1
|
Weiszmann J, Walther D, Clauw P, Back G, Gunis J, Reichardt I, Koemeda S, Jez J, Nordborg M, Schwarzerova J, Pierides I, Nägele T, Weckwerth W. Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes. PLANT PHYSIOLOGY 2023; 193:980-1000. [PMID: 37220420 PMCID: PMC10517190 DOI: 10.1093/plphys/kiad298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Acclimation and adaptation of metabolism to a changing environment are key processes for plant survival and reproductive success. In the present study, 241 natural accessions of Arabidopsis (Arabidopsis thaliana) were grown under two different temperature regimes, 16 °C and 6 °C, and growth parameters were recorded, together with metabolite profiles, to investigate the natural genome × environment effects on metabolome variation. The plasticity of metabolism, which was captured by metabolic distance measures, varied considerably between accessions. Both relative growth rates and metabolic distances were predictable by the underlying natural genetic variation of accessions. Applying machine learning methods, climatic variables of the original growth habitats were tested for their predictive power of natural metabolic variation among accessions. We found specifically habitat temperature during the first quarter of the year to be the best predictor of the plasticity of primary metabolism, indicating habitat temperature as the causal driver of evolutionary cold adaptation processes. Analyses of epigenome- and genome-wide associations revealed accession-specific differential DNA-methylation levels as potentially linked to the metabolome and identified FUMARASE2 as strongly associated with cold adaptation in Arabidopsis accessions. These findings were supported by calculations of the biochemical Jacobian matrix based on variance and covariance of metabolomics data, which revealed that growth under low temperatures most substantially affects the accession-specific plasticity of fumarate and sugar metabolism. Our findings indicate that the plasticity of metabolic regulation is predictable from the genome and epigenome and driven evolutionarily by Arabidopsis growth habitats.
Collapse
Affiliation(s)
- Jakob Weiszmann
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, 1030 Vienna, Austria
| | - Dirk Walther
- Bioinformatics, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Pieter Clauw
- Austrian Academy of Sciences, Gregor Mendel Institute (GMI), 1030 Vienna, Austria
| | - Georg Back
- Bioinformatics, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Joanna Gunis
- Austrian Academy of Sciences, Gregor Mendel Institute (GMI), 1030 Vienna, Austria
| | - Ilka Reichardt
- Genome Engineering Facility, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stefanie Koemeda
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbH (VBCF), 1030 Vienna, Austria
| | - Jakub Jez
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbH (VBCF), 1030 Vienna, Austria
| | - Magnus Nordborg
- Austrian Academy of Sciences, Gregor Mendel Institute (GMI), 1030 Vienna, Austria
| | - Jana Schwarzerova
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Brno University of Technology, Faculty of Electrical Engineering and Communication, Department of Biomedical Engineering, Technická 12, 616 00 Brno, Czech Republic
| | - Iro Pierides
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152 Planegg, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, 1030 Vienna, Austria
| |
Collapse
|
2
|
Garrido A, Conde A, De Vos RCH, Cunha A. The influence of light microclimate on the lipid profile and associated transcripts of photosynthetically active grape berry seeds. FRONTIERS IN PLANT SCIENCE 2023; 13:1022379. [PMID: 36684778 PMCID: PMC9846335 DOI: 10.3389/fpls.2022.1022379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Lipids and oils determine the quality and industrial value of grape seeds. Studies with legume seeds demonstrated the influence of light on lipid metabolism and its association with seed photosynthesis. Grape berry seeds are photosynthetically active till mature stage, but mostly during the green stage and veraison. The objective of this work was to compare the lipid profiles of seeds from white grape berries (cv. Alvarinho) growing at two contrasting light microclimates in the canopy (low and high light, LL and HL respectively), previously reported to have distinct photosynthetic competences. Berries were collected at three developmental stages (green, veraison and mature) and from both microclimates, and the seeds were analyzed for their lipid profiles in an untargeted manner using liquid chromatography coupled to high resolution mass spectrometry (LCMS). The seed lipid profiles differed greatly among berry developmental stages, and to a lesser extend between microclimates. The LL microclimate coincided with a higher relative levels of fatty acids specifically at mature stage, while the HL microclimate led to an up-regulation of ceramides at green stage and of triacylglycerols and glycerophospholipids at mature stage. The seed transcript levels of four key genes (VvACCase1, VvΔ9FAD, VvFAD6 and VvLOXO) involved in fatty acid metabolism were analyzed using real-time qPCR. The lipoxygenase gene (VvLOXO) was down- and up-regulated by HL, as compared to LL, in seeds at green and veraison stages, respectively. These results suggest that seed photosynthesis may play distinct roles during seed growth and development, possibly by fueling different lipid pathways: at green stage mainly towards the accumulation of membrane-bound lipid species that are essential for cell growth and maintenance of the photosynthetic machinery itself; and at veraison and mature stages mainly towards storage lipids that contribute to the final quality of the grape seeds.
Collapse
Affiliation(s)
- Andreia Garrido
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Artur Conde
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Ric C. H. De Vos
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University and Research (Wageningen-UR), Wageningen, Netherlands
| | - Ana Cunha
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| |
Collapse
|
3
|
Shahhoseini R, Daneshvar H. Phytochemical and physiological reactions of feverfew (Tanacetum parthenium (L.) Schultz Bip) to TiO 2 nanoparticles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:674-684. [PMID: 36563573 DOI: 10.1016/j.plaphy.2022.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/17/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Nanomaterials can be used as elicitors for improving the biosynthesis of secondary metabolites in medicinal plants. The present study was conducted to assay the titanium dioxide-nanoparticles (TiO2-NPs) effects on feverfew (Tanacetum parthenium) as an anti-cancer plant. The study showed that TiO2-NPs application increased the amounts of the main compounds and oxygenated monoterpene in essential oils, thereby causing an improvement in the quantity and quality of the essential oils compared to control. The highest effect was related to 1500 ppm TiO2-NPs concentration. Regarding parthenolide, TiO2-NPs had no positive effect on parthenolide content and the highest content was observed in control. Increasing the concentrations over 1500 ppm resulted in a decrease in chlorophyll content, capitule diameter, flower yield, and harvest index compared to other concentrations and control. Additionally, the results indicated that TiO2-NPs foliar spray reduced flower number, biological yield, fresh weight, and dry weights compared with untreated plants. The increase in quality and content of essential oil and lack of increase in parthenolide content, and reproductive and vegetative characteristics showed that TiO2-NPs mainly affected the content and composition of essential oil. Totally, the application of TiO2-NPs in terms of positive effect on the yield and metabolites (without damaging biological effects) can be recommended and followed up to the concentration of 1000 ppm. Overall, the results indicated that improving the synthesis of valuable medicinal metabolites using TiO2-NPs has promising results depending on the type of species, concentration used and target metabolites.
