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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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102
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103
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Perez de Souza L, Scossa F, Proost S, Bitocchi E, Papa R, Tohge T, Fernie AR. Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1132-1153. [PMID: 30480348 PMCID: PMC6850281 DOI: 10.1111/tpj.14178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.
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Affiliation(s)
| | - Federico Scossa
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Consiglio per la ricerca in agricoltura e l′analisi dell′economia agrariaCREA‐OFAVia di Fioranello 5200134RomeItaly
| | - Sebastian Proost
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Takayuki Tohge
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Graduate School of Biological SciencesNara Institute of Science and TechnologyIkoma, Nara630‐0192Japan
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
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104
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Lortzing V, Oberländer J, Lortzing T, Tohge T, Steppuhn A, Kunze R, Hilker M. Insect egg deposition renders plant defence against hatching larvae more effective in a salicylic acid-dependent manner. PLANT, CELL & ENVIRONMENT 2019; 42:1019-1032. [PMID: 30252928 DOI: 10.1111/pce.13447] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/15/2018] [Indexed: 05/06/2023]
Abstract
Plants can improve their antiherbivore defence by taking insect egg deposition as cue of impending feeding damage. Previous studies showed that Pieris brassicae larvae feeding upon egg-deposited Brassicaceae perform worse and gain less weight than larvae on egg-free plants. We investigated how P. brassicae oviposition on Arabidopsis thaliana affects the plant's molecular and chemical responses to larvae. A transcriptome comparison of feeding-damaged leaves without and with prior oviposition revealed about 200 differently expressed genes, including enhanced expression of PR5, which is involved in salicylic acid (SA)-signalling. SA levels were induced by larval feeding to a slightly greater extent in egg-deposited than egg-free plants. The adverse effect of egg-deposited wild-type (WT) plants on larval weight was absent in an egg-deposited PR5-deficient mutant or other mutants impaired in SA-mediated signalling, that is, sid2/ics1, ald1, and pad4. In contrast, the adverse effect of egg-deposited WT plants on larvae was retained in egg-deposited npr1 and wrky70 mutants impaired further downstream in SA-signalling. Oviposition induced accumulation of flavonols in WT plants with and without feeding damage, but not in the PR5-deficient mutant. We demonstrated that egg-mediated improvement of A. thaliana's antiherbivore defence involves SA-signalling in an NPR1-independent manner and is associated with accumulation of flavonols.
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Affiliation(s)
- Vivien Lortzing
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Jana Oberländer
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Tobias Lortzing
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Department Secondary Metabolism, Potsdam, Germany
| | - Anke Steppuhn
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Monika Hilker
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
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105
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Fàbregas N, Fernie AR. The metabolic response to drought. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1077-1085. [PMID: 30726961 DOI: 10.1093/jxb/ery437] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/28/2018] [Indexed: 05/23/2023]
Abstract
Metabolic regulation is one of the main mechanisms involved in the maintenance of cell osmotic potential under abiotic stress. To date, metabolite profiling approaches have been extensively used to characterize the molecular responses to abiotic stress in many plant species. However, studies revealing the specific metabolic responses of plants exposed to water-deficit stress remain limited. Here, we review the most recent developments that advance our understanding of the metabolic response to drought stress in Arabidopsis and rice. We provide an updated schematic overview of the specific metabolic signature of wild-type plants in response to drought.
