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Wang JX, Han WH, Xie R, Zhang FB, Ge ZW, Ji SX, Liu SS, Wang XW. Metabolic and Molecular Insights Into Nicotiana benthamiana Trichome Exudates: An Ammunition Depot for Plant Resistance Against Insect Pests. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39262218 DOI: 10.1111/pce.15135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/02/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
Nicotiana benthamiana, a widely acknowledged laboratory model plant for molecular studies, exhibits lethality to certain insect pests and can serve as a dead-end trap plant for pest control in the field. However, the underlying mechanism of N. benthamiana's resistance against insects remains unknown. Here, we elucidate that the lethal effect of N. benthamiana on the whitefly Bemisia tabaci arises from the toxic glandular trichome exudates. By comparing the metabolite profiles of trichome exudates, we found that 51 metabolites, including five O-acyl sugars (O-AS) with medium-chain acyl moieties, were highly accumulated in N. benthamiana. Silencing of two O-AS biosynthesis genes, branched-chain keto acid dehydrogenase (BCKD) and Isopropyl malate synthase-C (IPMS-C), significantly reduced the O-AS levels in N. benthamiana and its resistance against whiteflies. Additionally, we demonstrated that the higher expression levels of BCKD and IPMS-C in the trichomes of N. benthamiana contribute to O-AS synthesis and consequently enhance whitefly resistance. Furthermore, overexpression of NbBCKD and NbIPMS-C genes in the cultivated tobacco Nicotiana tabacum enhanced its resistance to whiteflies. Our study revealed the metabolic and molecular mechanisms underlying the lethal effect of N. benthamiana on whiteflies and presents a promising avenue for improving whitefly resistance.
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Affiliation(s)
- Jun-Xia Wang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Hao Han
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Rui Xie
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Feng-Bin Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhi-Wei Ge
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Shun-Xia Ji
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai MY. An agroecological structure model of compost-soil-plant interactions for sustainable organic farming. ISME COMMUNICATIONS 2023; 3:28. [PMID: 37002405 PMCID: PMC10066230 DOI: 10.1038/s43705-023-00233-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan.
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan.
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan.
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan.
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | | | | | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunya Taguchi
- Center for Frontier Medical Engineering, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Teruo Matsushita
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshiaki Ito
- Keiyo Gas Energy Solution Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Sankichi Horiuchi
- Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa, Chiba, 277-8567, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kenichi Mori
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Miroku Co., Ltd., Kitsuki, Oita, 873-0021, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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Cao P, Kim SJ, Xing A, Schenck CA, Liu L, Jiang N, Wang J, Last RL, Brandizzi F. Homeostasis of branched-chain amino acids is critical for the activity of TOR signaling in Arabidopsis. eLife 2019; 8:e50747. [PMID: 31808741 PMCID: PMC6937141 DOI: 10.7554/elife.50747] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/05/2019] [Indexed: 01/11/2023] Open
Abstract
The target of rapamycin (TOR) kinase is an evolutionarily conserved hub of nutrient sensing and metabolic signaling. In plants, a functional connection of TOR activation with glucose availability was demonstrated, while it is yet unclear whether branched-chain amino acids (BCAAs) are a primary input of TOR signaling as they are in yeast and mammalian cells. Here, we report on the characterization of an Arabidopsis mutant over-accumulating BCAAs. Through chemical interventions targeting TOR and by examining mutants of BCAA biosynthesis and TOR signaling, we found that BCAA over-accumulation leads to up-regulation of TOR activity, which causes reorganization of the actin cytoskeleton and actin-associated endomembranes. Finally, we show that activation of TOR is concomitant with alteration of cell expansion, proliferation and specialized metabolism, leading to pleiotropic effects on plant growth and development. These results demonstrate that BCAAs contribute to plant TOR activation and reveal previously uncharted downstream subcellular processes of TOR signaling.