Collapse
Affiliation(s)
- Reza Shahhoseini
- Department of Medicinal Plants, Arak University, 38156-8-8349, Arak, Iran.
| | - Hadiseh Daneshvar
- Department of Horticultural Sciences, University of Tehran, Karaj, Iran
| |
Collapse
|
4
|
Enzyme-treated chicory for cosmetics: application assessment and techno-economic analysis. AMB Express 2022; 12:152. [PMID: 36472772 PMCID: PMC9727056 DOI: 10.1186/s13568-022-01494-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
Chicory (Cichorium intybus L.) is an important industrial crop that produces large quantities of the dietary fiber inulin in its roots. Following inulin extraction, the bagasse is typically used as animal feed, but it contains numerous bioactive secondary metabolites with potential applications in healthcare and cosmetic products. Here we assessed the antimicrobial properties of chicory biomass pre-treated with various enzymes alone and in combination to release the bioactive compounds and increase their bioavailability. We found that pre-treatment significantly increased the antimicrobial activity of this industrial by-product, yielding an extract that inhibited typical skin pathogens in a cosmetic formula challenge test. We also evaluated the valorization of chicory biomass as a bioactive cosmetic ingredient. Economic feasibility was estimated by combining our experimental results with a conceptual techno-economic analysis. Our results suggest that chicory biomass can be utilized for the sustainable production of efficacious cosmetic ingredients.
Collapse
|
5
|
Comparative compositions of metabolites and dietary fibre components in doughs and breads produced from bread wheat, emmer and spelt and using yeast and sourdough processes. Food Chem 2021; 374:131710. [PMID: 34891089 DOI: 10.1016/j.foodchem.2021.131710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/19/2022]
Abstract
Wholemeal flours from blends of bread wheat, emmer and spelt were processed into bread using yeast-based and sourdough fermentation. The bread wheat flour contained significantly higher concentrations of total dietary fibre and fructans than the spelt and emmer flours, the latter having the lowest contents. Breadmaking using sourdough and yeast systems resulted in changes in composition from flour to dough to bread including increases in organic acids and mannitol in the sourdough system and increases in amino acids and sugars (released by hydrolysis of proteins and starch, respectively) in both processing systems. The concentrations of fructans and raffinose (the major endogenous FODMAPs) were reduced by yeast and sourdough fermentation, with yeast having the greater effect. Both systems resulted in greater increases in sugars and glycerol in emmer than in bread wheat and spelt, but the significance of these differences for human health has not been established.
Collapse
|
6
|
Garrido A, Engel J, Mumm R, Conde A, Cunha A, De Vos RCH. Metabolomics of Photosynthetically Active Tissues in White Grapes: Effects of Light Microclimate and Stress Mitigation Strategies. Metabolites 2021; 11:metabo11040205. [PMID: 33808188 PMCID: PMC8067353 DOI: 10.3390/metabo11040205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 12/17/2022] Open
Abstract
The effects of climate change are becoming a real concern for the viticulture sector, with impacts on both grapevine physiology and the quality of the fresh berries and wine. Short-term mitigation strategies, like foliar kaolin application and smart irrigation regimes, have been implemented to overcome these problems. We previously showed that these strategies also influence the photosynthetic activity of the berries themselves, specifically in the exocarp and seed. In the present work, we assessed the modulating effects of both canopy-light microclimate, kaolin and irrigation treatments on the metabolic profiles of the exocarp and seed, as well as the potential role of berry photosynthesis herein. Berries from the white variety Alvarinho were collected at two contrasting light microclimate positions within the vine canopy (HL—high light and LL—low light) from both irrigated and kaolin-treated plants, and their respective controls, at three fruit developmental stages (green, véraison and mature). Untargeted liquid chromatography mass spectrometry (LCMS) profiling of semi-polar extracts followed by multivariate statistical analysis indicate that both the light microclimate and irrigation influenced the level of a series of phenolic compounds, depending on the ripening stage of the berries. Moreover, untargeted gas chromatography mass spectrometry (GCMS) profiling of polar extracts show that amino acid and sugar levels were influenced mainly by the interaction of irrigation and kaolin treatments. The results reveal that both photosynthetically active berry tissues had a distinct metabolic profile in response to the local light microclimate, which suggests a specific role of photosynthesis in these tissues. A higher light intensity within the canopy mainly increased the supply of carbon precursors to the phenylpropanoid/flavonoid pathway, resulting in increased levels of phenolic compounds in the exocarp, while in seeds, light mostly influenced compounds related to carbon storage and seed development. In addition, our work provides new insights into the influence of abiotic stress mitigation strategies on the composition of exocarps and seeds, which are both important tissues for the quality of grape-derived products.
Collapse
Affiliation(s)
- Andreia Garrido
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- Correspondence: (A.G.); (A.C.)
| | - Jasper Engel
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University and Research (Wageningen-UR), P.O. Box 16, 6700 AA Wageningen, The Netherlands; (J.E.); (R.M.); (R.C.H.D.V.)
