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Bartley GE, Avena-Bustillos RJ, Du WX, Hidalgo M, Cain B, Breksa AP. Transcriptional regulation of chlorogenic acid biosynthesis in carrot root slices exposed to UV-B light. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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102
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Tohge T, Wendenburg R, Ishihara H, Nakabayashi R, Watanabe M, Sulpice R, Hoefgen R, Takayama H, Saito K, Stitt M, Fernie AR. Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae. Nat Commun 2016; 7:12399. [PMID: 27545969 PMCID: PMC4996938 DOI: 10.1038/ncomms12399] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 06/29/2016] [Indexed: 02/07/2023] Open
Abstract
Incidence of natural light stress renders it important to enhance our understanding of the mechanisms by which plants protect themselves from harmful effects of UV-B irradiation, as this is critical for fitness of land plant species. Here we describe natural variation of a class of phenylacylated-flavonols (saiginols), which accumulate to high levels in floral tissues of Arabidopsis. They were identified in a subset of accessions, especially those deriving from latitudes between 16° and 43° North. Investigation of introgression line populations using metabolic and transcript profiling, combined with genomic sequence analysis, allowed the identification of flavonol-phenylacyltransferase 2 (FPT2) that is responsible for the production of saiginols and conferring greater UV light tolerance in planta. Furthermore, analysis of polymorphism within the FPT duplicated region provides an evolutionary framework of the natural history of this locus in the Brassicaceae.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Hirofumi Ishihara
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ryo Nakabayashi
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1 Chuo-ku, Chiba 260-8675, Japan
| | - Mutsumi Watanabe
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ronan Sulpice
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Hiromitsu Takayama
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1 Chuo-ku, Chiba 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1 Chuo-ku, Chiba 260-8675, Japan.,RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Yokohama 230-0045, Japan
| | - Mark Stitt
- 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.,Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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103
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Galili G, Amir R, Fernie AR. The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:153-78. [PMID: 26735064 DOI: 10.1146/annurev-arplant-043015-112213] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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104
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Mal C, Deb A, Aftabuddin M, Kundu S. A network analysis of miRNA mediated gene regulation of rice: crosstalk among biological processes. MOLECULAR BIOSYSTEMS 2016; 11:2273-80. [PMID: 26066638 DOI: 10.1039/c5mb00222b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand the network architecture of miRNA mediated regulations at the genomic and functional levels of rice, we have made an unambiguous annotation of the experimentally verified miRNAs, predicted their targets and the possible biological functions they can affect. Some functions, namely translational and protein modifications and photosynthesis are targeted by higher percentage of miRNA. Using transformation procedures, we constructed a genome scale miRNA-miRNA functional synergistic network (MFSN). The analysis of MFSN modules help to identify miRNAs co-regulating target genes having several interrelated biological processes. Some of these target genes are also co-expressed under particular conditions. For example, the genes co-expressed under drought conditions as well as those targeted by miRNAs present in a MFSN module have interdependent biological processes namely, photosynthesis, cell-wall biogenesis, root development and xylan synthesis. The stress-induced miRNAs and their distributions, and the presence of transcription factors in the target set of MFSN modules were also analyzed.
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Affiliation(s)
- Chittabrata Mal
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India.
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105
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Hettwer K, Böttcher C, Frolov A, Mittasch J, Albert A, von Roepenack-Lahaye E, Strack D, Milkowski C. Dynamic metabolic changes in seeds and seedlings of Brassica napus (oilseed rape) suppressing UGT84A9 reveal plasticity and molecular regulation of the phenylpropanoid pathway. PHYTOCHEMISTRY 2016; 124:46-57. [PMID: 26833384 DOI: 10.1016/j.phytochem.2016.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/13/2016] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
In Brassica napus, suppression of the key biosynthetic enzyme UDP-glucose:sinapic acid glucosyltransferase (UGT84A9) inhibits the biosynthesis of sinapine (sinapoylcholine), the major phenolic component of seeds. Based on the accumulation kinetics of a total of 158 compounds (110 secondary and 48 primary metabolites), we investigated how suppression of the major sink pathway of sinapic acid impacts the metabolome of developing seeds and seedlings. In UGT84A9-suppressing (UGT84A9i) lines massive alterations became evident in late stages of seed development affecting the accumulation levels of 58 secondary and 7 primary metabolites. UGT84A9i seeds were characterized by decreased amounts of various hydroxycinnamic acid (HCA) esters, and increased formation of sinapic and syringic acid glycosides. This indicates glycosylation and β-oxidation as metabolic detoxification strategies to bypass intracellular accumulation of sinapic acid. In addition, a net loss of sinapic acid upon UGT84A9 suppression may point to a feedback regulation of HCA biosynthesis. Surprisingly, suppression of UGT84A9 under control of the seed-specific NAPINC promoter was maintained in cotyledons during the first two weeks of seedling development and associated with a reduced and delayed transformation of sinapine into sinapoylmalate. The lack of sinapoylmalate did not interfere with plant fitness under UV-B stress. Increased UV-B radiation triggered the accumulation of quercetin conjugates whereas the sinapoylmalate level was not affected.
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Affiliation(s)
- Karina Hettwer
- Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Christoph Böttcher
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Strasse 19, 14195 Berlin, Germany
| | - Andrej Frolov
- Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Juliane Mittasch
- Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; Martin-Luther-University Halle-Wittenberg, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Andreas Albert
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Edda von Roepenack-Lahaye
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Dieter Strack
- Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Carsten Milkowski
- Martin-Luther-University Halle-Wittenberg, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany.
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106
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Gene Expressing and sRNA Sequencing Show That Gene Differentiation Associates with a Yellow Acer palmatum Mutant Leaf in Different Light Conditions. BIOMED RESEARCH INTERNATIONAL 2016; 2015:843470. [PMID: 26788511 PMCID: PMC4692996 DOI: 10.1155/2015/843470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 11/17/2022]
Abstract
Acer palmatum Thunb., like other maples, is a widely ornamental-use small woody tree for leaf shapes and colors. Interestingly, we found a yellow-leaves mutant “Jingling Huangfeng” turned to green when grown in shade or low-density light condition. In order to study the potential mechanism, we performed high-throughput sequencing and obtained 1,082 DEGs in leaves grown in different light conditions that result in A. palmatum significant morphological and physiological changes. A total of 989 DEGs were annotated and clustered, of which many DEGs were found associating with the photosynthesis activity and pigment synthesis. The expression of CHS and FDR gene was higher while the expression of FLS gene was lower in full-sunlight condition; this may cause more colorful substance like chalcone and anthocyanin that were produced in full-light condition, thus turning the foliage to yellow. Moreover, this is the first available miRNA collection which contains 67 miRNAs of A. palmatum, including 46 conserved miRNAs and 21 novel miRNAs. To get better understanding of which pathways these miRNAs involved, 102 Unigenes were found to be potential targets of them. These results will provide valuable genetic resources for further study on the molecular mechanisms of Acer palmatum leaf coloration.
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108
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Su F, Gilard F, Guérard F, Citerne S, Clément C, Vaillant-Gaveau N, Dhondt-Cordelier S. Spatio-temporal Responses of Arabidopsis Leaves in Photosynthetic Performance and Metabolite Contents to Burkholderia phytofirmans PsJN. FRONTIERS IN PLANT SCIENCE 2016; 7:403. [PMID: 27066045 PMCID: PMC4811906 DOI: 10.3389/fpls.2016.00403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/14/2016] [Indexed: 05/13/2023]
Abstract
A valuable strategy to improve crop yield consists in the use of plant growth-promoting rhizobacteria (PGPRs). However, the influence of PGPR colonization on plant physiology is largely unknown. PGPR Burkholderia phytofirmans strain PsJN (Bp PsJN) colonized only Arabidopsis thaliana roots after seed or soil inoculation. Foliar bacteria were detected only after leaf infiltration. Since, different bacterial times of presence and/or locations in host plant could lead to different plant physiological responses, photosynthesis, and metabolite profiles in A. thaliana leaves were thus investigated following leaf, root, or seed inoculation with Bp PsJN. Only Bp PsJN leaf colonization transiently decreased cyclic electron transport and effective quantum yield of photosystem I (PSI), and prevented a decrease in net photosynthesis and stomatal opening compared to the corresponding control. Metabolomic analysis revealed that soluble sugars, amino acids or their derivatives accumulated differently in all Bp PsJN-inoculated plants. Octanoic acid accumulated only in case of inoculated plants. Modifications in vitamin, organic acid such as tricarboxylic acid intermediates, and hormone amounts were dependent on bacterial time of presence and location. Additionally, a larger array of amino acids and hormones (auxin, cytokinin, abscisic acid) were modified by seed inoculation with Bp PsJN. Our work thereby provides evidence that relative short-term inoculation with Bp PsJN altered physiological status of A. thaliana leaves, whereas long-term bacterization triggered modifications on a larger set of metabolites. Our data highlighted the changes displayed during this plant-microbe interaction to trigger physiological and metabolic responses that could explain the increase in plant growth or stress tolerance conferred by the presence of Bp PsJN.