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Affiliation(s)
- Pengfei Cao
- MSU-DOE Plant Research LabMichigan State UniversityEast LansingUnited States
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
| | - Sang-Jin Kim
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Anqi Xing
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Craig A Schenck
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Lu Liu
- MSU-DOE Plant Research LabMichigan State UniversityEast LansingUnited States
| | - Nan Jiang
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Jie Wang
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
| | - Robert L Last
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUnited States
| | - Federica Brandizzi
- MSU-DOE Plant Research LabMichigan State UniversityEast LansingUnited States
- Department of Plant BiologyMichigan State UniversityEast LansingUnited States
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
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Schaufelberger M, Galbier F, Herger A, de Brito Francisco R, Roffler S, Clement G, Diet A, Hörtensteiner S, Wicker T, Ringli C. Mutations in the Arabidopsis ROL17/isopropylmalate synthase 1 locus alter amino acid content, modify the TOR network, and suppress the root hair cell development mutant lrx1. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2313-2323. [PMID: 30753668 PMCID: PMC6463047 DOI: 10.1093/jxb/ery463] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/19/2018] [Indexed: 05/22/2023]
Abstract
The growth and development of organisms must be tightly controlled and adjusted to nutrient availability and metabolic activities. The Target of Rapamycin (TOR) network is a major control mechanism in eukaryotes and influences processes such as translation, mitochondrial activity, production of reactive oxygen species, and the cytoskeleton. In Arabidopsis thaliana, inhibition of the TOR kinase causes changes in cell wall architecture and suppression of phenotypic defects of the cell wall formation mutant lrx1 (leucine-rich repeat extensin 1). The rol17 (repressor of lrx1 17) mutant was identified as a new suppressor of lrx1 that induces also a short root phenotype. The ROL17 locus encodes isopropylmalate synthase 1, a protein involved in leucine biosynthesis. Dependent on growth conditions, mutations in ROL17 do not necessarily alter the level of leucine, but always cause development of the rol17 mutant phenotypes, suggesting that the mutation does not only influence leucine biosynthesis. Changes in the metabolome of rol17 mutants are also found in plants with inhibited TOR kinase activity. Furthermore, rol17 mutants show reduced sensitivity to the TOR kinase inhibitor AZD-8055, indicating a modified TOR network. Together, these data suggest that suppression of lrx1 by rol17 is the result of an alteration of the TOR network.
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Affiliation(s)
- Myriam Schaufelberger
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Florian Galbier
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Institute of Molecular Plant Biology, Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Aline Herger
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Rita de Brito Francisco
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Stefan Roffler
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Gilles Clement
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Anouck Diet
- Institute of Plant Sciences Paris-Saclay, CNRS, Université Paris Diderot, INRA, Université Paris Sud, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, Gif-sur-Yvette, France
| | - Stefan Hörtensteiner
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Christoph Ringli
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Correspondence:
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He Y, Cheng J, He Y, Yang B, Cheng Y, Yang C, Zhang H, Wang Z. Influence of isopropylmalate synthase OsIPMS1 on seed vigour associated with amino acid and energy metabolism in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:322-337. [PMID: 29947463 PMCID: PMC6335077 DOI: 10.1111/pbi.12979] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 06/24/2018] [Indexed: 05/21/2023]
Abstract
Seed vigour is an imperative trait for the direct seeding of rice. Isopropylmalate synthase (IPMS) catalyses the committed step of leucine (Leu) biosynthesis, but its effect on seed vigour remains unclear. In this study, rice OsIPMS1 and OsIPMS2 was cloned, and the roles of OsIPMS1 in seed vigour were mainly investigated. OsIPMS1 and OsIPMS2 catalyse Leu biosynthesis, and Leu feedback inhibits their IPMS activities. Disruption of OsIPMS1 resulted in low seed vigour under various conditions, which might be tightly associated with the reduction of amino acids in germinating seeds. Eleven amino acids that associated with stress tolerance, GA biosynthesis and tricarboxylic acid (TCA) cycle were significantly reduced in osipms1 mutants compared with those in wide type (WT) during seed germination. Transcriptome analysis indicated that a total of 1209 differentially expressed genes (DEGs) were altered in osipms1a mutant compared with WT at the early germination stage, wherein most of the genes were involved in glycolysis/gluconeogenesis, protein processing, pyruvate, carbon, fructose and mannose metabolism. Further analysis confirmed that the regulation of OsIPMS1 in seed vigour involved in starch hydrolysis, glycolytic activity and energy levels in germinating seeds. The effects of seed priming were tightly associated with the mRNA levels of OsIPMS1 in priming seeds. The OsIPMS1 might be used as a biomarker to determine the best stop time-point of seed priming in rice. This study provides novel insights into the function of OsIPMS1 on seed vigour and should have practical applications in seed priming of rice.