- Business Unit Biometris, Wageningen Plant Research, Wageningen University and Research (Wageningen-UR), P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Roland Mumm
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University and Research (Wageningen-UR), P.O. Box 16, 6700 AA Wageningen, The Netherlands; (J.E.); (R.M.); (R.C.H.D.V.)
| | - Artur Conde
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana Cunha
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Correspondence: (A.G.); (A.C.)
| | - Ric C. H. De Vos
- Business Unit Bioscience, Wageningen Plant Research, Wageningen University and Research (Wageningen-UR), P.O. Box 16, 6700 AA Wageningen, The Netherlands; (J.E.); (R.M.); (R.C.H.D.V.)
| |
Collapse
|
7
|
Andargie M, Vinas M, Rathgeb A, Möller E, Karlovsky P. Lignans of Sesame ( Sesamum indicum L.): A Comprehensive Review. Molecules 2021; 26:883. [PMID: 33562414 PMCID: PMC7914952 DOI: 10.3390/molecules26040883] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Major lignans of sesame sesamin and sesamolin are benzodioxol--substituted furofurans. Sesamol, sesaminol, its epimers, and episesamin are transformation products found in processed products. Synthetic routes to all lignans are known but only sesamol is synthesized industrially. Biosynthesis of furofuran lignans begins with the dimerization of coniferyl alcohol, followed by the formation of dioxoles, oxidation, and glycosylation. Most genes of the lignan pathway in sesame have been identified but the inheritance of lignan content is poorly understood. Health-promoting properties make lignans attractive components of functional food. Lignans enhance the efficiency of insecticides and possess antifeedant activity, but their biological function in plants remains hypothetical. In this work, extensive literature including historical texts is reviewed, controversial issues are critically examined, and errors perpetuated in literature are corrected. The following aspects are covered: chemical properties and transformations of lignans; analysis, purification, and total synthesis; occurrence in Seseamum indicum and related plants; biosynthesis and genetics; biological activities; health-promoting properties; and biological functions. Finally, the improvement of lignan content in sesame seeds by breeding and biotechnology and the potential of hairy roots for manufacturing lignans in vitro are outlined.
Collapse
Affiliation(s)
- Mebeaselassie Andargie
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| | - Maria Vinas
- Centro para Investigaciones en Granos y Semillas (CIGRAS), University of Costa Rica, 2060 San Jose, Costa Rica;
| | - Anna Rathgeb
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| | - Evelyn Möller
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37073 Goettingen, Germany; (A.R.); (E.M.)
| |
Collapse
|
8
|
Küstner L, Fürtauer L, Weckwerth W, Nägele T, Heyer AG. Subcellular dynamics of proteins and metabolites under abiotic stress reveal deferred response of the Arabidopsis thaliana hexokinase-1 mutant gin2-1 to high light. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:456-472. [PMID: 31386774 DOI: 10.1111/tpj.14491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/22/2019] [Accepted: 07/29/2019] [Indexed: 05/13/2023]
Abstract
Stress responses in plants imply spatio-temporal changes in enzymes and metabolites, including subcellular compartment-specific re-allocation processes triggered by sudden changes in environmental parameters. To investigate interactions of primary metabolism with abiotic stress, the gin2-1 mutant, defective in the sugar sensor hexokinase 1 (HXK1) was compared with its wildtype Landsberg erecta (Ler) based on time resolved, compartment-specific metabolome and proteome data obtained over a full diurnal cycle. The high light sensitive gin2-1 mutant was substantially delayed in subcellular re-distribution of metabolites upon stress, and this correlated with a massive reduction in proteins belonging to the ATP producing electron transport chain under high light, while fewer changes occurred in the cold. In the wildtype, compounds specifically protecting individual compartments could be identified, e.g., maltose and raffinose in plastids, myo-inositol in mitochondria, but gin2-1 failed to recruit these substances to the respective compartments, or responded only slowly to high irradiance. No such delay was obtained in the cold. At the whole cell level, concentrations of the amino acids, glycine and serine, provided strong evidence for an important role of the photorespiratory pathway during stress exposure, and different subcellular allocation of serine may contribute to the slow growth of the gin2-1 mutant under high irradiance.
Collapse
Affiliation(s)
- Lisa Küstner
- Department of Plant Biotechnology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Lisa Fürtauer
- Department Biology I, Plant Evolutionary Cell Biology, Ludwig-Maximilians-University Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Thomas Nägele
- Department Biology I, Plant Evolutionary Cell Biology, Ludwig-Maximilians-University Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Arnd G Heyer
- Department of Plant Biotechnology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| |
Collapse
|
9
|
Small-Scale Bioreactor for Sterile Hydroponics and Hairy Roots: Metabolic Diversity and Salicylic Acid Exudation by Hairy Roots of Hyoscyamus niger. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9153044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The volume and complexity of commercial bioreactors for sterile hydroponics and hairy roots are too large for comparative analysis of many cultures. Here a small-scale bioreactor fabricated from standard glass materials and suitable for both airlift and bubble aeration mode is described. The performance of the bioreactor was tested by growing oilseed rape (Brassica napus L.) and rose plants (Rosa canina L.) in sterile hydroponics and by cultivating hairy roots of henbane (Hyoscyamus niger L.) and sesame (Hyoscyamus niger L.). Plants grown in hydroponics for up to six weeks did not show chloroses or necroses. Hairy roots grew faster or comparably fast in bioreactors as compared to shaking flasks. Root exudates of roses and exudates of hairy roots of henbane were subjected to targeted and nontargeted analysis by HPLC coupled with optical and mass spectrometric detectors. The diversity and concentration of hairy root exudates were higher in bioreactors than in shaking flasks. The composition of hairy root exudates of three accessions of H. niger did not match the genetic relatedness among the accessions. Hairy roots of Hyoscyamus niger exuded salicylic acid in amounts varying among plant accessions and between bioreactors and shaking flask cultures.