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Affiliation(s)
- Norma Fàbregas
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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106
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Fang C, Luo J, Wang S. The Diversity of Nutritional Metabolites: Origin, Dissection, and Application in Crop Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:1028. [PMID: 31475024 PMCID: PMC6706459 DOI: 10.3389/fpls.2019.01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 05/21/2023]
Abstract
The chemical diversity of plants is very high, and plant-based foods provide almost all the nutrients necessary for human health, either directly or indirectly. With advancements in plant metabolomics studies, the concept of nutritional metabolites has been expanded and updated. Because the concentration of many nutrients is usually low in plant-based foods, especially those from crops, metabolome-assisted breeding techniques using molecular markers associated with the synthesis of nutritional metabolites have been developed and used to improve nutritional quality of crops. Here, we review the origins of the diversity of nutrient metabolites from a genomic perspective and the role of gene duplication and divergence. In addition, we systematically review recent advances in the metabolomic and genetic basis of metabolite production in major crops. With the development of genome sequencing and metabolic detection technologies, multi-omic integrative analysis of genomes, transcriptomes, and metabolomes has greatly facilitated the deciphering of the genetic basis of metabolic pathways and the diversity of nutrient metabolites. Finally, we summarize the application of nutrient diversity in crop breeding and discuss the future development of a viable alternative to metabolome-assisted breeding techniques that can be used to improve crop nutrient quality.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Shouchuang Wang,
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107
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Fang C, Fernie AR, Luo J. Exploring the Diversity of Plant Metabolism. TRENDS IN PLANT SCIENCE 2019; 24:83-98. [PMID: 30297176 DOI: 10.1016/j.tplants.2018.09.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
Plants produce a huge array of metabolites, far more than those produced by most other organisms. Unraveling this diversity and its underlying genetic variation has attracted increasing research attention. Post-genomic profiling platforms have enabled the marriage and mining of the enormous amount of phenotypic and genetic diversity. We review here achievements to date and challenges remaining that are associated with plant metabolic research using multi-omic strategies. We focus mainly on strategies adopted in investigating the diversity of plant metabolism and its underlying features. Recent advances in linking metabotypes with phenotypic and genotypic traits are also discussed. Taken together, we conclude that exploring the diversity of metabolism could provide new insights into plant evolution and domestication.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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108
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Brog YM, Osorio S, Yichie Y, Alseekh S, Bensal E, Kochevenko A, Zamir D, Fernie AR. A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:391-403. [PMID: 30230636 PMCID: PMC7379295 DOI: 10.1111/tpj.14095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 05/31/2023]
Abstract
We present a complementary resource for trait fine-mapping in tomato to those based on the intra-specific cross between cultivated tomato and the wild tomato species Solanum pennellii, which have been extensively used for quantitative genetics in tomato over the last 20 years. The current population of backcross inbred lines (BILs) is composed of 107 lines derived after three backcrosses of progeny of the wild species Solanum neorickii (LA2133) and cultivated tomato (cultivar TA209) and is freely available to the scientific community. These S. neorickii BILs were genotyped using the 10K SolCAP single nucleotide polymorphism chip, and 3111 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs harbor on average 4.3 introgressions per line, with a mean introgression length of 34.7 Mbp, allowing partitioning of the genome into 340 bins and thereby facilitating rapid trait mapping. We demonstrate the power of using this resource in comparison with archival data from the S. pennellii resources by carrying out metabolic quantitative trait locus analysis following gas chromatography-mass spectrometry on fruits harvested from the S. neorickii BILs. The metabolic candidate genes phenylalanine ammonia-lyase and cystathionine gamma-lyase were then tested and validated in F2 populations and via agroinfiltration-based overexpression in order to exemplify the fidelity of this method in identifying the genes that drive tomato metabolic phenotypes.