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Affiliation(s)
- Yongqi He
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Jinping Cheng
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Ying He
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Bin Yang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yanhao Cheng
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Can Yang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hongsheng Zhang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Zhoufei Wang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
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Guo R, Huang Z, Deng Y, Chen X, XuHan X, Lai Z. Comparative Transcriptome Analyses Reveal a Special Glucosinolate Metabolism Mechanism in Brassica alboglabra Sprouts. FRONTIERS IN PLANT SCIENCE 2016; 7:1497. [PMID: 27757119 PMCID: PMC5047911 DOI: 10.3389/fpls.2016.01497] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/20/2016] [Indexed: 05/20/2023]
Abstract
Brassica sprouts contain abundant phytochemicals, especially glucosinolates (GSs). Various methods have been used to enhance GS content in sprouts. However, the molecular basis of GS metabolism in sprouts remains an open question. Here we employed RNA-seq analysis to compare the transcriptomes of high-GS (JL-08) and low-GS (JL-09) Brassica alboglabra sprouts. Paired-end Illumina RNA-seq reads were generated and mapped to the Brassica oleracea reference genome. The differentially expressed genes were analyzed between JL-08 and JL-09. Among these, 1477 genes were up-regulated and 1239 down-regulated in JL-09 compared with JL-08. Enrichment analysis of these differentially expressed genes showed that the GS biosynthesis had the smallest enrichment factor and the highest Q-value of all metabolic pathways in Kyoto Encyclopedia of Genes and Genomes database, indicating the main metabolic difference between JL-08 and JL-09 is the GS biosynthetic pathway. Thirty-seven genes of the sequenced data were annotated as putatively involved in GS biosynthesis, degradation, and regulation, of which 11 were differentially expressed in JL-08 and JL-09. The expression level of GS degradation enzyme myrosinase in high-GS JL-08 was lower compared with low-GS JL-09. Surprisingly, in high-GS JL-08, the expression levels of GS biosynthesis genes were also lower than those in low-GS JL-09. As the GS contents in sprouts are determined by dynamic equilibrium of seed stored GS mobilization, de novo synthesis, degradation, and extra transport, the result of this study leads us to suggest that efforts to increase GS content should focus on either raising GS content in seeds or decreasing myrosinase activity, rather than improving the expression level of GS biosynthesis genes in sprouts.
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Affiliation(s)
- Rongfang Guo
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhongkai Huang
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yanping Deng
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xiaodong Chen
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xu XuHan
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institut de la Recherche Interdisciplinaire de ToulouseToulouse, France
- *Correspondence: Xu XuHan
| | - Zhongxiong Lai
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Zhongxiong Lai
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Babuin MF, Campestre MP, Rocco R, Bordenave CD, Escaray FJ, Antonelli C, Calzadilla P, Gárriz A, Serna E, Carrasco P, Ruiz OA, Menendez AB. Response to long-term NaHCO3-derived alkalinity in model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: transcriptomic profiling and physiological characterization. PLoS One 2014; 9:e97106. [PMID: 24835559 PMCID: PMC4024010 DOI: 10.1371/journal.pone.0097106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/14/2014] [Indexed: 11/19/2022] Open
Abstract
The current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation of a new homeostatic cellular condition after long-term alkaline stress. Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. Our results provided a set of selected, differentially expressed genes deserving further investigation and suggested that the L. japonicus ecotypes could constitute a useful model to search for common and distinct tolerance mechanisms to long-term alkaline stress response in plants.