Collapse
|
10
|
Ponnaiah M, Gilard F, Gakière B, El-Maarouf-Bouteau H, Bailly C. Regulatory actors and alternative routes for Arabidopsis seed germination are revealed using a pathway-based analysis of transcriptomic datasets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:163-175. [PMID: 30868664 DOI: 10.1111/tpj.14311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/07/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Regulation of seed germination by dormancy relies on a complex network of transcriptional and post-transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High-throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway-based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non-dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.
Collapse
Affiliation(s)
- Maharajah Ponnaiah
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, F-75005, Paris, France
| | - Françoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université d'Evry, Université Paris-Diderot, Université Paris-Sud, Sorbonne Paris-Cité, Saclay Plant Sciences, Orsay, France
| | - Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université d'Evry, Université Paris-Diderot, Université Paris-Sud, Sorbonne Paris-Cité, Saclay Plant Sciences, Orsay, France
| | | | - Christophe Bailly
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, F-75005, Paris, France
| |
Collapse
|
11
|
Huang Q, Hu D, Wang X, Chen Y, Wu Y, Pan L, Li H, Zhang J, Deng F, Guo X, Shen H. The modification of indoor PM 2.5 exposure to chronic obstructive pulmonary disease in Chinese elderly people: A meet-in-metabolite analysis. ENVIRONMENT INTERNATIONAL 2018; 121:1243-1252. [PMID: 30389378 DOI: 10.1016/j.envint.2018.10.046] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Exposure to airborne fine particulate matter (PM2.5) has been associated with a variety of adverse health outcomes including chronic obstructive pulmonary disease (COPD). However, the linkages between PM2.5 exposure, PM2.5-related biomarkers, COPD-related biomarkers and COPD remain poorly elucidated. OBJECTIVES To investigate the linkages between PM2.5 exposure and COPD outcome by using the meet-in-middle strategy based on urinary metabolic biomarkers. METHODS A cross-sectional study was designed to illustrate the mentioned quadripartite linkages. Indoor PM2.5 and its element components were assessed in 41 Chinese elderly participants including COPD patients and their healthy spouses. Metabolic biomarkers involved in PM2.5 exposure and COPD were identified by using urinary metabolomics. The associations between PM2.5- and COPD-related biomarkers were investigated by statistics and metabolic pathway analysis. RESULTS Seven metabolites were screened and identified with significant correlations to PM2.5 exposure, which were majorly involved in purine and amino acid metabolism as well as glycolysis. Ten COPD-related metabolic biomarkers were identified, which suggested that amino acid metabolism, lipid and fatty acid metabolism, and glucose metabolism were disturbed in the patients. Also, PM2.5 and its many elemental components were significantly associated with COPD-related biomarkers. We observed that the two kinds of biomarkers (PM2.5- and COPD-related) integrated in a locally connected network and the alterations of these metabolic biomarkers can biologically link PM2.5 exposure to COPD outcome. CONCLUSIONS Our study indicated the modification of PM2.5 to COPD via both modes of action of lowering participants' antioxidation capacity and decreasing their lung energy generation; this information would be valuable for the prevention strategy of COPD.
Collapse
Affiliation(s)
- Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dayu Hu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Xiaofei Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yahong Chen
- Respiratory Department, Peking University Third Hospital, No. 49 North Garden Road, Beijing 100191, China
| | - Yan Wu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Pan
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Hongyu Li
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Jie Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, No. 38 Xueyuan Road, Beijing 100191, China.
| | - Xinbiao Guo
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Heqing Shen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| |
Collapse
|
12
|
Wu Y, Zhang J, Peng S, Wang X, Luo L, Liu L, Huang Q, Tian M, Zhang X, Shen H. Multiple elements related to metabolic markers in the context of gestational diabetes mellitus in meconium. ENVIRONMENT INTERNATIONAL 2018; 121:1227-1234. [PMID: 30385065 DOI: 10.1016/j.envint.2018.10.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/03/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) is a typical fetus development niches dysfunction and many toxic/nutrient elements have been associated with its onset and progression. However, the classic epidemiologic approach is regarded as "black-box epidemiology" and fails to elucidate these elements' biological roles on the damaged fetus developmental microenvironment. OBJECTIVE We aimed to characterize the associations between meconium of multiple elements with GDM for illustrating their interruption effects on in-uterus microenvironment. METHODS In this case-control study (n = 137 cases; n = 197 controls), the participants were nested from a cross-sectional retrospection of 1359 recruitments in Xiamen, China. Twenty-one meconium elements were characterized using inductively coupled plasma mass spectrometry (ICP-MS) or inductively coupled plasma optical emission spectrometry (ICP-OES). For shifting the present paradigm from a black-box approach to a molecular approach, GDM-related metabolic markers were identified in our previous metabolome report. Based on the meet-in-middle strategy, the associations among the elements, metabolic markers and GDM incidence were assessed by using redundancy analysis and correlation-adjusted correlation; mediation analysis was further used to test the hypothesis that metabolic markers mediate the associations of the elements with GDM incidence. RESULTS Eight elements were related with the GDM occurrence in dose-dependent manners, which positively (Al, As, Ba, Cd, Hg, and Sn) or negatively (Ca and V) associated with GDM. Among them, As, Cd, Ba, and Ca significantly contributed to the variation of GDM-related metabolic markers. Additionally, the associations of Cd, Ba, Ca and As with GDM were mediated by the metabolic markers which majorly involved in the lipid metabolism and the Adenosine/l-Arginine/Nitric Oxide (ALANO) pathways. CONCLUSIONS The two-side mediations of meconium metabolic markers between the multiple elements and GDM occurrence indicated that maternal exposure to As, Ba, Cd, and Ca may be associated with the dysfunction of fetus development niche through disrupting lipid metabolism and ALANO pathways.