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Affiliation(s)
- Fan Su
- Unité de Recherche Vignes et Vins de Champagne – EA 4707, SFR Condorcet FR CNRS 3417, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-ArdenneReims, France
| | - Françoise Gilard
- UMR CNRS-INRA 9213, Saclay Plant Sciences, Institute of Plant Sciences Paris-Saclay IPS2 (Bâtiment 630), Université Paris-SudOrsay, France
| | - Florence Guérard
- UMR CNRS-INRA 9213, Saclay Plant Sciences, Institute of Plant Sciences Paris-Saclay IPS2 (Bâtiment 630), Université Paris-SudOrsay, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, ERL 3559 CNRS, INRA Versailles-GrignonVersailles, France
| | - Christophe Clément
- Unité de Recherche Vignes et Vins de Champagne – EA 4707, SFR Condorcet FR CNRS 3417, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-ArdenneReims, France
| | - Nathalie Vaillant-Gaveau
- Unité de Recherche Vignes et Vins de Champagne – EA 4707, SFR Condorcet FR CNRS 3417, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-ArdenneReims, France
| | - Sandrine Dhondt-Cordelier
- Unité de Recherche Vignes et Vins de Champagne – EA 4707, SFR Condorcet FR CNRS 3417, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-ArdenneReims, France
- *Correspondence: Sandrine Dhondt-Cordelier,
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109
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Jiang Z, Zheng Y, Qiu R, Yang Y, Xu M, Ye Y, Xu M. Short UV-B Exposure Stimulated Enzymatic and Nonenzymatic Antioxidants and Reduced Oxidative Stress of Cold-Stored Mangoes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10965-10972. [PMID: 26641945 DOI: 10.1021/acs.jafc.5b04460] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The effects of UV-B irradiation on reactive oxygen species (ROS) levels, antioxidant compound contents, antioxidative enzyme activities, and oxidative damage of cold-stored mangoes were examined. Superoxide anion production rate, hydrogen peroxide concentration, ion leakage level and malondialdehyde content of the cold-stored fruit preradiated with 5 KJ m(-2) UV-B for 4 h were significantly decreased as compared with control fruit. The activities of ROS generating enzymes remained unchanged in UV-B-irradiated mangoes as compared to the control, but superoxide dismutase and catalase activities, ascorbate and polyphenol contents and antioxidant capacities of the cold-stored mangoes were significantly enhanced by UV-B. The UV-B-enhanced antioxidant compounds and antioxidative enzymes were highly correlated with the reduced-ROS levels in UV-B-irradiated mangoes. The data indicated that a short UV-B exposure reduced oxidative stress and alleviated oxidative damage of the cold-stored mangoes by triggering both enzymatic and nonenzymatic antioxidant systems although ROS generation in the fruit was not affected.
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Affiliation(s)
- Zhifang Jiang
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
| | - Yaoqi Zheng
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
| | - Rongrong Qiu
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
| | - Yanjun Yang
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
| | - Mingfeng Xu
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
| | - Yu Ye
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
| | - Maojun Xu
- Key Laboratory for Quality and Safety of Agricultural Products of Hangzhou City, College of Life and Environmental Sciences and ‡Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medical Plants, College of Life and Environmental Sciences, Hangzhou Normal University , Hangzhou 310036, China
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110
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Sztatelman O, Grzyb J, Gabryś H, Banaś AK. The effect of UV-B on Arabidopsis leaves depends on light conditions after treatment. BMC PLANT BIOLOGY 2015; 15:281. [PMID: 26608826 PMCID: PMC4660668 DOI: 10.1186/s12870-015-0667-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/17/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Ultraviolet B (UV-B) irradiation can influence many cellular processes. Irradiation with high UV-B doses causes chlorophyll degradation, a decrease in the expression of genes associated with photosynthesis and its subsequent inhibition. On the other hand, sublethal doses of UV-B are used in post-harvest technology to prevent yellowing in storage. To address this inconsistency the effect of short, high-dose UV-B irradiation on detached Arabidopsis thaliana leaves was examined. RESULTS Two different experimental models were used. After short treatment with a high dose of UV-B the Arabidopsis leaves were either put into darkness or exposed to constant light for up to 4 days. UV-B inhibited dark-induced chlorophyll degradation in Arabidopsis leaves in a dose-dependent manner. The expression of photosynthesis-related genes, chlorophyll content and photosynthetic efficiency were higher in UV-B -treated leaves left in darkness. UV-B treatment followed by constant light caused leaf yellowing and induced the expression of senescence-related genes. Irrespective of light treatment a high UV-B dose led to clearly visible cell death 3 days after irradiation. CONCLUSIONS High doses of UV-B have opposing effects on leaves depending on their light status after UV treatment. In darkened leaves short UV-B treatment delays the appearance of senescence symptoms. When followed by light treatment, the same doses of UV-B result in chlorophyll degradation. This restricts the potential usability of UV treatment in postharvest technology to crops which are stored in darkness.
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Affiliation(s)
- Olga Sztatelman
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland.
- Current address: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, 02-106, Poland.
| | - Joanna Grzyb
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warszawa, 02-668, Poland.
| | - Halina Gabryś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland.
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland.
- The Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland.
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111
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Zhao Y, Zhao J, Zhao C, Zhou H, Li Y, Zhang J, Li L, Hu C, Li W, Peng X, Lu X, Lin F, Xu G. A metabolomics study delineating geographical location-associated primary metabolic changes in the leaves of growing tobacco plants by GC-MS and CE-MS. Sci Rep 2015; 5:16346. [PMID: 26549189 PMCID: PMC4637841 DOI: 10.1038/srep16346] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 10/12/2015] [Indexed: 11/17/2022] Open
Abstract
Ecological conditions and developmental senescence significantly affect the physiological metabolism of plants, yet relatively little is known about the influence of geographical location on dynamic changes in plant leaves during growth. Pseudotargeted gas chromatography-selected ion monitoring-mass spectrometry and capillary electrophoresis-mass spectrometry were used to investigate a time course of the metabolic responses of tobacco leaves to geographical location. Principal component analysis revealed obvious metabolic discrimination between growing districts relative to cultivars. A complex carbon and nitrogen metabolic network was modulated by environmental factors during growth. When the Xuchang and Dali Districts in China were compared, the results indicated that higher rates of photosynthesis, photorespiration and respiration were utilized in Xuchang District to generate the energy and carbon skeletons needed for the biosynthesis of nitrogen-containing metabolites. The increased abundance of defense-associated metabolites generated from the shikimate-phenylpropanoid pathway in Xuchang relative to Dali was implicated in protection against stress.
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Affiliation(s)
- Yanni Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jieyu Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116023, China
| | - Chunxia Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huina Zhou
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Yanli Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Junjie Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lili Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxiu Hu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Wenzheng Li
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research Center at Yunnan, Yuxi, 653100, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116023, China
| | - Xin Lu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fucheng Lin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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112
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Tohge T, Scossa F, Fernie AR. Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation. PLANT PHYSIOLOGY 2015; 169:1499-511. [PMID: 26371234 PMCID: PMC4634077 DOI: 10.1104/pp.15.01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/10/2015] [Indexed: 05/05/2023]
Abstract
Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
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113
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Harb J, Alseekh S, Tohge T, Fernie AR. Profiling of primary metabolites and flavonols in leaves of two table grape varieties collected from semiarid and temperate regions. PHYTOCHEMISTRY 2015. [PMID: 26196939 DOI: 10.1016/j.phytochem.2015.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cultivation of grapes in West Bank - Palestine is very old and a large number of grape varieties exist as a result of continuous domestication over thousands of years. This rich biodiversity has highly influenced the consumer behavior of local people, who consume both grape berries and leaves. However, studies that address the contents of health-promoting metabolites in leaves are scarce. Accordingly the aim of this study is to assess metabolite levels in leaves of two grape varieties that were collected from semiarid and temperate regions. Metabolic profiling was conducted using GC-MS and LC-MS. The obtained results show that abiotic stresses in the semiarid region led to clear changes in primary metabolites, in particular in amino acids, which exist at very high levels. By contrast, qualitative and genotype-dependent differences in secondary metabolites were observed, whereas abiotic stresses appear to have negligible effect on the content of these metabolites. The qualitative difference in the flavonol profiles between the two genotypes is most probably related to differential expression of specific genes, in particular flavonol 3-O-rhamnosyltransferase, flavonol-3-O-glycoside pentosyltransferases and flavonol-3-O-d-glucosidel-rhamnosyltransferase by 'Beituni' grape leaves, which led to much higher levels of flavonols with rutinoside, pentoside, and rhamnoside moieties with this genotype.
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Affiliation(s)
- Jamil Harb
- Department of Biology and Biochemistry, Birzeit University, Birzeit, West Bank, Palestine; Max-Planck-Institut für Mölekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Saleh Alseekh
- Max-Planck-Institut für Mölekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Takayuki Tohge
- Max-Planck-Institut für Mölekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Mölekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
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114
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Tohge T, Zhang Y, Peterek S, Matros A, Rallapalli G, Tandrón YA, Butelli E, Kallam K, Hertkorn N, Mock HP, Martin C, Fernie AR. Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:686-704. [PMID: 26108615 DOI: 10.1111/tpj.12920] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 05/12/2023]
Abstract
Given the potential health benefits of polyphenolic compounds in the diet, there is a growing interest in the generation of food crops enriched with health-protective flavonoids. We undertook a series of metabolite analyses of tomatoes ectopically expressing the Delila and Rosea1 transcription factor genes from snapdragon (Antirrhinum majus), paying particular attention to changes in phenylpropanoids compared to controls. These analyses revealed multiple changes, including depletion of rutin and naringenin chalcone, and enhanced levels of anthocyanins and phenylacylated flavonol derivatives. We isolated and characterized the chemical structures of the two most abundant anthocyanins, which were shown by NMR spectroscopy to be delphinidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside and petunidin-3-(4'''-O-trans-p-coumaroyl)-rutinoside-5-O-glucoside. By performing RNA sequencing on both purple fruit and wild-type fruit, we obtained important information concerning the relative expression of both structural and transcription factor genes. Integrative analysis of the transcript and metabolite datasets provided compelling evidence of the nature of all anthocyanin biosynthetic genes, including those encoding species-specific anthocyanin decoration enzymes. One gene, SlFdAT1 (Solyc12g088170), predicted to encode a flavonoid-3-O-rutinoside-4'''-phenylacyltransferase, was characterized by assays of recombinant protein and over-expression assays in tobacco. The combined data are discussed in the context of both our current understanding of phenylpropanoid metabolism in Solanaceous species, and evolution of flavonoid decorating enzymes and their transcriptional networks in various plant species.