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Affiliation(s)
- María Florencia Babuin
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - María Paula Campestre
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Rubén Rocco
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Cesar D. Bordenave
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Francisco J. Escaray
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Cristian Antonelli
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Pablo Calzadilla
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Andrés Gárriz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Eva Serna
- Unidad Central de Investigación en Medicina-INCLIVA, Universitat de Valencia, Valencia, Spain
| | - Pedro Carrasco
- Departamento de Bioquímica y Biología Vegetal-Universitat de Valencia, Valencia, Spain
| | - Oscar A. Ruiz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Ana B. Menendez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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8
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Gigolashvili T, Kopriva S. Transporters in plant sulfur metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:442. [PMID: 25250037 PMCID: PMC4158793 DOI: 10.3389/fpls.2014.00442] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/18/2014] [Indexed: 05/02/2023]
Abstract
Sulfur is an essential nutrient, necessary for synthesis of many metabolites. The uptake of sulfate, primary and secondary assimilation, the biosynthesis, storage, and final utilization of sulfur (S) containing compounds requires a lot of movement between organs, cells, and organelles. Efficient transport systems of S-containing compounds across the internal barriers or the plasma membrane and organellar membranes are therefore required. Here, we review a current state of knowledge of the transport of a range of S-containing metabolites within and between the cells as well as of their long distance transport. An improved understanding of mechanisms and regulation of transport will facilitate successful engineering of the respective pathways, to improve the plant yield, biotic interaction and nutritional properties of crops.
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Affiliation(s)
- Tamara Gigolashvili
- Department of Plant Molecular Physiology, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of CologneCologne Germany
- *Correspondence: Tamara Gigolashvili, Department of Plant Molecular Physiology, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, Zülpicher Street 47 B, 50674 Cologne, Germany e-mail:
| | - Stanislav Kopriva
- Plant Biochemistry Department, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of CologneCologne Germany
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9
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Abstract
Recursive pathways are broadly defined as those that catalyze a series of reactions such that the key, bond-forming functional group of the substrate is always regenerated in each cycle, allowing for a new cycle of reactions to begin. Recursive carbon-chain elongation pathways in nature produce fatty acids, polyketides, isoprenoids and α-keto acids (αKAs), which all use modular or iterative approaches for chain elongation. Recently, an artificial pathway for αKA elongation has been built that uses an engineered isopropylmalate synthase to recursively condense acetyl-CoA with αKAs. This synthetic approach expands the possibilities for recursive pathways beyond the modular or iterative synthesis of natural products and serves as a case study for understanding the challenges of building recursive pathways from nonrecursive enzymes. There exists the potential to design synthetic recursive pathways far beyond what nature has evolved.
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10
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de Kraker JW, Gershenzon J. From amino acid to glucosinolate biosynthesis: protein sequence changes in the evolution of methylthioalkylmalate synthase in Arabidopsis. THE PLANT CELL 2011; 23:38-53. [PMID: 21205930 PMCID: PMC3051243 DOI: 10.1105/tpc.110.079269] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 12/02/2010] [Accepted: 12/16/2010] [Indexed: 05/18/2023]
Abstract
Methylthioalkylmalate synthase (MAM) catalyzes the committed step in the side chain elongation of Met, yielding important precursors for glucosinolate biosynthesis in Arabidopsis thaliana and other Brassicaceae species. MAM is believed to have evolved from isopropylmalate synthase (IPMS), an enzyme involved in Leu biosynthesis, based on phylogenetic analyses and an overlap of catalytic abilities. Here, we investigated the changes in protein structure that have occurred during the recruitment of IPMS from amino acid to glucosinolate metabolism. The major sequence difference between IPMS and MAM is the absence of 120 amino acids at the C-terminal end of MAM that constitute a regulatory domain for Leu-mediated feedback inhibition. Truncation of this domain in Arabidopsis IPMS2 results in loss of Leu feedback inhibition and quaternary structure, two features common to MAM enzymes, plus an 8.4-fold increase in the k(cat)/K(m) for a MAM substrate. Additional exchange of two amino acids in the active site resulted in a MAM-like enzyme that had little residual IPMS activity. Hence, combination of the loss of the regulatory domain and a few additional amino acid exchanges can explain the evolution of MAM from IPMS during its recruitment from primary to secondary metabolism.