Collapse
Affiliation(s)
- Yan Wu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Siyuan Peng
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xiaofei Wang
- Department of Chemistry and The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Lianzhong Luo
- Department of Pharmacy, Xiamen Medical College, Xiamen, China
| | - Liangpo Liu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Qingyu Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Meiping Tian
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xueqin Zhang
- Xiamen Maternity and Child Health Care Hospital, Xiamen, China.
| | - Heqing Shen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, China.
| |
Collapse
|
13
|
Lamari N, Zhendre V, Urrutia M, Bernillon S, Maucourt M, Deborde C, Prodhomme D, Jacob D, Ballias P, Rolin D, Sellier H, Rabier D, Gibon Y, Giauffret C, Moing A. Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding. Metabolomics 2018; 14:132. [PMID: 30830438 PMCID: PMC6208756 DOI: 10.1007/s11306-018-1427-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/06/2018] [Indexed: 11/11/2022]
Abstract
INTRODUCTION In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context. OBJECTIVES Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass. METHODS Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping. RESULTS NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance. CONCLUSION After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.
Collapse
Affiliation(s)
- Nadia Lamari
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- 0000 0001 0768 2743grid.7886.1Present Address: Earth Institute, O’Brien Centre for Science, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Vanessa Zhendre
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Maria Urrutia
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- INRA, UR AgroImpact, Estrées-Mons, 80203 Péronne, France
- Present Address: Enza Zaden Centro de Investigacion S.L., 04710 Santa Maria del Aguila, Almería, Spain
| | - Stéphane Bernillon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Mickaël Maucourt
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Catherine Deborde
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Duyen Prodhomme
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Daniel Jacob
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Patricia Ballias
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Dominique Rolin
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | | | | | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | | | - Annick Moing
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| |
Collapse
|
14
|
Pais AL, Li X, (Jenny) Xiang Q. Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida L. Ecol Evol 2018; 8:5619-5636. [PMID: 29938079 PMCID: PMC6010843 DOI: 10.1002/ece3.4090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
Understanding intraspecific relationships between genetic and functional diversity is a major goal in the field of evolutionary biology and is important for conserving biodiversity. Linking intraspecific molecular patterns of plants to ecological pressures and trait variation remains difficult due to environment-driven plasticity. Next-generation sequencing, untargeted liquid chromatography-mass spectrometry (LC-MS) profiling, and interdisciplinary approaches integrating population genomics, metabolomics, and community ecology permit novel strategies to tackle this problem. We analyzed six natural populations of the disease-threatened Cornus florida L. from distinct ecological regions using genotype-by-sequencing markers and LC-MS-based untargeted metabolite profiling. We tested the hypothesis that higher genetic diversity in C. florida yielded higher chemical diversity and less disease susceptibility (screening hypothesis), and we also determined whether genetically similar subpopulations were similar in chemical composition. Most importantly, we identified metabolites that were associated with candidate loci or were predictive biomarkers of healthy or diseased plants after controlling for environment. Subpopulation clustering patterns based on genetic or chemical distances were largely congruent. While differences in genetic diversity were small among subpopulations, we did observe notable similarities in patterns between subpopulation averages of rarefied-allelic and chemical richness. More specifically, we found that the most abundant compound of a correlated group of putative terpenoid glycosides and derivatives was correlated with tree health when considering chemodiversity. Random forest biomarker and genomewide association tests suggested that this putative iridoid glucoside and other closely associated chemical features were correlated to SNPs under selection.
Collapse
Affiliation(s)
- Andrew L. Pais
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNorth Carolina
| | - Xu Li
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNorth Carolina
- Plants for Human Health InstituteNorth Carolina State UniversityKannapolisNorth Carolina
| | - Qiu‐Yun (Jenny) Xiang
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNorth Carolina
| |
Collapse
|
15
|
Mokochinski JB, Mazzafera P, Sawaya ACHF, Mumm R, de Vos RCH, Hall RD. Metabolic responses of Eucalyptus species to different temperature regimes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:397-411. [PMID: 29247597 PMCID: PMC6220972 DOI: 10.1111/jipb.12626] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/14/2017] [Indexed: 05/08/2023]
Abstract
Species and hybrids of Eucalyptus are the world's most widely planted hardwood trees. They are cultivated across a wide range of latitudes and therefore environmental conditions. In this context, comprehensive metabolomics approaches have been used to assess how different temperature regimes may affect the metabolism of three species of Eucalyptus, E. dunnii, E. grandis and E. pellita. Young plants were grown for 53 d in the greenhouse and then transferred to growth chambers at 10°C, 20°C or 30°C for another 7 d. In all three species the leaf chlorophyll content was positively correlated to temperature, and in E. pellita the highest temperature also resulted in a significant increase in stem biomass. Comprehensive metabolomics was performed using untargeted gas chromatography mass spectrometry (GC-MS) and liquid chromatography (LC)-MS. This approach enabled the comparison of the relative abundance of 88 polar primary metabolites from GC-MS and 625 semi-polar secondary metabolites from LC-MS. Using principal components analysis, a major effect of temperature was observed in each species which was larger than that resulting from the genetic background. Compounds mostly affected by temperature treatment were subsequently selected using partial least squares discriminant analysis and were further identified. These putative annotations indicated that soluble sugars and several polyphenols, including tannins, triterpenes and alkaloids were mostly influenced.