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Affiliation(s)
- Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Yang Zhang
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Silke Peterek
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Ghanasyam Rallapalli
- The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich, UK NR4 7UH, UK
| | - Yudelsy A Tandrón
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Eugenio Butelli
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Kalyani Kallam
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Norbert Hertkorn
- German Research Center for Environment and Health, GmbH, Institute of Ecological Chemistry, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764, Neuherberg, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, D-06466, Gatersleben, Germany
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
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115
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Hartmann A, Albert A, Ganzera M. Effects of elevated ultraviolet radiation on primary metabolites in selected alpine algae and cyanobacteria. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2015; 149:149-55. [PMID: 26065817 PMCID: PMC4509709 DOI: 10.1016/j.jphotobiol.2015.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 12/02/2022]
Abstract
Extremophilic green algae and cyanobacteria are the most abundant species in high mountain habitats, where rough climate conditions such as temperature differences, limited water retention and high ultraviolet (UV) radiation are the cause for a restricted biological diversity in favor of a few specialized autotrophic microorganisms. In this study, we investigated four algal species from alpine habitat in a sun simulator for their defense strategies in response to UV-A radiation (315-400nm) up to 13.4W/m(2) and UV-B radiation (280-315nm) up to 2.8W/m(2). Besides changes in pigment composition we discovered that primary polar metabolites like aromatic amino acids, nucleic bases and nucleosides are increasingly produced when the organisms are exposed to elevated UV radiation. Respective compounds were isolated and identified, and in order to quantify them an HPLC-DAD method was developed and validated. Our results show that especially tyrosine and guanosine were found to be generally two to three times upregulated in the UV-B exposed samples compared to the non-treated control.
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Affiliation(s)
- Anja Hartmann
- Institute of Pharmacy, Pharmacognosy, University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas Albert
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Markus Ganzera
- Institute of Pharmacy, Pharmacognosy, University of Innsbruck, 6020 Innsbruck, Austria.
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116
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Mucha S, Walther D, Müller TM, Hincha DK, Glawischnig E. Substantial reprogramming of the Eutrema salsugineum (Thellungiella salsuginea) transcriptome in response to UV and silver nitrate challenge. BMC PLANT BIOLOGY 2015; 15:137. [PMID: 26063239 PMCID: PMC4464140 DOI: 10.1186/s12870-015-0506-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/24/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cruciferous plants synthesize a large variety of tryptophan-derived phytoalexins in response to pathogen infection, UV irradiation, or high dosages of heavy metals. The major phytoalexins of Eutrema salsugineum (Thellungiella salsuginea), which has recently been established as an extremophile model plant, are probably derivatives of indole glucosinolates, in contrast to Arabidopsis, which synthesizes characteristic camalexin from the glucosinolate precursor indole-3-acetaldoxime. RESULTS The transcriptional response of E. salsugineum to UV irradiation and AgNO3 was monitored by RNAseq and microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated. The putative Eutrema WRKY33 ortholog was functionally tested and shown to complement camalexin deficiency in Atwrky33 mutant. CONCLUSIONS In E. salsugineum, UV irradiation or heavy metal application resulted in substantial transcriptional reprogramming. Consistently induced genes of indole glucosinolate biosynthesis and modification will serve as candidate genes for the biosynthesis of Eutrema-specific phytoalexins.
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MESH Headings
- Biosynthetic Pathways/genetics
- Brassicaceae/drug effects
- Brassicaceae/genetics
- Brassicaceae/radiation effects
- Cellular Reprogramming/drug effects
- Cellular Reprogramming/radiation effects
- Gene Expression Regulation, Plant/drug effects
- Gene Expression Regulation, Plant/radiation effects
- Gene Knockout Techniques
- Glucosinolates/biosynthesis
- Indoles/metabolism
- Metals, Heavy/toxicity
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Sesquiterpenes/metabolism
- Silver Nitrate/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Stress, Physiological/radiation effects
- Thiazoles/metabolism
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- Transcription, Genetic/radiation effects
- Transcriptome/drug effects
- Transcriptome/genetics
- Transcriptome/radiation effects
- Tryptophan/biosynthesis
- Ultraviolet Rays
- Phytoalexins
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Affiliation(s)
- Stefanie Mucha
- Lehrstuhl für Genetik, Technische Universität München, D-85354, Freising, Germany.
| | - Dirk Walther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Germany.
| | - Teresa M Müller
- Lehrstuhl für Genetik, Technische Universität München, D-85354, Freising, Germany.
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Germany.
| | - Erich Glawischnig
- Lehrstuhl für Genetik, Technische Universität München, D-85354, Freising, Germany.
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117
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Kaling M, Kanawati B, Ghirardo A, Albert A, Winkler JB, Heller W, Barta C, Loreto F, Schmitt-Kopplin P, Schnitzler JP. UV-B mediated metabolic rearrangements in poplar revealed by non-targeted metabolomics. PLANT, CELL & ENVIRONMENT 2015; 38:892-904. [PMID: 24738572 DOI: 10.1111/pce.12348] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 03/26/2014] [Accepted: 03/27/2014] [Indexed: 05/04/2023]
Abstract
Plants have to cope with various abiotic stresses including UV-B radiation (280-315 nm). UV-B radiation is perceived by a photoreceptor, triggers morphological responses and primes plant defence mechanisms such as antioxidant levels, photoreapir or accumulation of UV-B screening pigments. As poplar is an important model system for trees, we elucidated the influence of UV-B on overall metabolite patterns in poplar leaves grown under high UV-B radiation. Combining non-targeted metabolomics with gas exchange analysis and confocal microscopy, we aimed understanding how UV-B radiation triggers metabolome-wide changes, affects isoprene emission, photosynthetic performance, epidermal light attenuation and finally how isoprene-free poplars adjust their metabolome under UV-B radiation. Exposure to UV-B radiation caused a comprehensive rearrangement of the leaf metabolome. Several hundreds of metabolites were up- and down-regulated over various pathways. Our analysis, revealed the up-regulation of flavonoids, anthocyanins and polyphenols and the down-regulation of phenolic precursors in the first 36 h of UV-B treatment. We also observed a down-regulation of steroids after 12 h. The accumulation of phenolic compounds leads to a reduced light transmission in UV-B-exposed plants. However, the accumulation of phenolic compounds was reduced in non-isoprene-emitting plants suggesting a metabolic- or signalling-based interaction between isoprenoid and phenolic pathways.
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Affiliation(s)
- Moritz Kaling
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany; Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
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118
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Wargent JJ, Nelson BCW, McGhie TK, Barnes PW. Acclimation to UV-B radiation and visible light in Lactuca sativa involves up-regulation of photosynthetic performance and orchestration of metabolome-wide responses. PLANT, CELL & ENVIRONMENT 2015; 38:929-40. [PMID: 24945714 DOI: 10.1111/pce.12392] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 05/07/2023]
Abstract
UV-B radiation is often viewed as a source of stress for higher plants. In particular, photosynthetic function has been described as a common target for UV-B impairment; yet as our understanding of UV-B photomorphogenesis increases, there are opportunities to expand the emerging paradigm of regulatory UV response. Lactuca sativa is an important dietary crop species and is often subjected to rapid sunlight exposure at field transfer. Acclimation to UV-B and visible light conditions in L. sativa was dissected using gas exchange and chlorophyll fluorescence measurements, in addition to non-destructive assessments of UV epidermal shielding (SUV ). After UV-B treatment, seedlings were subjected to wide-range metabolomic analysis using liquid chromatography hybrid quadrupole time-of-flight high-resolution mass spectrometry (LC-QTOF-HRMS). During the acclimation period, net photosynthetic rate increased in UV-treated plants, epidermal UV shielding increased in both subsets of plants transferred to the acclimatory conditions (UV+/UV- plants) and Fv /Fm declined slightly in UV+/UV- plants. Metabolomic analysis revealed that a key group of secondary compounds was up-regulated by higher light conditions, yet several of these compounds were elevated further by UV-B radiation. In conclusion, acclimation to UV-B radiation involves co-protection from the effects of visible light, and responses to UV-B radiation at a photosynthetic level may not be consistently viewed as damaging to plant development.