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11
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Larson EM, Idnurm A. Two origins for the gene encoding alpha-isopropylmalate synthase in fungi. PLoS One 2010; 5:e11605. [PMID: 20657649 PMCID: PMC2904702 DOI: 10.1371/journal.pone.0011605] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2010] [Accepted: 06/22/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The biosynthesis of leucine is a biochemical pathway common to prokaryotes, plants and fungi, but absent from humans and animals. The pathway is a proposed target for antimicrobial therapy. METHODOLOGY/PRINCIPAL FINDINGS Here we identified the leuA gene encoding alpha-isopropylmalate synthase in the zygomycete fungus Phycomyces blakesleeanus using a genetic mapping approach with crosses between wild type and leucine auxotrophic strains. To confirm the function of the gene, Phycomyces leuA was used to complement the auxotrophic phenotype exhibited by mutation of the leu3+ gene of the ascomycete fungus Schizosaccharomyces pombe. Phylogenetic analysis revealed that the leuA gene in Phycomyces, other zygomycetes, and the chytrids is more closely related to homologs in plants and photosynthetic bacteria than ascomycetes or basidiomycetes, and suggests that the Dikarya have acquired the gene more recently. CONCLUSIONS/SIGNIFICANCE The identification of leuA in Phycomyces adds to the growing body of evidence that some primary metabolic pathways or parts of them have arisen multiple times during the evolution of fungi, probably through horizontal gene transfer events.
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Affiliation(s)
- Erica M. Larson
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
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12
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Gene expression profiling of phytoplasma-infected Madagascar periwinkle leaves using differential display. Mol Biol Rep 2010; 38:2993-3000. [PMID: 20127177 DOI: 10.1007/s11033-010-9964-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 01/15/2010] [Indexed: 10/19/2022]
Abstract
Phytoplasmas are small (0.2-0.8 μm), wall-less, pleiomorphic prokaryotes responsible of numerous economically important plant diseases. They are characterized by a very small genome and are obligate parasites of phloem tissues and some insects that act as vectors of infection. To investigate molecular mechanisms involved in pathogenesis, the differential display technique was here applied to identify plant genes whose transcription was significantly altered in leaves of Madagascar periwinkle (Catharanthus roseus (L.) G.Don) infected by 'Candidatus Phytoplasma pyri'. We detected, reamplified, cloned, and sequenced 16 putative differentially expressed cDNA fragments. Northern blot analysis revealed that seven of the 16 genes identified were up-regulated following phytoplasma infection, while three genes were down-regulated. The remaining six genes did not show significant changes in the level of expression. Identified genes are mainly involved in plant defence/stress responses, protein metabolism and transport, transcriptional regulation, vesicle trafficking, and carbohydrate metabolism. The possible role played by these genes in the phytoplasma infection is discussed.
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13
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Verkerk R, Schreiner M, Krumbein A, Ciska E, Holst B, Rowland I, De Schrijver R, Hansen M, Gerhäuser C, Mithen R, Dekker M. Glucosinolates in Brassica vegetables: the influence of the food supply chain on intake, bioavailability and human health. Mol Nutr Food Res 2009; 53 Suppl 2:S219. [PMID: 19035553 DOI: 10.1002/mnfr.200800065] [Citation(s) in RCA: 341] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Glucosinolates (GLSs) are found in Brassica vegetables. Examples of these sources include cabbage, Brussels sprouts, broccoli, cauliflower and various root vegetables (e.g. radish and turnip). A number of epidemiological studies have identified an inverse association between consumption of these vegetables and the risk of colon and rectal cancer. Animal studies have shown changes in enzyme activities and DNA damage resulting from consumption of Brassica vegetables or isothiocyanates, the breakdown products (BDP) of GLSs in the body. Mechanistic studies have begun to identify the ways in which the compounds may exert their protective action but the relevance of these studies to protective effects in the human alimentary tract is as yet unproven. In vitro studies with a number of specific isothiocyanates have suggested mechanisms that might be the basis of their chemoprotective effects. The concentration and composition of the GLSs in different plants, but also within a plant (e.g. in the seeds, roots or leaves), can vary greatly and also changes during plant development. Furthermore, the effects of various factors in the supply chain of Brassica vegetables including breeding, cultivation, storage and processing on intake and bioavailability of GLSs are extensively discussed in this paper.