Collapse
Affiliation(s)
- Joao Benhur Mokochinski
- Department of Plant Biology, Institute of BiologyState University of Campinas, UNICAMPCampinas 13083‐862Brazil
- Bioscience, Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of BiologyState University of Campinas, UNICAMPCampinas 13083‐862Brazil
| | - Alexandra Christine Helena Frankland Sawaya
- Department of Plant Biology, Institute of BiologyState University of Campinas, UNICAMPCampinas 13083‐862Brazil
- Faculty of Pharmaceutical ScienceState University of Campinas, UNICAMPCampinas 13083‐862Brazil
| | - Roland Mumm
- Bioscience, Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
| | | | - Robert David Hall
- Bioscience, Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
- Laboratory of Plant PhysiologyWageningen University and ResearchWageningenThe Netherlands
| |
Collapse
|
16
|
Hussain RMF, Kim HK, Khurshid M, Akhtar MT, Linthorst HJM. Overexpression of AtWRKY50 is correlated with enhanced production of sinapic derivatives in Arabidopsis. Metabolomics 2018; 14:25. [PMID: 30830336 DOI: 10.1007/s11306-018-1317-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 01/03/2018] [Indexed: 12/22/2022]
Abstract
INTRODUCTION WRKY proteins belong to a plant-specific class of transcription factors. Seventy-four WKRY genes have been identified in Arabidopsis and many WRKY proteins are known to be involved in responses to stress, especially to biotic stress. They may act either as transcriptional activators or as repressors of genes that play roles in the stress response. A number of studies have proposed the connection of Arabidopsis WRKY transcription factors in induced pathogenesis-related (PR) gene expression, although no direct evidence has been presented for specific WRKY-PR promoter interactions. OBJECTIVE We previously identified AtWRKY50 as a transcriptional activator of SAR gene PR1. Although PR1 accumulates to high levels in plants after attack by pathogens, its function is still elusive. Here we investigated the effects of overexpression of several WRKY proteins, including AtWRKY50, on the metabolome of Arabidopsis thaliana. METHODS The influence of overexpression of WRKY proteins on the metabolites of Arabidopsis was investigated by using an NMR spectroscopy-based metabolomic approach. The 1H NMR data was analysed using the multivariate data analysis methods, such as principal component analysis, hierarchical cluster analysis and partial least square-discriminant analysis. RESULTS The results showed that the metabolome of transgenic Arabidopsis seedlings overexpressing AtWRKY50 was different from wild type Arabidopsis and transgenic Arabidopsis overexpressing other WRKY genes. Amongst other metabolites, sinapic acid and 1-O-sinapoyl-β-D-glucose especially appeared to be the most prominent discriminating metabolites, accumulating to levels 2 to 3 times higher in the AtWRKY50 overexpressor lines. CONCLUSION Our results indicate a possible involvement of AtWRKY50 in secondary metabolite production in Arabidopsis, in particular of hydroxycinnamates such as sinapic acid and 1-O-sinapoyl-β-D-glucose.
Collapse
Affiliation(s)
- Rana M F Hussain
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Hye K Kim
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Muhammad Khurshid
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Institute of Biochemistry and Biotechnology, University of the Punjab, Quaid-e-Azam campus, P.O Box 54590, Lahore, Pakistan
| | - Muhammad T Akhtar
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Huub J M Linthorst
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| |
Collapse
|
17
|
Ahuja I, de Vos RCH, Rohloff J, Stoopen GM, Halle KK, Ahmad SJN, Hoang L, Hall RD, Bones AM. Arabidopsis myrosinases link the glucosinolate-myrosinase system and the cuticle. Sci Rep 2016; 6:38990. [PMID: 27976683 PMCID: PMC5157024 DOI: 10.1038/srep38990] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/16/2016] [Indexed: 11/23/2022] Open
Abstract
Both physical barriers and reactive phytochemicals represent two important components of a plant's defence system against environmental stress. However, these two defence systems have generally been studied independently. Here, we have taken an exclusive opportunity to investigate the connection between a chemical-based plant defence system, represented by the glucosinolate-myrosinase system, and a physical barrier, represented by the cuticle, using Arabidopsis myrosinase (thioglucosidase; TGG) mutants. The tgg1, single and tgg1 tgg2 double mutants showed morphological changes compared to wild-type plants visible as changes in pavement cells, stomatal cells and the ultrastructure of the cuticle. Extensive metabolite analyses of leaves from tgg mutants and wild-type Arabidopsis plants showed altered levels of cuticular fatty acids, fatty acid phytyl esters, glucosinolates, and indole compounds in tgg single and double mutants as compared to wild-type plants. These results point to a close and novel association between chemical defence systems and physical defence barriers.
Collapse
Affiliation(s)
- Ishita Ahuja
- Department of Biology, Norwegian University of Science and Technology (NTNU), Realfagbygget, NO-7491 Trondheim, Norway
- Plant Research International, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ric C. H. de Vos
- Plant Research International, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Jens Rohloff
- Department of Biology, Norwegian University of Science and Technology (NTNU), Realfagbygget, NO-7491 Trondheim, Norway
| | - Geert M. Stoopen
- Plant Research International, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- RIKILT, Wageningen UR, Akkermaalsbos 2, 6708 WB Wageningen, The Netherlands
| | - Kari K. Halle
- Department of Mathematical Sciences, NTNU, Trondheim, Norway
| | | | - Linh Hoang
- Cellular and Molecular Imaging Core Facility (CMIC), Laboratory for Electron Microscopy, NTNU, Trondheim, Norway
| | - Robert D. Hall
- Plant Research International, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Atle M. Bones
- Department of Biology, Norwegian University of Science and Technology (NTNU), Realfagbygget, NO-7491 Trondheim, Norway
| |
Collapse
|
18
|
Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data. Sci Rep 2016; 6:29033. [PMID: 27363486 PMCID: PMC4929559 DOI: 10.1038/srep29033] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/14/2016] [Indexed: 12/22/2022] Open
Abstract
Many metabolomics studies focus on aboveground parts of the plant, while metabolism within roots and the chemical composition of the rhizosphere, as influenced by exudation, are not deeply investigated. In this study, we analysed exudate metabolic patterns of Arabidopsis thaliana and their variation in genetically diverse accessions. For this project, we used the 19 parental accessions of the Arabidopsis MAGIC collection. Plants were grown in a hydroponic system, their exudates were harvested before bolting and subjected to UPLC/ESI-QTOF-MS analysis. Metabolite profiles were analysed together with the genome sequence information. Our study uncovered distinct metabolite profiles for root exudates of the 19 accessions. Hierarchical clustering revealed similarities in the exudate metabolite profiles, which were partly reflected by the genetic distances. An association of metabolite absence with nonsense mutations was detected for the biosynthetic pathways of an indolic glucosinolate hydrolysis product, a hydroxycinnamic acid amine and a flavonoid triglycoside. Consequently, a direct link between metabolic phenotype and genotype was detected without using segregating populations. Moreover, genomics can help to identify biosynthetic enzymes in metabolomics experiments. Our study elucidates the chemical composition of the rhizosphere and its natural variation in A. thaliana, which is important for the attraction and shaping of microbial communities.