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Affiliation(s)
- J J Wargent
- Institute of Agriculture & Environment, Massey University, Palmerston North, 4410, New Zealand
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119
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Takahashi S, Kojo KH, Kutsuna N, Endo M, Toki S, Isoda H, Hasezawa S. Differential responses to high- and low-dose ultraviolet-B stress in tobacco Bright Yellow-2 cells. FRONTIERS IN PLANT SCIENCE 2015; 6:254. [PMID: 25954287 PMCID: PMC4404814 DOI: 10.3389/fpls.2015.00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/31/2015] [Indexed: 05/14/2023]
Abstract
Ultraviolet (UV)-B irradiation leads to DNA damage, cell cycle arrest, growth inhibition, and cell death. To evaluate the UV-B stress-induced changes in plant cells, we developed a model system based on tobacco Bright Yellow-2 (BY-2) cells. Both low-dose UV-B (low UV-B: 740 J m(-2)) and high-dose UV-B (high UV-B: 2960 J m(-2)) inhibited cell proliferation and induced cell death; these effects were more pronounced at high UV-B. Flow cytometry showed cell cycle arrest within 1 day after UV-B irradiation; neither low- nor high-UV-B-irradiated cells entered mitosis within 12 h. Cell cycle progression was gradually restored in low-UV-B-irradiated cells but not in high-UV-B-irradiated cells. UV-A irradiation, which activates cyclobutane pyrimidine dimer (CPD) photolyase, reduced inhibition of cell proliferation by low but not high UV-B and suppressed high-UV-B-induced cell death. UV-B induced CPD formation in a dose-dependent manner. The amounts of CPDs decreased gradually within 3 days in low-UV-B-irradiated cells, but remained elevated after 3 days in high-UV-B-irradiated cells. Low UV-B slightly increased the number of DNA single-strand breaks detected by the comet assay at 1 day after irradiation, and then decreased at 2 and 3 days after irradiation. High UV-B increased DNA fragmentation detected by the terminal deoxynucleotidyl transferase dUTP nick end labeling assay 1 and 3 days after irradiation. Caffeine, an inhibitor of ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) checkpoint kinases, reduced the rate of cell death in high-UV-B-irradiated cells. Our data suggest that low-UV-B-induced CPDs and/or DNA strand-breaks inhibit DNA replication and proliferation of BY-2 cells, whereas larger contents of high-UV-B-induced CPDs and/or DNA strand-breaks lead to cell death.
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Affiliation(s)
- Shinya Takahashi
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
- Alliance for Research on North Africa, University of TsukubaTsukuba, Japan
- Ph. D. Program in Life Science Innovation, University of TsukubaTsukuba, Japan
| | - Kei H. Kojo
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
- LPixel Inc.Bunkyo-ku, Japan
| | - Natsumaro Kutsuna
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
- LPixel Inc.Bunkyo-ku, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Hiroko Isoda
- Alliance for Research on North Africa, University of TsukubaTsukuba, Japan
- Ph. D. Program in Life Science Innovation, University of TsukubaTsukuba, Japan
| | - Seiichiro Hasezawa
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
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120
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Kim T, Dreher K, Nilo-Poyanco R, Lee I, Fiehn O, Lange BM, Nikolau BJ, Sumner L, Welti R, Wurtele ES, Rhee SY. Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PLANT PHYSIOLOGY 2015; 167:1685-1698. [PMID: 25670818 PMCID: PMC4378150 DOI: 10.1104/pp.114.252361] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/06/2015] [Indexed: 05/29/2023]
Abstract
Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.
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Affiliation(s)
- Taehyong Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Kate Dreher
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Ricardo Nilo-Poyanco
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Insuk Lee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Oliver Fiehn
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Bernd Markus Lange
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Basil J Nikolau
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Lloyd Sumner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Ruth Welti
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Eve S Wurtele
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.K., K.D., R.N.-P., S.Y.R.);Department of Biotechnology, Yonsei University, Seoul 120-749, South Korea (I.L.); Genome Center, University of California, Davis, California 95616 (O.F.); M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (B.M.L.); Center for Metabolic Biology, Department of Biochemistry, Biophysics, and Molecular Biology (B.J.N.), and Department of Genetics, Development, and Cell Biology (E.S.W.), Iowa State University, Ames, Iowa 50011; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (L.S.); andDivision of Biology, Kansas State University, Manhattan, Kansas 66506 (R.W.)
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Nakabayashi R, Saito K. Integrated metabolomics for abiotic stress responses in plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:10-6. [PMID: 25618839 DOI: 10.1016/j.pbi.2015.01.003] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 05/22/2023]
Abstract
Plants are considered to biosynthesize specialized (traditionally called secondary) metabolites to adapt to environmental stresses such as biotic and abiotic stresses. The majority of specialized metabolites induced by abiotic stress characteristically exhibit antioxidative activity in vitro, but their function in vivo is largely yet to be experimentally confirmed. In this review, we highlight recent advances in the identification of the role of abiotic stress-responsive specialized metabolites with an emphasis on flavonoids. Integrated 'omics' analysis, centered on metabolomics with a series of plant resources differing in their flavonoid accumulation, showed experimentally that flavonoids play a major role in antioxidation in vivo. In addition, the results also suggest the role of flavonoids in the vacuole. To obtain more in-depth insights, chemical and biological challenges need to be addressed for the identification of unknown specialized metabolites and their in vivo functions.
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Affiliation(s)
- Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.
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Hashmi U, Shafqat S, Khan F, Majid M, Hussain H, Kazi AG, John R, Ahmad P. Plant exomics: concepts, applications and methodologies in crop improvement. PLANT SIGNALING & BEHAVIOR 2015; 10:e976152. [PMID: 25482786 PMCID: PMC4622497 DOI: 10.4161/15592324.2014.976152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/17/2014] [Accepted: 08/18/2014] [Indexed: 05/17/2023]
Abstract
Molecular breeding has a crucial role in improvement of crops. Conventional breeding techniques have failed to ameliorate food production. Next generation sequencing has established new concepts of molecular breeding. Exome sequencing has proven to be a significant tool for assessing natural evolution in plants, studying host pathogen interactions and betterment of crop production as exons assist in interpretation of allelic variation with respect to their phenotype. This review covers the platforms for exome sequencing, next generation sequencing technologies that have revolutionized exome sequencing and led toward development of third generation sequencing. Also discussed in this review are the uses of these sequencing technologies to improve wheat, rice and cotton yield and how these technologies are used in exploring the biodiversity of crops, providing better understanding of plant-host pathogen interaction and assessing the process of natural evolution in crops and it also covers how exome sequencing identifies the gene pool involved in symbiotic and other co-existential systems. Furthermore, we conclude how integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone and in the end how these integration will transform the future of crops.
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Key Words
- BAC, bacterial artificial chromosome
- BGR, bacterial grain rot
- CBOL, consortium for 860 the barcode of life
- ETI, effector-triggered immunity
- HPRT, hypoxanthineguanine phosphoribosyl transferase
- MMs, molecular markers
- NGS, next generation sequencing
- NITSR, nuclear internal transcribed spacer region
- OPC, open promoter complex
- QTL, quantitative trait locus
- SMRT, single molecule real time
- SNPs, single nucleotide poly-morphisms
- SOLiD, sequencing by oligonucleotide ligation and detection
- WES, whole exome sequencing
- WGS, whole genome sequencing
- WGS, whole genome shotgun
- biodiversity
- crop improvement
- dNMPs, deoxyribosenucleoside monophosphates
- exome sequencing
- plant biotechnology
- plant-host pathogen interactions
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Affiliation(s)
- Uzair Hashmi
- Atta ur Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Samia Shafqat
- Atta ur Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Faria Khan
- Atta ur Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Misbah Majid
- Atta ur Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Harris Hussain
- Atta ur Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Alvina Gul Kazi
- Atta ur Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Riffat John
- Department of Botany; University of Kashmir; Jammu and Kashmir, India
| | - Parvaiz Ahmad
- Department of Botany; S.P. College Srinagar; Jammu and Kashmir, India
- Correspondence to: Parvaiz Ahmad;
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Cavalcanti JHF, Esteves-Ferreira AA, Quinhones CGS, Pereira-Lima IA, Nunes-Nesi A, Fernie AR, Araújo WL. Evolution and functional implications of the tricarboxylic acid cycle as revealed by phylogenetic analysis. Genome Biol Evol 2014; 6:2830-48. [PMID: 25274566 PMCID: PMC4224347 DOI: 10.1093/gbe/evu221] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The tricarboxylic acid (TCA) cycle, a crucial component of respiratory metabolism, is composed of a set of eight enzymes present in the mitochondrial matrix. However, most of the TCA cycle enzymes are encoded in the nucleus in higher eukaryotes. In addition, evidence has accumulated demonstrating that nuclear genes were acquired from the mitochondrial genome during the course of evolution. For this reason, we here analyzed the evolutionary history of all TCA cycle enzymes in attempt to better understand the origin of these nuclear-encoded proteins. Our results indicate that prior to endosymbiotic events the TCA cycle seemed to operate only as isolated steps in both the host (eubacterial cell) and mitochondria (alphaproteobacteria). The origin of isoforms present in different cell compartments might be associated either with gene-transfer events which did not result in proper targeting of the protein to mitochondrion or with duplication events. Further in silico analyses allow us to suggest new insights into the possible roles of TCA cycle enzymes in different tissues. Finally, we performed coexpression analysis using mitochondrial TCA cycle genes revealing close connections among these genes most likely related to the higher efficiency of oxidative phosphorylation in this specialized organelle. Moreover, these analyses allowed us to identify further candidate genes which might be used for metabolic engineering purposes given the importance of the TCA cycle during development and/or stress situations.
