of these defense signaling hormones is preserved at the metabolome level. We provide complete chemical ionization spectra for 203 Arabidopsis metabolites from central metabolism, which uniformly feature the unfragmented pseudomolecular ion as the base peak. This unbiased, soft ionization technique is a powerful screening tool to identify adaptive metabolic trends in photosynthetic tissue and represents an important advance in methodology to measure plant metabolic flux.
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Affiliation(s)
- Matthew E Bergman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Sonia E Evans
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Benjamin Davis
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Rehma Hamid
- Department of Biology, University of Toronto—Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Ibadat Bajwa
- Department of Biology, University of Toronto—Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Amreetha Jayathilake
- Department of Biology, University of Toronto—Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Anmol Kaur Chahal
- Department of Biology, University of Toronto—Mississauga, Mississauga, Ontario, Canada L5L 1C6
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8
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Allen H, Zeef L, Morreel K, Goeminne G, Kumar M, Gomez LD, Dean AP, Eckmann A, Casiraghi C, McQueen-Mason SJ, Boerjan W, Turner SR. Flexible and digestible wood caused by viral-induced alteration of cell wall composition. Curr Biol 2022; 32:3398-3406.e6. [PMID: 35732179 PMCID: PMC9616729 DOI: 10.1016/j.cub.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022]
Abstract
Woody plant material represents a vast renewable resource that has the potential to produce biofuels and other bio-based products with favorable net CO2 emissions.1,2 Its potential has been demonstrated in a recent study that generated novel structural materials from flexible moldable wood.3 Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility.4 Although ARW disease is associated with the presence of an RNA virus5 known as apple rubbery wood virus (ARWV), how the unique symptoms develop is unknown. We demonstrate that the symptoms of ARWV infections arise from reduced lignification within the secondary cell wall of xylem fibers and result in increased wood digestibility. In contrast, the mid-lamellae region and xylem ray cells are largely unaffected by the infection. Gene expression and proteomic data from symptomatic xylem clearly show the downregulation of phenylalanine ammonia lyase (PAL), the enzyme catalyzing the first committed step in the phenylpropanoid pathway leading to lignin biosynthesis. A large increase in soluble phenolics in symptomatic xylem, including the lignin precursor phenylalanine, is also consistent with PAL downregulation. ARWV infection results in the accumulation of many host-derived virus-activated small interfering RNAs (vasiRNAs). PAL-derived vasiRNAs are among the most abundant vasiRNAs in symptomatic xylem and are likely the cause of reduced PAL activity. Apparently, the mechanism used by the virus to alter lignin exhibits similarities to the RNAi strategy used to alter lignin in genetically modified trees to generate comparable improvements in wood properties.6, 7, 8 Video abstract
Apple rubbery wood (ARW) symptoms are caused by decreased lignin in woody tissue RNA-seq, proteomics, and metabolomics suggest phenylalanine levels decrease Virus-activated small interfering RNAs (vasiRNAs) are generated in response to ARWV infection VasiRNAs cause siRNA-based downregulation of phenylalanine ammonia
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Affiliation(s)
- Holly Allen
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leo Zeef
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Metabolomics Core Gent, VIB, 9052 Zwijnaarde, Belgium
| | - Manoj Kumar
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew P Dean
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Axel Eckmann
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cinzia Casiraghi
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York YO10 5DD, UK
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Simon R Turner
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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9
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The ease and complexity of identifying and using specialized metabolites for crop engineering. Emerg Top Life Sci 2022; 6:153-162. [PMID: 35302160 PMCID: PMC9023015 DOI: 10.1042/etls20210248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Plants produce a broad variety of specialized metabolites with distinct biological activities and potential applications. Despite this potential, most biosynthetic pathways governing specialized metabolite production remain largely unresolved across the plant kingdom. The rapid advancement of genetics and biochemical tools has enhanced our ability to identify plant specialized metabolic pathways. Further advancements in transgenic technology and synthetic biology approaches have extended this to a desire to design new pathways or move existing pathways into new systems to address long-running difficulties in crop systems. This includes improving abiotic and biotic stress resistance, boosting nutritional content, etc. In this review, we assess the potential and limitations for (1) identifying specialized metabolic pathways in plants with multi-omics tools and (2) using these enzymes in synthetic biology or crop engineering. The goal of these topics is to highlight areas of research that may need further investment to enhance the successful application of synthetic biology for exploiting the myriad of specialized metabolic pathways.