Collapse
|
19
|
Riach AC, Perera MVL, Florance HV, Penfield SD, Hill JK. Analysis of plant leaf metabolites reveals no common response to insect herbivory by Pieris rapae in three related host-plant species. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2547-56. [PMID: 25711707 PMCID: PMC4986865 DOI: 10.1093/jxb/erv045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Studying the biochemical responses of different plant species to insect herbivory may help improve our understanding of the evolution of defensive metabolites found in host plants and their role in plant-herbivore interactions. Untargeted metabolic fingerprints measured as individual mass features were used to compare metabolite reactions in three Brassicales host-plant species (Cleome spinosa, Brassica oleracea, and Lunaria annua) to larval herbivore attack (Pieris rapae; Lepidoptera). Principal component analyses of metabolic fingerprints were able to distinguish among the three plant species and between uneaten control plants and plants that had been eaten. A large number of mass features (1186, 13% of mass features measured in control plants) were common to the three plant species. However, there were few similarities in the mass features that were induced (i.e. changed in abundance) following herbivory. Of the 87 and 68 induced mass features in B. oleracea and C. spinosa, respectively, there were only three that were induced in both plant species. By contrast, L. annua only had one mass feature induced by herbivory, and this was not induced in the other two plant species. The growth of the P. rapae larvae was poorer on the host plant L. annua than on B. oleracea and C. spinosa. The absence of common metabolites among the plants meant these induced responses could not be related to the performance of the herbivore. Thus, the response to herbivory by the same herbivore in these three host plants has evolved to be idiosyncratic in terms of the specific metabolites induced.
Collapse
Affiliation(s)
- A C Riach
- Department of Biology, University of York, York YO10 5DD, UK
| | - M V L Perera
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - H V Florance
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - S D Penfield
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - J K Hill
- Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
20
|
Panighel A, De Rosso M, Dalla Vedova A, Flamini R. Putative identification of new p-coumaroyl glycoside flavonoids in grape by ultra-high performance liquid chromatography/high-resolution mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:357-366. [PMID: 26406348 DOI: 10.1002/rcm.7115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 06/05/2023]
Abstract
RATIONALE Grape polyphenols are antioxidant compounds, markers in vine chemotaxonomy, and involved in color stabilization of red wines. Sugar acylation usually confers higher stability on glycoside derivatives and this effect is enhanced by an aromatic substituent such as p-coumaric acid. Until now, only p-coumaroyl anthocyanins have been found in grape. METHODS A method of 'suspect screening analysis' by ultra-high-performance liquid chromatography/high-resolution mass spectrometry (UHPLC/QTOFMS) has recently been developed to study grape metabolomics. In the present study, this approach was used to identify new polyphenols in grape by accurate mass measurement, MS/MS fragmentation, and study of correlations between fragments observed and putative structures. RESULTS Three putative p-coumaroyl flavonoids were identified in Raboso Piave grape extract: a dihydrokaempferide-3-O-p-coumaroylhexoside-like flavanone, isorhamnetin-3-O-p-coumaroylglucoside, and a chrysoeriol-p-coumaroylhexoside-like flavone. Accurate MS provided structural characterization of functional groups, and literature data indicates their probable position in the molecule. A fragmentation scheme is proposed for each compound. CONCLUSIONS Compounds were identified by overlapping various analytical methods according to recommendations in the MS-based metabolomics literature. Stereochemistry and the definitive position of substituents in the molecule can only be confirmed by isolation and characterization or synthesis of each compound. These findings suggest addressing research of acylated polyphenol glycosides to other grape varieties.
Collapse
Affiliation(s)
- Annarita Panighel
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| | - Mirko De Rosso
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| | - Antonio Dalla Vedova
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| | - Riccardo Flamini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano (TV), Italy
| |
Collapse
|
21
|
Sotelo-Silveira M, Chauvin AL, Marsch-Martínez N, Winkler R, de Folter S. Metabolic fingerprinting of Arabidopsis thaliana accessions. FRONTIERS IN PLANT SCIENCE 2015; 6:365. [PMID: 26074932 PMCID: PMC4444734 DOI: 10.3389/fpls.2015.00365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/08/2015] [Indexed: 05/02/2023]
Abstract
In the post-genomic era much effort has been put on the discovery of gene function using functional genomics. Despite the advances achieved by these technologies in the understanding of gene function at the genomic and proteomic level, there is still a big genotype-phenotype gap. Metabolic profiling has been used to analyze organisms that have already been characterized genetically. However, there is a small number of studies comparing the metabolic profile of different tissues of distinct accessions. Here, we report the detection of over 14,000 and 17,000 features in inflorescences and leaves, respectively, in two widely used Arabidopsis thaliana accessions. A predictive Random Forest Model was developed, which was able to reliably classify tissue type and accession of samples based on LC-MS profile. Thereby we demonstrate that the morphological differences among A. thaliana accessions are reflected also as distinct metabolic phenotypes within leaves and inflorescences.