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Affiliation(s)
- João Henrique Frota Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Alberto A Esteves-Ferreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Carla G S Quinhones
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Italo A Pereira-Lima
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, MG, Brazil
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Hectors K, Van Oevelen S, Geuns J, Guisez Y, Jansen MAK, Prinsen E. Dynamic changes in plant secondary metabolites during UV acclimation in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2014; 152:219-30. [PMID: 24517099 DOI: 10.1111/ppl.12168] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/22/2013] [Accepted: 01/14/2014] [Indexed: 05/02/2023]
Abstract
Plants respond to environmental stress by synthesizing a range of secondary metabolites for defense purposes. Here we report on the effect of chronic ultraviolet (UV) radiation on the accumulation of plant secondary metabolites in Arabidopsis thaliana leaves. In the natural environment, UV is a highly dynamic environmental parameter and therefore we hypothesized that plants are continuously readjusting levels of secondary metabolites. Our data show distinct kinetic profiles for accumulation of tocopherols, polyamines and flavonoids upon UV acclimation. The lipid-soluble antioxidant α-tocopherol accumulated fast and remained elevated. Polyamines accumulated fast and transiently. This fast response implies a role for α-tocopherol and polyamines in short-term UV response. In contrast, an additional sustained accumulation of flavonols took place. The distinct accumulation patterns of these secondary metabolites confirm that the UV acclimation process is a dynamic process, and indicates that commonly used single time-point analyses do not reveal the full extent of UV acclimation. We demonstrate that UV stimulates the accumulation of specific flavonol glycosides, i.e. kaempferol and (to a lesser extent) quercetin di- and triglycosides, all specifically rhamnosylated at position seven. All metabolites were identified by Ultra Performance Liquid Chromatography (UPLC)-coupled tandem mass spectrometry. Some of these flavonol glycosides reached steady-state levels in 3-4 days, while concentrations of others are still increasing after 12 days of UV exposure. A biochemical pathway for these glycosides is postulated involving 7-O-rhamnosylation for the synthesis of all eight metabolites identified. We postulate that this 7-O-rhamnosylation has an important function in UV acclimation.
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Affiliation(s)
- Kathleen Hectors
- Laboratory of Molecular Plant Physiology & Biotechnology, Department of Biology, University of Antwerp, Antwerpen, Belgium; Laboratory of Plant Growth & Development, Department of Biology, University of Antwerp, Antwerpen, Belgium
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Zhao Y, Zhao C, Li Y, Chang Y, Zhang J, Zeng Z, Lu X, Xu G. Study of metabolite differences of flue-cured tobacco from different regions using a pseudotargeted gas chromatography with mass spectrometry selected-ion monitoring method. J Sep Sci 2014; 37:2177-84. [PMID: 24865655 DOI: 10.1002/jssc.201400097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/02/2014] [Accepted: 05/17/2014] [Indexed: 12/16/2023]
Abstract
A pseudotargeted method based on gas chromatography and mass spectrometry with selected-ion monitoring was established to investigate the metabolite differences of flue-cured tobacco from three different growing regions. The mixed solvent of acetonitrile/isopropanol/water (3:3:2, v/v/v) was chosen as the optimal extraction system based on the good repeatability and extraction efficiency. A self-developed software coupled with commercial software was used to establish the pseudotargeted method including 289 peaks and 47 groups. Multivariable statistical analysis indicated that tobacco samples can be obviously separated based on the geographical origins. On the basis of a Mann-Whitney U test, organic acids, phenols, and alkaloids had higher levels in Hunan province. In contrast, a large proportion of amino acids (including L-tyrosine, L-proline, and serine), sucrose, and linoleic acid were the highest in Yunnan province. Meanwhile, multiple metabolic pathways (including carbohydrate metabolism, tricarboxylic acid cycle, and nitrogen metabolism) were influenced by growing regions. Twenty-eight differential metabolites, which had great contributions to the classification of tobacco samples of three growing regions, were further defined. The results demonstrated that the developed pseudotargeted method was a powerful tool to investigate the metabolic profiling of tobacco leaves and discriminate tobacco leaves of different growing regions.
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Affiliation(s)
- Yanni Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Fukushima A, Kusano M, Mejia RF, Iwasa M, Kobayashi M, Hayashi N, Watanabe-Takahashi A, Narisawa T, Tohge T, Hur M, Wurtele ES, Nikolau BJ, Saito K. Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis. PLANT PHYSIOLOGY 2014; 165:948-961. [PMID: 24828308 PMCID: PMC4081348 DOI: 10.1104/pp.114.240986] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/05/2014] [Indexed: 05/19/2023]
Abstract
Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally, and improving gene annotation remains a major challenge in plant science. As metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation in the plant metabolism, it provides clues to the function(s) of genes of interest. We chose 50 Arabidopsis mutants, including a set of characterized and uncharacterized mutants, that resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry. To make the data set available as an efficient public functional genomics tool for hypothesis generation, we developed the Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). It allows the evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools. Nonprocessed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by the Metabolomics Standards Initiative and are freely downloadable. Proof-of-concept analysis suggests that MeKO is highly useful for the generation of hypotheses for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.riken.jp/meko/.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Ramon Francisco Mejia
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Mami Iwasa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Naomi Hayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Akiko Watanabe-Takahashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Tomoko Narisawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Takayuki Tohge
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Manhoi Hur
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Eve Syrkin Wurtele
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Basil J Nikolau
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (A.F., Mi.K., R.F.M., M.I., Ma.K., N.H., A.W.-T., T.N., T.T., K.S.);Japan Science and Technology Agency, National Bioscience Database Center, Chiyoda-ku, Tokyo 102-0081, Japan (A.F.);Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan (Mi.K.);Nissan Chemical Industries, Funabashi, Chiba 274-8507, Japan (M.I.);Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T.);Department of Genetics Development and Cell Biology (M.H., E.S.W.), Center for Metabolic Biology (E.S.W., B.J.N.), Center for Biorenewable Chemicals (E.S.W., B.J.N.), and Biochemistry, Biophysics, and Molecular Biology (B.J.N.), Iowa State University, Ames, Iowa 50011; andGraduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 263-8522, Japan (K.S.)
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127
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Chu Y, Kwon T, Nam J. Enzymatic and metabolic engineering for efficient production of syringin, sinapyl alcohol 4-O-glucoside, in Arabidopsis thaliana. PHYTOCHEMISTRY 2014; 102:55-63. [PMID: 24667164 DOI: 10.1016/j.phytochem.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 02/21/2014] [Accepted: 03/04/2014] [Indexed: 06/03/2023]
Abstract
To promote efficient production of syringin, a plant-derived bioactive monolignol glucoside, synergistic effects of enzymatic and metabolic engineering were combined. Recombinant UGT72E3/E2 chimeras, generated by exchanging parts of the C-terminal domain including the Putative Secondary Plant Glycosyltransferase (PSPG) motif of UGT72E3 and UGT72E2, were expressed in leaves of transgenic Arabidopsis plants; syringin production was measured in vivo and by enzymatic assays in vitro. In both tests, UGT72E3/2 displayed substrate specificity for sinapyl alcohol like the parental enzyme UGT72E3, and the syringin production was significantly increased compared to UGT72E3. In particular, in the in vitro assay, which was performed in the presence of a high concentration of sinapyl alcohol, the production of syringin by UGT72E3/2 was 4-fold higher than by UGT72E3. Furthermore, to enhance metabolic flow through the phenylpropanoid pathway and maintain a high basal concentration of sinapyl alcohol in the leaves, UGT72E3/2 was combined with the sinapyl alcohol synthesis pathway gene F5H encoding ferulate 5-hydroxylase and the lignin biosynthesis transcriptional activator MYB58. The resulting UGT72E3/2+F5H+MYB58 OE plants, which simultaneously overexpress these three genes, accumulated a 56-fold higher level of syringin in their leaves than wild-type plants.
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Affiliation(s)
- Yang Chu
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, South Korea
| | - Tackmin Kwon
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, South Korea
| | - Jaesung Nam
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, South Korea.
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128
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Martins SCV, Araújo WL, Tohge T, Fernie AR, DaMatta FM. In high-light-acclimated coffee plants the metabolic machinery is adjusted to avoid oxidative stress rather than to benefit from extra light enhancement in photosynthetic yield. PLoS One 2014; 9:e94862. [PMID: 24733284 PMCID: PMC3986255 DOI: 10.1371/journal.pone.0094862] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 03/20/2014] [Indexed: 12/31/2022] Open
Abstract
Coffee (Coffea arabica L.) has been traditionally considered as shade-demanding, although it performs well without shade and even out-yields shaded coffee. Here we investigated how coffee plants adjust their metabolic machinery to varying light supply and whether these adjustments are supported by a reprogramming of the primary and secondary metabolism. We demonstrate that coffee plants are able to adjust its metabolic machinery to high light conditions through marked increases in its antioxidant capacity associated with enhanced consumption of reducing equivalents. Photorespiration and alternative pathways are suggested to be key players in reductant-consumption under high light conditions. We also demonstrate that both primary and secondary metabolism undergo extensive reprogramming under high light supply, including depression of the levels of intermediates of the tricarboxylic acid cycle that were accompanied by an up-regulation of a range of amino acids, sugars and sugar alcohols, polyamines and flavonoids such as kaempferol and quercetin derivatives. When taken together, the entire dataset is consistent with these metabolic alterations being primarily associated with oxidative stress avoidance rather than representing adjustments in order to facilitate the plants from utilizing the additional light to improve their photosynthetic performance.