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Affiliation(s)
- Ruud Verkerk
- Product Design and Quality Management Group, Wageningen University, Wageningen, The Netherlands.
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14
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Yindeeyoungyeon W, Likitvivatanavong S, Palittapongarnpim P. Characterization of alpha-isopropylmalate synthases containing different copy numbers of tandem repeats in Mycobacterium tuberculosis. BMC Microbiol 2009; 9:122. [PMID: 19505340 PMCID: PMC2704214 DOI: 10.1186/1471-2180-9-122] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 06/09/2009] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Alpha-isopropylmalate synthase (alpha-IPMS) is the key enzyme that catalyzes the first committed step in the leucine biosynthetic pathway. The gene encoding alpha-IPMS in Mycobacterium tuberculosis, leuA, is polymorphic due to the insertion of 57-bp repeat units referred to as Variable Number of Tandem Repeats (VNTR). The role of the VNTR found within the M. tuberculosis genome is unclear. To investigate the role of the VNTR in leuA, we compared two alpha-IPMS proteins with different numbers of amino acid repeats, one with two copies and the other with 14 copies. We have cloned leuA with 14 copies of the repeat units into the pET15b expression vector with a His6-tag at the N-terminus, as was previously done for the leuA gene with two copies of the repeat units. RESULTS The recombinant His6-alpha-IPMS proteins with two and 14 copies (alpha-IPMS-2CR and alpha-IPMS-14CR, respectively) of the repeat units were purified by immobilized metal ion affinity chromatography and gel filtration. Both enzymes were found to be dimers by gel filtration. Both enzymes work well at pH values of 7-8.5 and temperatures of 37-42 degrees C. However, alpha-IPMS-14CR tolerates pH values and temperatures outside of this range better than alpha-IPMS-2CR does. alpha-IPMS-14CR has higher affinity than alpha-IPMS-2CR for the two substrates, alpha-ketoisovalerate and acetyl CoA. Furthermore, alpha-IPMS-2CR was feedback inhibited by the end product l-leucine, whereas alpha-IPMS-14CR was not. CONCLUSION The differences in the kinetic properties and the l-leucine feedback inhibition between the two M. tuberculosis alpha-IPMS proteins containing low and high numbers of VNTR indicate that a large VNTR insertion affects protein structure and function. Demonstration of l-leucine binding to alpha-IPMS-14CR would confirm whether or not alpha-IPMS-14CR responds to end-product feedback inhibition.