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Affiliation(s)
- Yaacov Micha Brog
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ – University of Malaga – Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Campus de Teatinos29071MálagaSpain
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - Yoav Yichie
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
- Center of Plant Systems Biology and Biotechnology4000PlovdivBulgaria
| | - Elad Bensal
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Andriy Kochevenko
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - Dani Zamir
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
- Center of Plant Systems Biology and Biotechnology4000PlovdivBulgaria
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109
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Soubeyrand E, Johnson TS, Latimer S, Block A, Kim J, Colquhoun TA, Butelli E, Martin C, Wilson MA, Basset GJ. The Peroxidative Cleavage of Kaempferol Contributes to the Biosynthesis of the Benzenoid Moiety of Ubiquinone in Plants. THE PLANT CELL 2018; 30:2910-2921. [PMID: 30429224 PMCID: PMC6354277 DOI: 10.1105/tpc.18.00688] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/13/2018] [Indexed: 05/24/2023]
Abstract
Land plants possess the unique capacity to derive the benzenoid moiety of the vital respiratory cofactor, ubiquinone (coenzyme Q), from phenylpropanoid metabolism via β-oxidation of p-coumarate to form 4-hydroxybenzoate. Approximately half of the ubiquinone in plants comes from this pathway; the origin of the rest remains enigmatic. In this study, Phe-[Ring-13C6] feeding assays and gene network reconstructions uncovered a connection between the biosynthesis of ubiquinone and that of flavonoids in Arabidopsis (Arabidopsis thaliana). Quantification of ubiquinone in Arabidopsis and tomato (Solanum lycopersicum) mutants in flavonoid biosynthesis pinpointed the corresponding metabolic branch-point as lying between flavanone-3-hydroxylase and flavonoid-3'-hydroxylase. Further isotopic labeling and chemical rescue experiments demonstrated that the B-ring of kaempferol is incorporated into ubiquinone. Moreover, heme-dependent peroxidase activities were shown to be responsible for the cleavage of B-ring of kaempferol to form 4-hydroxybenzoate. By contrast, kaempferol 3-β-d-glucopyranoside, dihydrokaempferol, and naringenin were refractory to peroxidative cleavage. Collectively, these data indicate that kaempferol contributes to the biosynthesis of a vital respiratory cofactor, resulting in an extraordinary metabolic arrangement where a specialized metabolite serves as a precursor for a primary metabolite. Evidence is also provided that the ubiquinone content of tomato fruits can be manipulated via deregulation of flavonoid biosynthesis.
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Affiliation(s)
- Eric Soubeyrand
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida 32611
| | - Timothy S Johnson
- Department of Environmental Horticulture, University of Florida, Gainesville, Florida 32611
| | - Scott Latimer
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida 32611
| | - Anna Block
- Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, U.S. Department of Agriculture, Gainesville, Florida 32608
| | - Jeongim Kim
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida 32611
| | - Thomas A Colquhoun
- Department of Environmental Horticulture, University of Florida, Gainesville, Florida 32611
| | - Eugenio Butelli
- John Innes Centre, Colney Research Park, Norwich, United Kingdom
| | - Cathie Martin
- John Innes Centre, Colney Research Park, Norwich, United Kingdom
| | - Mark A Wilson
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Gilles J Basset
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida 32611
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110
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Zhang Y, Fernie AR. On the role of the tricarboxylic acid cycle in plant productivity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1199-1216. [PMID: 29917310 DOI: 10.1111/jipb.12690] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/18/2018] [Indexed: 05/10/2023]
Abstract
The tricarboxylic acid (TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were reduced or knocked out in order to ascertain their in vivo function. Some of the resultant plants exhibited improved photosynthesis and plant growth, under controlled greenhouse conditions. In addition, overexpression of the endogenous genes, or heterologous forms of a number of the enzymes, has been carried out in tomato fruit and the roots of a range of species, and in some instances improvement in fruit yield and postharvest properties and plant performance, under nutrient limitation, have been reported, respectively. Given a number of variants, in nature, we discuss possible synthetic approaches involving introducing these variants, or at least a subset of them, into plants. We additionally discuss the likely consequences of introducing synthetic metabolons, wherein certain pairs of reactions are artificially permanently assembled into plants, and speculate as to future strategies to further improve plant productivity by manipulation of the core metabolic pathway.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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111
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Looking at Flavonoid Biodiversity in Horticultural Crops: A Colored Mine with Nutritional Benefits. PLANTS 2018; 7:plants7040098. [PMID: 30405037 PMCID: PMC6313872 DOI: 10.3390/plants7040098] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 12/22/2022]
Abstract
Flavonoids represent a wide group of plant secondary metabolites implicated in many physiological roles, from the attraction of pollinators to the protection against biotic or abiotic stresses. Flavonoids are synthetized in a number of horticultural crops that are important components of our daily diet. In the last decades, the consumption of vegetables rich in antioxidants has been strongly promoted from the perspective of prevention/protection against chronic diseases. Therefore, due to their nutritional importance, several attempts have been made to enhance flavonoid levels in species of agronomic interest. In this review, we focus on the flavonoid biodiversity among the major horticultural species, which is responsible of differences among closely related species and influences the qualitative/quantitative composition. We also review the role of flavonoids in the nutritional quality of plant products, contributing to their organoleptic and nutritional properties, and the main strategies of biofortification to increase their content.