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Affiliation(s)
- Samuel C. V. Martins
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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129
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Singh S, Agrawal SB, Agrawal M. UVR8 mediated plant protective responses under low UV-B radiation leading to photosynthetic acclimation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 137:67-76. [PMID: 24780386 DOI: 10.1016/j.jphotobiol.2014.03.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 11/27/2022]
Abstract
The UV-B photoreceptor UVR8 regulates the expression of several genes leading to acclimation responses in plants. Direct role of UVR8 in maintaining the photosynthesis is not defined but it is known to increase the expression of some chloroplastic proteins like SIG5 and ELIP. It provides indirect protection to photosynthesis by regulating the synthesis of secondary metabolites and photomorphogenesis. Signaling cascades controlled by UVR8 mediate many protective responses thus promotes plant acclimation against stress and secures its survival.
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Affiliation(s)
- Suruchi Singh
- Laboratory of Air Pollution and Global Climate Change, Department of Botany, Banaras Hindu University, Varanasi 221005, India
| | - S B Agrawal
- Laboratory of Air Pollution and Global Climate Change, Department of Botany, Banaras Hindu University, Varanasi 221005, India.
| | - Madhoolika Agrawal
- Laboratory of Air Pollution and Global Climate Change, Department of Botany, Banaras Hindu University, Varanasi 221005, India
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130
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Nakabayashi R, Yonekura-Sakakibara K, Urano K, Suzuki M, Yamada Y, Nishizawa T, Matsuda F, Kojima M, Sakakibara H, Shinozaki K, Michael AJ, Tohge T, Yamazaki M, Saito K. Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:367-79. [PMID: 24274116 PMCID: PMC4282528 DOI: 10.1111/tpj.12388] [Citation(s) in RCA: 649] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 11/11/2013] [Accepted: 11/20/2013] [Indexed: 05/18/2023]
Abstract
The notion that plants use specialized metabolism to protect against environmental stresses needs to be experimentally proven by addressing the question of whether stress tolerance by specialized metabolism is directly due to metabolites such as flavonoids. We report that flavonoids with radical scavenging activity mitigate against oxidative and drought stress in Arabidopsis thaliana. Metabolome and transcriptome profiling and experiments with oxidative and drought stress in wild-type, single overexpressors of MYB12/PFG1 (PRODUCTION OF FLAVONOL GLYCOSIDES1) or MYB75/PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT1), double overexpressors of MYB12 and PAP1, transparent testa4 (tt4) as a flavonoid-deficient mutant, and flavonoid-deficient MYB12 or PAP1 overexpressing lines (obtained by crossing tt4 and the individual MYB overexpressor) demonstrated that flavonoid overaccumulation was key to enhanced tolerance to such stresses. Antioxidative activity assays using 2,2-diphenyl-1-picrylhydrazyl, methyl viologen, and 3,3'-diaminobenzidine clearly showed that anthocyanin overaccumulation with strong in vitro antioxidative activity mitigated the accumulation of reactive oxygen species in vivo under oxidative and drought stress. These data confirm the usefulness of flavonoids for enhancing both biotic and abiotic stress tolerance in crops.
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Affiliation(s)
- Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Chuo-ku, Chiba, 260-8675, Japan
- CREST, Japan Science and Technology Agency4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Keiko Yonekura-Sakakibara
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kaoru Urano
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Makoto Suzuki
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yutaka Yamada
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Fumio Matsuda
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- †Graduate School of Information Science and Technology, Osaka University1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Anthony J Michael
- Department of Pharmacology, University of Texas Southwestern Medical CenterDallas, TX, 75390, USA
| | - Takayuki Tohge
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- ‡Max-Planck Institute for Molecular Plant Physiology14476, Potsdam, Germany
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Chuo-ku, Chiba, 260-8675, Japan
- CREST, Japan Science and Technology Agency4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Chuo-ku, Chiba, 260-8675, Japan
- *(e-mail )
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131
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Ernst M, Silva DB, Silva RR, Vêncio RZN, Lopes NP. Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing. Nat Prod Rep 2014; 31:784-806. [DOI: 10.1039/c3np70086k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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132
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KOBAYASHI M, KANTO T, FUJIKAWA T, YAMADA M, ISHIWATA M, SATOU M, HISAMATSU T. Supplemental UV Radiation Controls Rose Powdery Mildew Disease under the Greenhouse Conditions. ACTA ACUST UNITED AC 2014. [DOI: 10.2525/ecb.51.157] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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133
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Park HL, Lee SW, Jung KH, Hahn TR, Cho MH. Transcriptomic analysis of UV-treated rice leaves reveals UV-induced phytoalexin biosynthetic pathways and their regulatory networks in rice. PHYTOCHEMISTRY 2013; 96:57-71. [PMID: 24035516 DOI: 10.1016/j.phytochem.2013.08.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 08/08/2013] [Accepted: 08/20/2013] [Indexed: 05/13/2023]
Abstract
Rice produces diterpenoid and flavonoid phytoalexins for defense against pathogen attack. The production of phytoalexins in rice is also induced by UV-irradiation. To understand the metabolic networks involved in UV-induced phytoalexin biosynthesis and their regulation, phytochemical and transcriptomic analyses of UV-treated rice leaves were performed. In response to UV treatment, the accumulation of flavonoids was observed in rice leaves, which may serve as antioxidants against UV-induced oxidative stress. The phytochemical analysis confirmed sakuranetin accumulation and also demonstrated the induction of phenylamide synthesis in rice leaves by UV-irradiation. Transcriptomic analysis established that aromatic amino acid biosynthetic genes were immediately up-regulated after UV treatment. The genes involved in the phenylpropanoid pathway and flavonoid biosynthesis were also up-regulated. These findings suggest that the aromatic amino acid and flavonoid biosynthetic pathways are coordinately activated for the production of flavonoids and phenolic phytoalexins such as sakuranetin and phenylamides. An in silico analysis of UV-induced O-methyltransferase and acyltransferase genes suggested that these genes may be implicated in sakuranetin and phenylamide synthesis, respectively. The transcriptomic analysis also showed up-regulation of both methylerythritol phosphate pathway and the diterpenoid phytoalexin biosynthetic genes in response to UV treatment. A functional gene network analysis of phytoalexin biosynthetic and UV-induced genes for signaling components and transcription factors using RiceNet suggested that regulatory networks comprising signal perceiving receptor kinases, G-proteins, signal transducing mitogen-activated protein kinases and calcium signaling components, and transcription factors control flavonoid and phytoalexin biosynthesis in rice leaves under UV-C stress conditions.
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Affiliation(s)
- Hye Lin Park
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea
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134
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Jin X, Wang RS, Zhu M, Jeon BW, Albert R, Chen S, Assmann SM. Abscisic acid-responsive guard cell metabolomes of Arabidopsis wild-type and gpa1 G-protein mutants. THE PLANT CELL 2013; 25:4789-811. [PMID: 24368793 PMCID: PMC3903988 DOI: 10.1105/tpc.113.119800] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 10/18/2013] [Accepted: 11/27/2013] [Indexed: 05/03/2023]
Abstract
Individual metabolites have been implicated in abscisic acid (ABA) signaling in guard cells, but a metabolite profile of this specialized cell type is lacking. We used liquid chromatography-multiple reaction monitoring mass spectrometry for targeted analysis of 85 signaling-related metabolites in Arabidopsis thaliana guard cell protoplasts over a time course of ABA treatment. The analysis utilized ∼ 350 million guard cell protoplasts from ∼ 30,000 plants of the Arabidopsis Columbia accession (Col) wild type and the heterotrimeric G-protein α subunit mutant, gpa1, which has ABA-hyposensitive stomata. These metabolomes revealed coordinated regulation of signaling metabolites in unrelated biochemical pathways. Metabolites clustered into different temporal modules in Col versus gpa1, with fewer metabolites showing ABA-altered profiles in gpa1. Ca(2+)-mobilizing agents sphingosine-1-phosphate and cyclic adenosine diphosphate ribose exhibited weaker ABA-stimulated increases in gpa1. Hormone metabolites were responsive to ABA, with generally greater responsiveness in Col than in gpa1. Most hormones also showed different ABA responses in guard cell versus mesophyll cell metabolomes. These findings suggest that ABA functions upstream to regulate other hormones, and are also consistent with G proteins modulating multiple hormonal signaling pathways. In particular, indole-3-acetic acid levels declined after ABA treatment in Col but not gpa1 guard cells. Consistent with this observation, the auxin antagonist α-(phenyl ethyl-2-one)-indole-3-acetic acid enhanced ABA-regulated stomatal movement and restored partial ABA sensitivity to gpa1.