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10
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Huang XQ, Li R, Fu J, Dudareva N. A peroxisomal heterodimeric enzyme is involved in benzaldehyde synthesis in plants. Nat Commun 2022; 13:1352. [PMID: 35292635 PMCID: PMC8924275 DOI: 10.1038/s41467-022-28978-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/12/2022] [Indexed: 11/09/2022] Open
Abstract
Benzaldehyde, the simplest aromatic aldehyde, is one of the most wide-spread volatiles that serves as a pollinator attractant, flavor, and antifungal compound. However, the enzyme responsible for its formation in plants remains unknown. Using a combination of in vivo stable isotope labeling, classical biochemical, proteomics and genetic approaches, we show that in petunia benzaldehyde is synthesized via the β-oxidative pathway in peroxisomes by a heterodimeric enzyme consisting of α and β subunits, which belong to the NAD(P)-binding Rossmann-fold superfamily. Both subunits are alone catalytically inactive but, when mixed in equal amounts, form an active enzyme, which exhibits strict substrate specificity towards benzoyl-CoA and uses NADPH as a cofactor. Alpha subunits can form functional heterodimers with phylogenetically distant β subunits, but not all β subunits partner with α subunits, at least in Arabidopsis. Analysis of spatial, developmental and rhythmic expression of genes encoding α and β subunits revealed that expression of the gene for the α subunit likely plays a key role in regulating benzaldehyde biosynthesis. Benzaldehyde is a simple aromatic aldehyde that attracts pollinators, has antifungal properties and contributes to flavor in many plants. Here the authors show that benzaldehyde is synthesized in petunia via the benzoic acid β-oxidative pathway by a peroxisomal heterodimeric enzyme consisting of α and β subunits.
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Affiliation(s)
- Xing-Qi Huang
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Renqiuguo Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Jianxin Fu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.,School of Landscape Architecture, Zhejiang Agriculture & Forestry University, 311300, Hangzhou, P.R. China
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA. .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
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11
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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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12
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Adaptive mechanisms of plant specialized metabolism connecting chemistry to function. Nat Chem Biol 2021; 17:1037-1045. [PMID: 34552220 DOI: 10.1038/s41589-021-00822-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/21/2021] [Indexed: 12/29/2022]
Abstract
As sessile organisms, plants evolved elaborate metabolic systems that produce a plethora of specialized metabolites as a means to survive challenging terrestrial environments. Decades of research have revealed the genetic and biochemical basis for a multitude of plant specialized metabolic pathways. Nevertheless, knowledge is still limited concerning the selective advantages provided by individual and collective specialized metabolites to the reproductive success of diverse host plants. Here we review the biological functions conferred by various classes of plant specialized metabolites in the context of the interaction of plants with their surrounding environment. To achieve optimal multifunctionality of diverse specialized metabolic processes, plants use various adaptive mechanisms at subcellular, cellular, tissue, organ and interspecies levels. Understanding these mechanisms and the evolutionary trajectories underlying their occurrence in nature will ultimately enable efficient bioengineering of desirable metabolic traits in chassis organisms.
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Study of the l-Phenylalanine Ammonia-Lyase Penetration Kinetics and the Efficacy of Phenylalanine Catabolism Correction Using In Vitro Model Systems. Pharmaceutics 2021; 13:pharmaceutics13030383. [PMID: 33805682 PMCID: PMC7999051 DOI: 10.3390/pharmaceutics13030383] [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: 02/21/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/02/2022] Open
Abstract
The kinetics of l-phenylalanine ammonia-lyase (PAL) penetration into the monolayer of liver cells after its release from capsules was studied. The studies showed the absence of the effect of the capsule shell based on plant hydrocolloids on the absorption of l-phenylalanine ammonia-lyase in systems simulating the liver surface. After 120 min of incubation, in all variants of the experiment, from 87.0 to 96.8% of the enzyme penetrates the monolayer of liver cells. The combined analysis of the results concludes that the developed encapsulated form of l-phenylalanine ammonia-lyase is characterized by high efficiency in correcting the disturbed catabolism of phenylalanine in phenylketonuria, which is confirmed by the results of experiments carried out on in vitro model systems. PAL is approved for the treatment of adult patients with phenylketonuria. The encapsulated l-phenylalanine ammonia-lyase form can find therapeutic application in the phenylketonuria treatment after additional in vitro and in vivo studies, in particular, the study of preparation safety indicators. Furthermore, it demonstrated high efficacy in tumor regression and the treatment of tyrosine-related metabolic disorders such as tyrosinemia. Several therapeutically valuable metabolites biosynthesized by PAL via its catalytic action are included in food supplements, antimicrobial peptides, drugs, amino acids, and their derivatives. PAL, with improved pharmacodynamic and pharmacokinetic properties, is a highly effective medical drug.