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112
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Chen J, Wang J, Chen W, Sun W, Peng M, Yuan Z, Shen S, Xie K, Jin C, Sun Y, Liu X, Fernie AR, Yu S, Luo J. Metabolome Analysis of Multi-Connected Biparental Chromosome Segment Substitution Line Populations. PLANT PHYSIOLOGY 2018; 178:612-625. [PMID: 30139795 PMCID: PMC6181037 DOI: 10.1104/pp.18.00490] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/14/2018] [Indexed: 05/05/2023]
Abstract
Metabolomic analysis coupled with advanced genetic populations represents a powerful tool with which to investigate the plant metabolome. However, genetic analyses of the rice (Oryza sativa) metabolome have been conducted mainly using natural accessions or a single biparental population. Here, the flag leaves from three interconnected chromosome segment substitution line populations with a common recurrent genetic background were used to dissect rice metabolic diversity. We effectively used multiple interconnected biparental populations, constructed by introducing genomic segments into Zhenshan 97 from ACC10 (A/Z), Minghui 63 (M/Z), and Nipponbare (N/Z), to map metabolic quantitative trait loci (mQTL). A total of 1,587 mQTL were generated, of which 684, 479, and 722 were obtained from the A/Z, M/Z, and N/Z chromosome segment substitution line populations, respectively, and we designated 99 candidate genes for 367 mQTL. In addition, 1,001 mQTL were generated specifically from joint linkage analysis with 25 candidate genes assigned. Several of these candidates were validated, such as LOC_Os07g01020 for the in vivo content of pyridoxine and its derivative and LOC_Os04g25980 for cis-zeatin glucosyltransferase activity. We propose a novel biosynthetic pathway for O-methylapigenin C-pentoside and demonstrated that LOC_Os04g11970 encodes a component of this pathway through fine-mapping. We postulate that the methylated apigenin may confer plant disease resistance. This study demonstrates the power of using multiple interconnected populations to generate a large number of veritable mQTL. The combined results are discussed in the context of functional metabolomics and the possible features of assigned candidates underlying respective metabolites.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Wei Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yangyang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, Hainan 572208, China
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113
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Brandt S, Fachinger S, Tohge T, Fernie AR, Braun HP, Hildebrandt TM. Extended darkness induces internal turnover of glucosinolates in Arabidopsis thaliana leaves. PLoS One 2018; 13:e0202153. [PMID: 30092103 PMCID: PMC6084957 DOI: 10.1371/journal.pone.0202153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/27/2018] [Indexed: 11/20/2022] Open
Abstract
Prolonged darkness leads to carbohydrate starvation, and as a consequence plants degrade proteins and lipids to oxidize amino acids and fatty acids as alternative substrates for mitochondrial ATP production. We investigated, whether the internal breakdown of glucosinolates, a major class of sulfur-containing secondary metabolites, might be an additional component of the carbohydrate starvation response in Arabidopsis thaliana (A. thaliana). The glucosinolate content of A. thaliana leaves was strongly reduced after seven days of darkness. We also detected a significant increase in the activity of myrosinase, the enzyme catalyzing the initial step in glucosinolate breakdown, coinciding with a strong induction of the main leaf myrosinase isoforms TGG1 and TGG2. In addition, nitrilase activity was increased suggesting a turnover via nitriles and carboxylic acids. Internal degradation of glucosinolates might also be involved in diurnal or developmental adaptations of the glucosinolate profile. We observed a diurnal rhythm for myrosinase activity in two-week-old plants. Furthermore, leaf myrosinase activity and protein abundance of TGG2 varied during plant development, whereas leaf protein abundance of TGG1 remained stable indicating regulation at the transcriptional as well as post-translational level.