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Affiliation(s)
- Wandee Yindeeyoungyeon
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathumthani 12120, Thailand
| | | | - Prasit Palittapongarnpim
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathumthani 12120, Thailand
- Department of Microbiology, Mahidol University, Bangkok 10400, Thailand
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15
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Slocombe SP, Schauvinhold I, McQuinn RP, Besser K, Welsby NA, Harper A, Aziz N, Li Y, Larson TR, Giovannoni J, Dixon RA, Broun P. Transcriptomic and reverse genetic analyses of branched-chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana. PLANT PHYSIOLOGY 2008; 148:1830-46. [PMID: 18931142 PMCID: PMC2593661 DOI: 10.1104/pp.108.129510] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Accepted: 10/13/2008] [Indexed: 05/18/2023]
Abstract
Acyl sugars containing branched-chain fatty acids (BCFAs) are exuded by glandular trichomes of many species in Solanaceae, having an important defensive role against insects. From isotope-feeding studies, two modes of BCFA elongation have been proposed: (1) fatty acid synthase-mediated two-carbon elongation in the high acyl sugar-producing tomato species Solanum pennellii and Datura metel; and (2) alpha-keto acid elongation-mediated one-carbon increments in several tobacco (Nicotiana) species and a Petunia species. To investigate the molecular mechanisms underlying BCFAs and acyl sugar production in trichomes, we have taken a comparative genomic approach to identify critical enzymatic steps followed by gene silencing and metabolite analysis in S. pennellii and Nicotiana benthamiana. Our study verified the existence of distinct mechanisms of acyl sugar synthesis in Solanaceae. From microarray analyses, genes associated with alpha-keto acid elongation were found to be among the most strongly expressed in N. benthamiana trichomes only, supporting this model in tobacco species. Genes encoding components of the branched-chain keto-acid dehydrogenase complex were expressed at particularly high levels in trichomes of both species, and we show using virus-induced gene silencing that they are required for BCFA production in both cases and for acyl sugar synthesis in N. benthamiana. Functional analysis by down-regulation of specific KAS I genes and cerulenin inhibition indicated the involvement of the fatty acid synthase complex in BCFA production in S. pennellii. In summary, our study highlights both conserved and divergent mechanisms in the production of important defense compounds in Solanaceae and defines potential targets for engineering acyl sugar production in plants for improved pest tolerance.
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Affiliation(s)
- Stephen P Slocombe
- Department of Biology, Area 7, University of York, York YO10 5YW, United Kingdom
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16
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Lou P, Zhao J, He H, Hanhart C, Pino Del Carpio D, Verkerk R, Custers J, Koornneef M, Bonnema G. Quantitative trait loci for glucosinolate accumulation in Brassica rapa leaves. THE NEW PHYTOLOGIST 2008; 179:1017-1032. [PMID: 18564302 DOI: 10.1111/j.1469-8137.2008.02530.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Glucosinolates and their breakdown products have been recognized for their effects on plant defense, human health, flavor and taste of cruciferous vegetables. Despite this importance, little is known about the regulation of the biosynthesis and degradation in Brassica rapa. Here, the identification of quantitative trait loci (QTL) for glucosinolate accumulation in B. rapa leaves in two novel segregating double haploid (DH) populations is reported: DH38, derived from a cross between yellow sarson R500 and pak choi variety HK Naibaicai; and DH30, from a cross between yellow sarson R500 and Kairyou Hakata, a Japanese vegetable turnip variety. An integrated map of 1068 cM with 10 linkage groups, assigned to the international agreed nomenclature, is developed based on the two individual DH maps with the common parent using amplified fragment length polymorphism (AFLP) and single sequence repeat (SSR) markers. Eight different glucosinolate compounds were detected in parents and F(1)s of the DH populations and found to segregate quantitatively in the DH populations. QTL analysis identified 16 loci controlling aliphatic glucosinolate accumulation, three loci controlling total indolic glucosinolate concentration and three loci regulating aromatic glucosinolate concentrations. Both comparative genomic analyses based on Arabidopsis-Brassica rapa synteny and mapping of candidate orthologous genes in B. rapa allowed the selection of genes involved in the glucosinolate biosynthesis pathway that may account for the identified QTL.