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Affiliation(s)
- Xiaofen Jin
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Rui-Sheng Wang
- Physics Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Reka Albert
- Physics Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sixue Chen
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, Florida 32610
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
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135
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Zhao N, Wang G, Norris A, Chen X, Chen F. Studying Plant Secondary Metabolism in the Age of Genomics. CRITICAL REVIEWS IN PLANT SCIENCES 2013; 32:369-382. [PMID: 0 DOI: 10.1080/07352689.2013.789648] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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136
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Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, Fernie AR. The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 72:21-34. [PMID: 23473981 DOI: 10.1016/j.plaphy.2013.02.001] [Citation(s) in RCA: 475] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/01/2013] [Indexed: 05/19/2023]
Abstract
Flavonoids are representative plant secondary products. In the model plant Arabidopsis thaliana, at least 54 flavonoid molecules (35 flavonols, 11 anthocyanins and 8 proanthocyanidins) are found. Scaffold structures of flavonoids in Arabidopsis are relatively simple. These include kaempferol, quercetin and isorhamnetin for flavonols, cyanidin for anthocyanins and epicatechin for proanthocyanidins. The chemical diversity of flavonoids increases enormously by tailoring reactions which modify these scaffolds, including glycosylation, methylation and acylation. Genes responsible for the formation of flavonoid aglycone structures and their subsequent modification reactions have been extensively characterized by functional genomic efforts - mostly the integration of transcriptomics and metabolic profiling followed by reverse genetic experimentation. This review describes the state-of-art of flavonoid biosynthetic pathway in Arabidopsis regarding both structural and genetic diversity, focusing on the genes encoding enzymes for the biosynthetic reactions and vacuole translocation.
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Affiliation(s)
- Kazuki Saito
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chiba 260-8675, Japan.
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137
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Brunetti C, George RM, Tattini M, Field K, Davey MP. Metabolomics in plant environmental physiology. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4011-20. [PMID: 23922358 DOI: 10.1093/jxb/ert244] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Changes in plant metabolism are at the heart of plant developmental processes, underpinning many of the ways in which plants respond to the environment. As such, the comprehensive study of plant metabolism, or metabolomics, is highly valuable in identifying phenotypic effects of abiotic and biotic stresses on plants. When study is in reference to analysing samples that are relevant to environmental or ecologically based hypotheses, it is termed 'environmental metabolomics'. The emergence of environmental metabolomics as one of the latest of the omics technologies has been one of the most critically important recent developments in plant physiology. Its applications broach the entire landscape of plant ecology, from the understanding of plant plasticity and adaptation through to community composition and even genetic modification in crops. The multitude of novel studies published utilizing metabolomics methods employ a variety of techniques, from the initial stages of tissue sampling, through to sample preservation, transportation, and analysis. This review introduces the concept and applications of plant environmental metabolomics as an ecologically important investigative tool. It examines the main techniques used in situ within field sites, with particular reference to sampling and processing, and those more appropriate for use in laboratory-based settings with emphasis on secondary metabolite analysis.
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Affiliation(s)
- Cecilia Brunetti
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell' Ambiente (DISPAA), Sez. Coltivazioni Arboree, Università di Firenze, Viale delle Idee 30, I-50019 Sesto Fiorentino, Firenze, Italy
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138
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Higashi Y, Saito K. Network analysis for gene discovery in plant-specialized metabolism. PLANT, CELL & ENVIRONMENT 2013; 36:1597-606. [PMID: 23336321 DOI: 10.1111/pce.12069] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 05/03/2023]
Abstract
Recent omics technologies provide information on multiple components of biological networks. Web-based data mining tools are continuously being developed. Because genes involved in specialized (secondary) metabolism are often co-ordinately regulated at the transcriptional level, a number of gene discovery studies have been successfully conducted using network analysis, especially by integrating gene co-expression network analysis and metabolomic investigation. In addition, next-generation sequencing technologies are currently utilized in functional genomics investigations of Arabidopsis and non-model plant species including medicinal plants. Systems-based approaches are expected to gain importance in medicinal plant research. This review discussed network analysis in Arabidopsis and gene discovery in plant-specialized metabolism in non-model plants.
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Affiliation(s)
- Yasuhiro Higashi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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139
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Jung ES, Lee S, Lim SH, Ha SH, Liu KH, Lee CH. Metabolite profiling of the short-term responses of rice leaves (Oryza sativa cv. Ilmi) cultivated under different LED lights and its correlations with antioxidant activities. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:61-9. [PMID: 23849114 DOI: 10.1016/j.plantsci.2013.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/19/2013] [Accepted: 05/07/2013] [Indexed: 05/24/2023]
Abstract
Metabolite profiling of rice leaves (Oryza sativa cv. Ilmi) was performed to investigate the short-term responses to different light-emitting diode (LED) lights, blue (B), green (G), red (R), white (W), shade (S), by using gas chromatography-ion trap-mass spectrometry (GC-IT-MS) and ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) with multivariate analysis. Clear grouping patterns of each light-grown sample, except G and W, were shown in partial least squares-discriminant analysis (PLS-DA). Thirty-two primary metabolites and eleven secondary metabolites were selected and visualized using heatmap. Antioxidant activities of rice leaves followed the order B=W=G>R>S and isoorientin-2''-O-glucoside, isovitexin-2''-O-glucoside, isoorientin-2''-O-(6'''-ρ-coumaroyl)-glucoside, and isoscoparin-2''-O-glucoside showed similar relative differences and had higher Pearson's correlation coefficients than other metabolites in correlation network. According to the orthogonal projection to latent structures-discriminant analysis (OPLS-DA) between B and R, the levels of amino acids, organic acids, fatty acids, and flavonoid glycosides were relatively high in B, whereas the glucose and fructose levels were high in R.
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Affiliation(s)
- Eun Sung Jung
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
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140
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Veljanovski V, Constabel CP. Molecular cloning and biochemical characterization of two UDP-glycosyltransferases from poplar. PHYTOCHEMISTRY 2013; 91:148-57. [PMID: 23375153 DOI: 10.1016/j.phytochem.2012.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/16/2012] [Accepted: 12/21/2012] [Indexed: 05/26/2023]
Abstract
Two pathogen-induced uridine diphosphate glycosyltransferases (UGTs) identified previously via co-expression with induced proanthocyanidin (PA) synthesis in poplar were cloned and characterized. Phylogenetic analysis grouped both genes with other known flavonoid UGTs that act on flavonols and anthocyanins. Recombinant enzymes were produced in order to test if they could glycoslate flavonoids. PtUGT78L1 accepted the flavonols quercetin and kaempferol as well as cyanidin, and used UDP-galactose as a sugar donor. PtUGT78M1 did not accept any of the flavonoids tested as a substrate, but did transfer glucose from UDP-glucose to the universal substrate 2,4,6-trichlorophenol. However, neither enzyme acted on the flavan-3-ols catechin or epicatechin, intermediates in the PA biosynthetic pathway.
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Affiliation(s)
- Vasko Veljanovski
- Centre for Forest Biology and Department of Biology, University of Victoria, Victoria, BC, Canada
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141
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Tilbrook K, Arongaus AB, Binkert M, Heijde M, Yin R, Ulm R. The UVR8 UV-B Photoreceptor: Perception, Signaling and Response. THE ARABIDOPSIS BOOK 2013; 11:e0164. [PMID: 23864838 PMCID: PMC3711356 DOI: 10.1199/tab.0164] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ultraviolet-B radiation (UV-B) is an intrinsic part of sunlight that is accompanied by significant biological effects. Plants are able to perceive UV-B using the UV-B photoreceptor UVR8 which is linked to a specific molecular signaling pathway and leads to UV-B acclimation. Herein we review the biological process in plants from initial UV-B perception and signal transduction through to the known UV-B responses that promote survival in sunlight. The UVR8 UV-B photoreceptor exists as a homodimer that instantly monomerises upon UV-B absorption via specific intrinsic tryptophans which act as UV-B chromophores. The UVR8 monomer interacts with COP1, an E3 ubiquitin ligase, initiating a molecular signaling pathway that leads to gene expression changes. This signaling output leads to UVR8-dependent responses including UV-B-induced photomorphogenesis and the accumulation of UV-B-absorbing flavonols. Negative feedback regulation of the pathway is provided by the WD40-repeat proteins RUP1 and RUP2, which facilitate UVR8 redimerization, disrupting the UVR8-COP1 interaction. Despite rapid advancements in the field of recent years, further components of UVR8 UV-B signaling are constantly emerging, and the precise interplay of these and the established players UVR8, COP1, RUP1, RUP2 and HY5 needs to be defined. UVR8 UV-B signaling represents our further understanding of how plants are able to sense their light environment and adjust their growth accordingly.
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Affiliation(s)
- Kimberley Tilbrook
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Adriana B. Arongaus
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Melanie Binkert
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Marc Heijde
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Ruohe Yin
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
| | - Roman Ulm
- Department of Botany and Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland
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142
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Saito K. Phytochemical genomics--a new trend. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:373-80. [PMID: 23628002 DOI: 10.1016/j.pbi.2013.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 05/04/2023]
Abstract
Phytochemical genomics is a recently emerging field, which investigates the genomic basis of the synthesis and function of phytochemicals (plant metabolites), particularly based on advanced metabolomics. The chemical diversity of the model plant Arabidopsis thaliana is larger than previously expected, and the gene-to-metabolite correlations have been elucidated mostly by an integrated analysis of transcriptomes and metabolomes. For example, most genes involved in the biosynthesis of flavonoids in Arabidopsis have been characterized by this method. A similar approach has been applied to the functional genomics for production of phytochemicals in crops and medicinal plants. Great promise is seen in metabolic quantitative loci analysis in major crops such as rice and tomato, and identification of novel genes involved in the biosynthesis of bioactive specialized metabolites in medicinal plants.