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Lynch JH, Huang XQ, Dudareva N. Silent constraints: the hidden challenges faced in plant metabolic engineering. Curr Opin Biotechnol 2021; 69:112-117. [PMID: 33429160 DOI: 10.1016/j.copbio.2020.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 01/12/2023]
Abstract
Metabolic engineering is embraced as a method to sustainably enhance production of valuable phytochemicals with beneficial properties. However, successful production of these compounds in plants is not always predictable even when the pathways are fully known, frequently due to the lack of comprehensive understanding of plant metabolism as a whole, and interconnections between different primary, secondary, and hormone metabolic networks. Here, we highlight critical hidden constraints, including substrate availability, silent metabolism, and metabolic crosstalk, that impair engineering strategies. We explore how these constraints have historically been manifested in engineering attempts and propose how modern advancements will enable future strategies to overcome these impediments.
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Affiliation(s)
- Joseph H Lynch
- 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
| | - Xing-Qi Huang
- 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
| | - Natalia Dudareva
- 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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15
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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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16
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Yuan J, Sun X, Guo T, Chao Y, Han L. Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves. PeerJ 2020; 8:e8426. [PMID: 32002335 PMCID: PMC6979412 DOI: 10.7717/peerj.8426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa.
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Affiliation(s)
- Jianbo Yuan
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Xinbo Sun
- College of Agronomy, Hebei Agricultural University, Key Laboratory of Crop Growth Regulation of Hebei Province, China
| | - Tao Guo
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yuehui Chao
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Liebao Han
- College of Grassland Science, Beijing Forestry University, Beijing, China
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17
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Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop ( Humulus lupulus L.). Int J Mol Sci 2019; 21:ijms21010233. [PMID: 31905722 PMCID: PMC6981390 DOI: 10.3390/ijms21010233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 12/19/2022] Open
Abstract
The hop plant (Humulus lupulus L.) produces several valuable secondary metabolites, such as prenylflavonoid, bitter acids, and essential oils. These compounds are biosynthesized in glandular trichomes (lupulin glands) endowed with pharmacological properties and widely implicated in the beer brewing industry. The present study is an attempt to generate exhaustive information of transcriptome dynamics and gene regulatory mechanisms involved in biosynthesis and regulation of these compounds, developmental changes including trichome development at three development stages, namely leaf, bract, and mature lupulin glands. Using high-throughput RNA-Seq technology, a total of 61.13, 50.01, and 20.18 Mb clean reads in the leaf, bract, and lupulin gland libraries, respectively, were obtained and assembled into 43,550 unigenes. The putative functions were assigned to 30,996 transcripts (71.17%) based on basic local alignment search tool similarity searches against public sequence databases, including GO, KEGG, NR, and COG families, which indicated that genes are principally involved in fundamental cellular and molecular functions, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in leaf, bract, and lupulin glands tissues of hop. The expression profile of transcript encoding enzymes of BCAA metabolism, MEP, and shikimate pathway was most up-regulated in lupulin glands compared with leaves and bracts. Similarly, the expression levels of the transcription factors and structural genes that directly encode enzymes involved in xanthohumol, bitter acids, and terpenoids biosynthesis pathway were found to be significantly enhanced in lupulin glands, suggesting that production of these metabolites increases after the leaf development. In addition, numerous genes involved in primary metabolism, lipid metabolism, photosynthesis, generation of precursor metabolites/energy, protein modification, transporter activity, and cell wall component biogenesis were differentially regulated in three developmental stages, suggesting their involvement in the dynamics of the lupulin gland development. The identification of differentially regulated trichome-related genes provided a new foundation for molecular research on trichome development and differentiation in hop. In conclusion, the reported results provide directions for future functional genomics studies for genetic engineering or molecular breeding for augmentation of secondary metabolite content in hop.
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Ma D, Reichelt M, Yoshida K, Gershenzon J, Constabel CP. Two R2R3-MYB proteins are broad repressors of flavonoid and phenylpropanoid metabolism in poplar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:949-965. [PMID: 30176084 DOI: 10.1111/tpj.14081] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/15/2018] [Accepted: 08/20/2018] [Indexed: 05/18/2023]
Abstract
The phenylpropanoid pathway leads to the production of many important plant secondary metabolites including lignin, chlorogenic acids, flavonoids, and phenolic glycosides. Early studies have demonstrated that flavonoid biosynthesis is transcriptionally regulated, often by a MYB, bHLH, and WDR transcription factor complex. In poplar, several R2R3 MYB transcription factors are known to be involved in flavonoid biosynthesis. Previous work determined that poplar MYB134 and MYB115 are major activators of the proanthocyanidin pathway, and also induce the expression of repressor-like MYB transcription factors. Here we characterize two new repressor MYBs, poplar MYB165 and MYB194, paralogs which comprise a subgroup of R2R3-MYBs distinct from previously reported poplar repressors. Both MYB165 and MYB194 repressed the activation of flavonoid promoters by MYB134 in transient activation assays, and both interacted with a co-expressed bHLH transcription factor, bHLH131, in yeast two-hybrid assays. Overexpression of MYB165 and MYB194 in hybrid poplar resulted in greatly reduced accumulation of several phenylpropanoids including anthocyanins, proanthocyanidins, phenolic glycosides, and hydroxycinnamic acid esters. Transcriptome analysis of MYB165- and MYB194-overexpressing poplars confirmed repression of many phenylpropanoid enzyme genes. In addition, other MYB genes as well as several shikimate pathway enzyme genes were downregulated by MYB165-overexpression. By contrast, leaf aromatic amino acid concentrations were greater in MYB165-overexpressing poplars. Our findings indicate that MYB165 is a major repressor of the flavonoid and phenylpropanoid pathway in poplar, and may also affect the shikimate pathway. The coordinated action of repressor and activator MYBs could be important for the fine tuning of proanthocyanidin biosynthesis during development or following stress.