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Affiliation(s)
- Ping Lou
- Laboratory of Plant Breeding, Wageningen University, 6700AJ, Wageningen, the Netherlands
| | - Jianjun Zhao
- Laboratory of Plant Breeding, Wageningen University, 6700AJ, Wageningen, the Netherlands
- Horticultural College, Hebei Agricultural University, 071001, Baoding, China
- Laboratory of Genetics, Wageningen University, 6703BD, Wageningen, the Netherlands
| | - Hongju He
- Product Design and Quality Management Group, Wageningen University, 6700EV, Wageningen, the Netherlands
- National Engineering Research Center for Vegetables, 100081, Beijing, China
| | - Corrie Hanhart
- Laboratory of Genetics, Wageningen University, 6703BD, Wageningen, the Netherlands
| | - Dunia Pino Del Carpio
- Laboratory of Plant Breeding, Wageningen University, 6700AJ, Wageningen, the Netherlands
| | - Ruud Verkerk
- Product Design and Quality Management Group, Wageningen University, 6700EV, Wageningen, the Netherlands
| | - Jan Custers
- Plant Research International, Wageningen University and Research Centre, 6708PB, Wageningen, the Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, 6703BD, Wageningen, the Netherlands
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Guusje Bonnema
- Laboratory of Plant Breeding, Wageningen University, 6700AJ, Wageningen, the Netherlands
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17
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de Kraker JW, Luck K, Textor S, Tokuhisa JG, Gershenzon J. Two Arabidopsis genes (IPMS1 and IPMS2) encode isopropylmalate synthase, the branchpoint step in the biosynthesis of leucine. PLANT PHYSIOLOGY 2007; 143:970-86. [PMID: 17189332 PMCID: PMC1803721 DOI: 10.1104/pp.106.085555] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Heterologous expression of the Arabidopsis (Arabidopsis thaliana) IPMS1 (At1g18500) and IPMS2 (At1g74040) cDNAs in Escherichia coli yields isopropylmalate synthases (IPMSs; EC 2.3.3.13). These enzymes catalyze the first dedicated step in leucine (Leu) biosynthesis, an aldol-type condensation of acetyl-coenzyme A (CoA) and 2-oxoisovalerate yielding isopropylmalate. Most biochemical properties of IPMS1 and IPMS2 are similar: broad pH optimum around pH 8.5, Mg2+ as cofactor, feedback inhibition by Leu, Km for 2-oxoisovalerate of approximately 300 microM, and a Vmax of approximately 2 x 10(3) micromol min(-1) g(-1). However, IPMS1 and IPMS2 differ in their Km for acetyl-CoA (45 microM and 16 microM, respectively) and apparent quaternary structure (dimer and tetramer, respectively). A knockout insertion mutant for IPMS1 showed an increase in valine content but no changes in Leu content; two insertion mutants for IPMS2 did not show any changes in soluble amino acid content. Apparently, in planta each gene can adequately compensate for the absence of the other, consistent with available microarray and reverse transcription-polymerase chain reaction data that show that both genes are expressed in all organs at all developmental stages. Both encoded proteins accept 2-oxo acid substrates in vitro ranging in length from glyoxylate to 2-oxohexanoate, and catalyze at a low rate the condensation of acetyl-CoA and 4-methylthio-2-oxobutyrate, i.e. a reaction involved in glucosinolate chain elongation normally catalyzed by methylthioalkylmalate synthases. The evolutionary relationship between IPMS and methylthioalkylmalate synthase enzymes is discussed in view of their amino acid sequence identity (60%) and overlap in substrate specificity.
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Affiliation(s)
- Jan-Willem de Kraker
- Max Planck Institute for Chemical Ecology, Beutenberg Campus, D-07745 Jena, Germany
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18
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Lewin A, Grieve IC. Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data. BMC Bioinformatics 2006; 7:426. [PMID: 17018143 PMCID: PMC1622761 DOI: 10.1186/1471-2105-7-426] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 10/03/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene Ontology (GO) terms are often used to assess the results of microarray experiments. The most common way to do this is to perform Fisher's exact tests to find GO terms which are over-represented amongst the genes declared to be differentially expressed in the analysis of the microarray experiment. However, due to the high degree of dependence between GO terms, statistical testing is conservative, and interpretation is difficult. RESULTS We propose testing groups of GO terms rather than individual terms, to increase statistical power, reduce dependence between tests and improve the interpretation of results. We use the publicly available package POSOC to group the terms. Our method finds groups of GO terms significantly over-represented amongst differentially expressed genes which are not found by Fisher's tests on individual GO terms. CONCLUSION Grouping Gene Ontology terms improves the interpretation of gene set enrichment for microarray data.
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Affiliation(s)
- Alex Lewin
- Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London W2 1PG, UK
| | - Ian C Grieve
- MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital, London W12 ONN, UK
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