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Affiliation(s)
- Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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143
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Nunes-Nesi A, Araújo WL, Obata T, Fernie AR. Regulation of the mitochondrial tricarboxylic acid cycle. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:335-43. [PMID: 23462640 DOI: 10.1016/j.pbi.2013.01.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/24/2013] [Accepted: 01/26/2013] [Indexed: 05/04/2023]
Abstract
Recent years have seen considerable advances in our understanding of the particular physiological roles of the constituent enzymes of the tricarboxylic acid (TCA) cycle. Despite acquiring a fairly comprehensive overview of the functional importance of these proteins relatively little is known concerning how this important pathway is regulated. In this review we concentrate on the mitochondrial reactions since this organelle is the only one in which a full cycle can, at least theoretically, operate. We summarize what is known about the regulation of the enzymes of the pathway both from historical kinetic studies as well as discussing more recent transcriptional and proteomic studies and our enhanced understanding of subcellular compartmentation within the context of metabolic regulation.
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Affiliation(s)
- Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, Brazil
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144
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Transcriptome data modeling for targeted plant metabolic engineering. Curr Opin Biotechnol 2013; 24:285-90. [DOI: 10.1016/j.copbio.2012.10.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/24/2012] [Accepted: 10/29/2012] [Indexed: 12/31/2022]
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145
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Kusano M, Fukushima A. Current challenges and future potential of tomato breeding using omics approaches. BREEDING SCIENCE 2013; 63:31-41. [PMID: 23641179 PMCID: PMC3621443 DOI: 10.1270/jsbbs.63.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/30/2012] [Indexed: 05/16/2023]
Abstract
As tomatoes are one of the most important vegetables in the world, improvements in the quality and yield of tomato are strongly required. For this purpose, omics approaches such as metabolomics and transcriptomics are used not only for basic research to understand relationships between important traits and metabolism but also for the development of next generation breeding strategies of tomato plants, because an increase in the knowledge improves the taste and quality, stress resistance and/or potentially health-beneficial metabolites and is connected to improvements in the biochemical composition of tomatoes. Such omics data can be applied to network analyses to potentially reveal unknown cellular regulatory networks in tomato plants. The high-quality tomato genome that was sequenced in 2012 will likely accelerate the application of omics strategies, including next generation sequencing for tomato breeding. In this review, we highlight the current studies of omics network analyses of tomatoes and other plant species, in particular, a gene coexpression network. Key applications of omics approaches are also presented as case examples to improve economically important traits for tomato breeding.
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Affiliation(s)
- Miyako Kusano
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
- Corresponding author (e-mail: )
| | - Atsushi Fukushima
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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146
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Tohge T, Watanabe M, Hoefgen R, Fernie AR. The evolution of phenylpropanoid metabolism in the green lineage. Crit Rev Biochem Mol Biol 2013; 48:123-52. [PMID: 23350798 DOI: 10.3109/10409238.2012.758083] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Phenolic secondary metabolites are only produced by plants wherein they play important roles in both biotic and abiotic defense in seed plants as well as being potentially important bioactive compounds with both nutritional and medicinal benefits reported for animals and humans as a consequence of their potent antioxidant activity. During the long evolutionary period in which plants have adapted to the environmental niches in which they exist (and especially during the evolution of land plants from their aquatic algal ancestors), several strategies such as gene duplication and convergent evolution have contributed to the evolution of this pathway. In this respect, diversity and redundancy of several key genes of phenolic secondary metabolism such as polyketide synthases, cytochrome P450s, Fe(2+)/2-oxoglutarate-dependent dioxygenases and UDP-glycosyltransferases have played an essential role. Recent technical developments allowing affordable whole genome sequencing as well as a better inventory of species-by-species chemical diversity have resulted in a dramatic increase in the number of tools we have to assess how these pathways evolved. In parallel, reverse genetics combined with detailed molecular phenotyping is 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. In this review, phenolic metabolite-related gene sequences (for a total of 65 gene families including shikimate biosynthetic genes) are compared across 23 independent species, and the phenolic metabolic complement of various plant species are compared with one another, in attempt to better understand the evolution of diversity in this crucial pathway.
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Affiliation(s)
- Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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147
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Nakabayashi R, Sawada Y, Yamada Y, Suzuki M, Hirai MY, Sakurai T, Saito K. Combination of Liquid Chromatography–Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry with 13C-Labeling for Chemical Assignment of Sulfur-Containing Metabolites in Onion Bulbs. Anal Chem 2013; 85:1310-5. [DOI: 10.1021/ac302733c] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ryo Nakabayashi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
| | - Yuji Sawada
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
| | - Yutaka Yamada
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
| | - Makoto Suzuki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
| | - Masami Yokota Hirai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
| | - Kazuki Saito
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045,
Japan
- Graduate School of
Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana,
Chuo-ku, Chiba 260-8675, Japan
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148
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Fukushima A, Kusano M. Recent progress in the development of metabolome databases for plant systems biology. FRONTIERS IN PLANT SCIENCE 2013; 4:73. [PMID: 23577015 PMCID: PMC3616245 DOI: 10.3389/fpls.2013.00073] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/15/2013] [Indexed: 05/19/2023]
Abstract
Metabolomics has grown greatly as a functional genomics tool, and has become an invaluable diagnostic tool for biochemical phenotyping of biological systems. Over the past decades, a number of databases involving information related to mass spectra, compound names and structures, statistical/mathematical models and metabolic pathways, and metabolite profile data have been developed. Such databases complement each other and support efficient growth in this area, although the data resources remain scattered across the World Wide Web. Here, we review available metabolome databases and summarize the present status of development of related tools, particularly focusing on the plant metabolome. Data sharing discussed here will pave way for the robust interpretation of metabolomic data and advances in plant systems biology.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Plant Science CenterYokohama, Kanagawa, Japan
- *Correspondence: Atsushi Fukushima, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. e-mail:
| | - Miyako Kusano
- RIKEN Plant Science CenterYokohama, Kanagawa, Japan
- Department of Genome System Sciences, Graduate School of Nanobioscience, Kihara Institute for Biological ResearchYokohama, Kanagawa, Japan
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149
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Fukushima A. DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene 2012; 518:209-14. [PMID: 23246976 DOI: 10.1016/j.gene.2012.11.028] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
Abstract
Large-scale "omics" data, such as microarrays, can be used to infer underlying cellular regulatory networks in organisms, enabling us to better understand the molecular basis of disease and important traits. Correlation approaches, such as a hierarchical cluster analysis, have been widely used to analyze omics data. In addition to the changes in the mean levels of molecules in the omics data, it is important to know about the changes in the correlation relationship among molecules between 2 experimental conditions. The development of a tool to identify differential correlation patterns in omics data in an efficient and unbiased manner is therefore desirable. We developed the DiffCorr package, a simple method for identifying pattern changes between 2 experimental conditions in correlation networks, which builds on a commonly used association measure, such as Pearson's correlation coefficient. DiffCorr calculates correlation matrices for each dataset, identifies the first principal component-based "eigen-molecules" in the correlation networks, and tests differential correlation between the 2 groups based on Fisher's z-test. We illustrated its utility by demonstrating biologically relevant, differentially correlated molecules in transcriptome coexpression and metabolite-to-metabolite correlation networks. DiffCorr can explore differential correlations between 2 conditions in the context of post-genomics data types, namely transcriptomics and metabolomics. DiffCorr is simple to use in calculating differential correlations and is suitable for the first step towards inferring causal relationships and detecting biomarker candidates. The package can be downloaded from the following website: http://diffcorr.sourceforge.net/.
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150
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Valledor L, Cañal MJ, Pascual J, Rodríguez R, Meijón M. Early induced protein 1 (PrELIP1) and other photosynthetic, stress and epigenetic regulation genes are involved in Pinus radiata D. don UV-B radiation response. PHYSIOLOGIA PLANTARUM 2012; 146:308-20. [PMID: 22471584 DOI: 10.1111/j.1399-3054.2012.01629.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The continuous atmospheric and environmental deterioration is likely to increase, among others, the influx of ultraviolet B (UV-B) radiation. The plants have photoprotective responses, which are complex mechanisms involving different physiological responses, to avoid the damages caused by this radiation that may lead to plant death. We have studied the adaptive responses to UV-B in Pinus radiata, given the importance of this species in conifer forests and reforestation programs. We analyzed the photosynthetic activity, pigments content, and gene expression of candidate genes related to photosynthesis, stress and gene regulation in needles exposed to UV-B during a 96 h time course. The results reveal a clear increase of pigments under UV-B stress while photosynthetic activity decreased. The expression levels of the studied genes drastically changed after UV-B exposure, were stress related genes were upregulated while photosynthesis (RBCA and RBCS) and epigenetic regulation were downregulated (MSI1, CSDP2, SHM4). The novel gene PrELIP1, fully sequenced for this work, was upregulated and expressed mainly in the palisade parenchyma of needles. This gene has conserved domains related to the dissipation of the UV-B radiation that give to this protein a key role during photoprotection response of the needles in Pinus radiata.
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Affiliation(s)
- Luis Valledor
- Área de Fisiología Vegetal, Dpto. B.O.S., Facultad de Biología, Universidad de Oviedo, C/ Cat. Rodrigo Uria s/n, E-33071, Oviedo, Asturias, Spain
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