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Affiliation(s)
- Dawei Ma
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8P 5C2, Canada
| | - Michael Reichelt
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Kazuko Yoshida
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8P 5C2, Canada
| | - Jonathan Gershenzon
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - C Peter Constabel
- Centre for Forest Biology & Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8P 5C2, Canada
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19
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Advances in metabolic flux analysis toward genome-scale profiling of higher organisms. Biosci Rep 2018; 38:BSR20170224. [PMID: 30341247 PMCID: PMC6250807 DOI: 10.1042/bsr20170224] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 10/06/2018] [Accepted: 10/14/2018] [Indexed: 11/25/2022] Open
Abstract
Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.
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20
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Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells. Metab Eng 2018; 49:36-46. [DOI: 10.1016/j.ymben.2018.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/16/2018] [Accepted: 07/08/2018] [Indexed: 12/15/2022]
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21
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Schenck CA, Maeda HA. Tyrosine biosynthesis, metabolism, and catabolism in plants. PHYTOCHEMISTRY 2018; 149:82-102. [PMID: 29477627 DOI: 10.1016/j.phytochem.2018.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid (AAA) required for protein synthesis in all organisms, but synthesized de novo only in plants and microorganisms. In plants, Tyr also serves as a precursor of numerous specialized metabolites that have diverse physiological roles as electron carriers, antioxidants, attractants, and defense compounds. Some of these Tyr-derived plant natural products are also used in human medicine and nutrition (e.g. morphine and vitamin E). While the Tyr biosynthesis and catabolic pathways have been extensively studied in microbes and animals, respectively, those of plants have received much less attention until recently. Accumulating evidence suggest that the Tyr biosynthetic pathways differ between microbes and plants and even within the plant kingdom, likely to support the production of lineage-specific plant specialized metabolites derived from Tyr. The interspecies variations of plant Tyr pathway enzymes can now be used to enhance the production of Tyr and Tyr-derived compounds in plants and other synthetic biology platforms.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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22
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Cna'ani A, Shavit R, Ravid J, Aravena-Calvo J, Skaliter O, Masci T, Vainstein A. Phenylpropanoid Scent Compounds in Petunia x hybrida Are Glycosylated and Accumulate in Vacuoles. FRONTIERS IN PLANT SCIENCE 2017; 8:1898. [PMID: 29163617 PMCID: PMC5675896 DOI: 10.3389/fpls.2017.01898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/19/2017] [Indexed: 05/24/2023]
Abstract
Floral scent has been studied extensively in the model plant Petunia. However, little is known about the intracellular fate of scent compounds. Here, we characterize the glycosylation of phenylpropanoid scent compounds in Petunia x hybrida. This modification reduces scent compounds' volatility, reactivity, and autotoxicity while increasing their water-solubility. Gas chromatography-mass spectrometry (GC-MS) analyses revealed that flowers of petunia cultivars accumulate substantial amounts of glycosylated scent compounds and that their increasing level parallels flower development. In contrast to the pool of accumulated aglycones, which drops considerably at the beginning of the light period, the collective pool of glycosides starts to increase at that time and does not decrease thereafter. The glycoside pool is dynamic and is generated or catabolized during peak scent emission, as inferred from phenylalanine isotope-feeding experiments. Using several approaches, we show that phenylpropanoid scent compounds are stored as glycosides in the vacuoles of petal cells: ectopic expression of Aspergillus niger β-glucosidase-1 targeted to the vacuole resulted in decreased glycoside accumulation; GC-MS analysis of intact vacuoles isolated from petal protoplasts revealed the presence of glycosylated scent compounds. Accumulation of glycosides in the vacuoles seems to be a common mechanism for phenylpropanoid metabolites.
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Affiliation(s)
- Alon Cna'ani
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Reut Shavit
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jasmin Ravid
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Javiera Aravena-Calvo
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Oded Skaliter
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Tania Masci
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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