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Affiliation(s)
- Saskia Brandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Sara Fachinger
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
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114
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Alseekh S, Fernie AR. Metabolomics 20 years on: what have we learned and what hurdles remain? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:933-942. [PMID: 29734513 DOI: 10.1111/tpj.13950] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 05/11/2023]
Abstract
The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by the use of these approaches, and document the knowledge and technology gaps that are currently constraining its further development. Finally, we detail why we think that the time is ripe to refocus our efforts on the understanding of metabolic function.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Centre of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Centre of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
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115
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Tohge T, Borghi M, Fernie AR. The natural variance of the Arabidopsis floral secondary metabolites. Sci Data 2018; 5:180051. [PMID: 29611844 PMCID: PMC5881409 DOI: 10.1038/sdata.2018.51] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/07/2018] [Indexed: 12/15/2022] Open
Abstract
Application of mass spectrometry-based metabolomics enables the detection of genotype-related natural variance in metabolism. Differences in secondary metabolite composition of flowers of 64 Arabidopsis thaliana (Arabidopsis) natural accessions, representing a considerable portion of the natural variation in this species are presented. The raw metabolomic data of the accessions and reference extracts derived from flavonoid knockout mutants have been deposited in the MetaboLights database. Additionally, summary tables of floral secondary metabolite data are presented in this article to enable efficient re-use of the dataset either in metabolomics cross-study comparisons or correlation-based integrative analysis of other metabolomic and phenotypic features such as transcripts, proteins and growth and flowering related phenotypes.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Monica Borghi
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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116
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Abstract
A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture. Our research group has focused on metabolomics-based functional genomics over the last 15 years and we have developed a new research area called 'Phytochemical Genomics'. In this review, the development of a research platform for plant metabolomics is discussed first, to provide a better understanding of the chemical diversity of plants. Then, representative applications of metabolomics to functional genomics in a model plant, Arabidopsis thaliana, are described. The extension of integrated multi-omics analyses to non-model specialized plants, e.g., medicinal plants, is presented, including the identification of novel genes, metabolites and networks for the biosynthesis of flavonoids, alkaloids, sulfur-containing metabolites and terpenoids. Further, functional genomics studies on a variety of medicinal plants is presented. I also discuss future trends in pharmacognosy and related sciences.
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Affiliation(s)
- Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University.,RIKEN Center for Sustainable Resource Science
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117
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Abstract
Recent technological developments and methodological advances of both liquid chromatography (LC) and mass spectrometry (MS) have allowed LC-MS-based plant metabolomics to become a common tool for investigating quantity, quality, and chemical diversity of plant metabolites. Targeted LC-MS metabolite analysis focuses on the detection and quantitation of the researcher's target metabolites. Whilst the word "target analysis" has been used for the analytical measurement to obtain the absolute concentrations evaluated by authentic and/or stable-isotope-labeled standards, over time the phrase came to be also used in a broad sense for the measurement of annotatable metabolites by structural information obtained from the combination of different strategies such as MS/MS analysis, reference extracts, mutant analysis and database search. Here, we describe a general protocol for targeted LC-MS metabolite profiling of plant secondary metabolites. Additionally, we introduce some examples of peak annotation using the combination approach.
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118
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Tohge T, Perez de Souza L, Fernie AR. On the natural diversity of phenylacylated-flavonoid and their in planta function under conditions of stress. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:279-290. [PMID: 29755304 PMCID: PMC5932100 DOI: 10.1007/s11101-017-9531-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 08/26/2017] [Indexed: 05/02/2023]
Abstract
Plants contain light signaling systems and undergo metabolic perturbation and reprogramming under light stress in order to adapt to environmental changes. Flavonoids are one of the largest classes of natural phytochemical compounds having several biological functions conferring stress defense to plants and health benefits in animal diets. A recent study of phenylacylated-flavonoids (also called hydroxycinnamoylated-flavonoids) of natural accessions of Arabidopsis suggested that phenylacylation of flavonoids relates to selection under different natural light conditions. Phenylacylated-flavonoids which are decorated with hydroxycinnamoyl units, namely cinnamoyl, 4-coumaroyl, caffeoyl, feruloyl and sinapoyl moieties, are widely distributed in the plant kingdom. Currently, more than 400 phenylacylated flavonoids have been reported. Phenylacylation renders enhanced phytochemical functions such as ultraviolet-absorbance and antioxidant activity, although, the physiological role of phenylacylation of flavonoids in plants is largely unknown. In this review, we provide an overview of the occurrence and natural diversity of phenylacylated-flavonoids as well as postulating their biological functions both in planta and with respect to biological activity following their consumption.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Leonardo Perez de Souza
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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119
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Peng M, Shahzad R, Gul A, Subthain H, Shen S, Lei L, Zheng Z, Zhou J, Lu D, Wang S, Nishawy E, Liu X, Tohge T, Fernie AR, Luo J. Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance. Nat Commun 2017; 8:1975. [PMID: 29213047 PMCID: PMC5719032 DOI: 10.1038/s41467-017-02168-x] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/10/2017] [Indexed: 01/08/2023] Open
Abstract
Decoration of phytochemicals contributes to the majority of metabolic diversity in nature, whereas how this process alters the biological functions of their precursor molecules remains to be investigated. Flavones, an important yet overlooked subclass of flavonoids, are most commonly conjugated with sugar moieties by UDP-dependent glycosyltransferases (UGTs). Here, we report that the natural variation of rice flavones is mainly determined by OsUGT706D1 (flavone 7-O-glucosyltransferase) and OsUGT707A2 (flavone 5-O-glucosyltransferase). UV-B exposure and transgenic evaluation demonstrate that their allelic variation contributes to UV-B tolerance in nature. Biochemical characterization of over 40 flavonoid UGTs reveals their differential evolution in angiosperms. These combined data provide biochemical insight and genetic regulation into flavone biosynthesis and additionally suggest that adoption of the positive alleles of these genes into breeding programs will likely represent a potential strategy aimed at producing stress-tolerant plants.
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Affiliation(s)
- Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Raheel Shahzad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ambreen Gul
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hizar Subthain
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Long Lei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhigang Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Junjie Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Dandan Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Elsayed Nishawy
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Desert Research Center, Genetics Resource Department, Egyptian Deserts Gene Bank, Cairo, 11735, Egypt
| | - Xianqing Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Takayuki Tohge
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 572208, China.
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120
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Abstract
Plant metabolic studies have traditionally focused on the role and regulation of the enzymes catalyzing key reactions within specific pathways. Within the past 20 years, reverse genetic approaches have allowed direct determination of the effects of the deficiency, or surplus, of a given protein on the biochemistry of a plant. In parallel, top-down approaches have also been taken, which rely on screening broad, natural genetic diversity for metabolic diversity. Here, we compare and contrast the various strategies that have been adopted to enhance our understanding of the natural diversity of metabolism. We also detail how these approaches have enhanced our understanding of both specific and global aspects of the genetic regulation of metabolism. Finally, we discuss how such approaches are providing important insights into the evolution of plant secondary metabolism.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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121
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Tohge T, de Souza LP, Fernie AR. Current understanding of the pathways of flavonoid biosynthesis in model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4013-4028. [PMID: 28922752 DOI: 10.1093/jxb/erx177] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Flavonoids are a signature class of secondary metabolites formed from a relatively simple collection of scaffolds. They are extensively decorated by chemical reactions including glycosylation, methylation, and acylation. They are present in a wide variety of fruits and vegetables and as such in Western populations it is estimated that 20-50 mg of flavonoids are consumed daily per person. In planta they have demonstrated to contribute to both flower color and UV protection. Their consumption has been suggested to presenta wide range of health benefits. Recent technical advances allowing affordable whole genome sequencing, as well as a better inventory of species-by-species chemical diversity, have greatly advanced our understanding as to how flavonoid biosynthesis pathways vary across species. In parallel, reverse genetics combined with detailed molecular phenotyping is currently allowing us to elucidate the functional importance of individual genes and metabolites and by this means to provide further mechanistic insight into their biological roles. Here we provide an inventory of current knowledge of pathways of flavonoid biosynthesis in both the model plant Arabidopsis thaliana and a range of crop species, including tomato, maize, rice, and bean.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm
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122
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Perez de Souza L, Naake T, Tohge T, Fernie AR. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 2017; 6:1-20. [PMID: 28520864 PMCID: PMC5499862 DOI: 10.1093/gigascience/gix037] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/19/2023] Open
Abstract
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway toward improving our coverage of the plant metabolome.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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123
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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124
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Tohge T, Fernie AR. Leveraging Natural Variance towards Enhanced Understanding of Phytochemical Sunscreens. TRENDS IN PLANT SCIENCE 2017; 22:308-315. [PMID: 28173981 DOI: 10.1016/j.tplants.2017.01.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/23/2016] [Accepted: 01/08/2017] [Indexed: 05/28/2023]
Abstract
The dependency of plants on sunlight renders exposure to UV a constant hazard. Light of this wavelength is damaging to proteins, RNA, and DNA, with damage to the latter resulting in a high mutagenic potential. To acclimate to environmental changes in light wavelengths and intensity, plants accumulate the production of UV-B-protectant phytochemicals, such as flavonoids and vitamins. Here, we review current and emerging knowledge concerning the biochemical response of plants to UV-B exposure. We additionally outline our opinion that the adoption of broad natural variance represents a powerful strategy by which to identify both novel UV-B-relevant metabolites and the genes regulating their abundance. Finally, we discuss how such information may guide future metabolic engineering strategies aimed at producing stress-tolerant plants.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
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125
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Jin M, Zhang X, Zhao M, Deng M, Du Y, Zhou Y, Wang S, Tohge T, Fernie AR, Willmitzer L, Brotman Y, Yan J, Wen W. Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis. BMC PLANT BIOLOGY 2017; 17:17. [PMID: 28100172 PMCID: PMC5242060 DOI: 10.1186/s12870-017-0972-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/05/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway. RESULTS We repeatedly detected 25 QTL corresponding to 23 distinct flavonoids across different environments or populations. In addition, a total of 39 genes were revealed both by an expression based network analysis and genetic mapping. Finally, the function of three candidate genes, including two UDP-glycosyltransferases (UGT) and an oxygenase which belongs to the flavone synthase super family, was revealed via preliminary molecular functional characterization. CONCLUSION We explored the genetic influences on the flavonoid biosynthesis based on integrating the genomic, transcriptomic and metabolomic information which provided a rich source of potential candidate genes. The integrated genomics based genetic mapping strategy is highly efficient for defining the complexity of functional genetic variants and their respective regulatory networks as well as in helping to select candidate genes and allelic variance before embarking on laborious transgenic validations.
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Affiliation(s)
- Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Takayuki Tohge
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China
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