Collapse
Affiliation(s)
- Mariana Sotelo-Silveira
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)Irapuato, México
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la RepúblicaMontevideo, Uruguay
| | - Anne-Laure Chauvin
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)Irapuato, México
| | | | - Robert Winkler
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad IrapuatoIrapuato, Mexico
- *Correspondence: Robert Winkler, Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36821 Irapuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)Irapuato, México
- Stefan de Folter, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, Mexico
| |
Collapse
|
22
|
Flamini R, De Rosso M, Panighel A, Dalla Vedova A, De Marchi F, Bavaresco L. Profiling of grape monoterpene glycosides (aroma precursors) by ultra-high performance-liquid chromatography-high resolution mass spectrometry (UHPLC/QTOF). JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1214-22. [PMID: 25476938 DOI: 10.1002/jms.3441] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/25/2014] [Accepted: 07/11/2014] [Indexed: 05/22/2023]
Abstract
A 'suspect screening analysis' method for grape metabolomics by ultra-high performance-liquid chromatography (UHPLC) and high-resolution quadrupole-time of flight (QTOF) mass spectrometry was recently developed. This method was applied to study grape monoterpene glycosides, the main grape aroma precursors. Since standard compounds were not available, they were tentatively identified by overlapping various analytical approaches, in agreement with the indications recommended in mass spectrometry (MS)-based metabolomics. Accurate mass and isotopic pattern, MS/MS fragmentation, correlation between fragments observed and putative structures and between liquid chromatography coupled with mass spectrometry (LC/MS) and gas chromatography/mass spectrometry signals were studied. Seventeen monoterpene glycosides were identified without performing the hydrolytic artifacts commonly used to study these compounds which may affect sample profile. This is the first time that a detailed study of these aroma precursors has been carried out by direct LC/MS analysis.
Collapse
Affiliation(s)
- Riccardo Flamini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Viticoltura (CRA-VIT), Viale XXVIII aprile 26, 31015, Conegliano, TV, Italy
| | | | | | | | | | | |
Collapse
|
23
|
Quéro A, Jousse C, Lequart-Pillon M, Gontier E, Guillot X, Courtois B, Courtois J, Pau-Roblot C. Improved stability of TMS derivatives for the robust quantification of plant polar metabolites by gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 970:36-43. [PMID: 25237783 DOI: 10.1016/j.jchromb.2014.08.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022]
Abstract
Plant metabolite profiling is commonly carried out by GC-MS of methoximated trimethylsilyl (TMS) derivatives. This technique is robust and enables a library search for spectra produced by electron ionization. However, recent articles have described problems associated with the low stability of some TMS derivatives. This limits the use of GC-MS for metabolomic studies that need large sets of qualitative and quantitative analyses. The aim of this work is to determine the experimental conditions in which the stability of TMS derivatives could be improved. This would facilitate the analysis of the large-scale experimental designs needed in the metabolomics approach. For good repeatability, the sampling conditions and the storage temperature of samples during analysis were investigated. Multiple injections of one sample from one vial led to high variations while injection of one sample from different vials improved the analysis. However, before injection, some amino acid TMS derivatives were degraded during the storage of vials in the autosampler. Only 10% of the initial quantity of glutamine 3 TMS and glutamate 3 TMS and 66% of α-alanine 2 TMS was detected 48 h after derivatization. When stored at 4 °C until injection, all TMS derivatives remained stable for 12 h; at -20 °C, they remained stable for 72 h. From the integration of all these results, a detailed analytical procedure is thus proposed. It enables a robust quantification of polar metabolites, useful for further plant metabolomics studies using GC-MS.
Collapse
Affiliation(s)
- Anthony Quéro
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, IUT d'Amiens, Dept. GB, Avenue des Facultés, Le Bailly, 80025 Amiens Cedex, France
| | - Cyril Jousse
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens Cedex, France
| | - Michelle Lequart-Pillon
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens Cedex, France
| | - Eric Gontier
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens Cedex, France
| | - Xavier Guillot
- Laboulet Semences S.A., 1 rue Carnot, 80270 Airaines, France
| | - Bernard Courtois
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, IUT d'Amiens, Dept. GB, Avenue des Facultés, Le Bailly, 80025 Amiens Cedex, France
| | - Josiane Courtois
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, IUT d'Amiens, Dept. GB, Avenue des Facultés, Le Bailly, 80025 Amiens Cedex, France
| | - Corinne Pau-Roblot
- Unité de Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens Cedex, France.
| |
Collapse
|
24
|
Houshyani B, van der Krol AR, Bino RJ, Bouwmeester HJ. Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence. BMC PLANT BIOLOGY 2014; 14:170. [PMID: 24947327 PMCID: PMC4091741 DOI: 10.1186/1471-2229-14-170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/09/2014] [Indexed: 05/14/2023]
Abstract
BACKGROUND Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types. RESULTS In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis. CONCLUSION Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.
Collapse
Affiliation(s)
- Benyamin Houshyani
- Wageningen University, Plant Sciences Group, Laboratory of Plant Physiology, P.O. Box 658, Wageningen 6700 AR, The Netherlands
| | - Alexander R van der Krol
- Wageningen University, Plant Sciences Group, Laboratory of Plant Physiology, P.O. Box 658, Wageningen 6700 AR, The Netherlands
| | - Raoul J Bino
- Wageningen University, Plant Sciences Group, Laboratory of Plant Physiology, P.O. Box 658, Wageningen 6700 AR, The Netherlands
| | - Harro J Bouwmeester
- Wageningen University, Plant Sciences Group, Laboratory of Plant Physiology, P.O. Box 658, Wageningen 6700 AR, The Netherlands
| |
Collapse
|
25
|
Dynamic metabolic and transcriptional profiling of Rhodococcus sp. strain YYL during the degradation of tetrahydrofuran. Appl Environ Microbiol 2014; 80:2656-64. [PMID: 24532074 DOI: 10.1128/aem.04131-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Although tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD(+), and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through (1)H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms.
Collapse
|
26
|
Ikeda S, Abe T, Nakamura Y, Kibinge N, Hirai Morita A, Nakatani A, Ono N, Ikemura T, Nakamura K, Altaf-Ul-Amin M, Kanaya S. Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database. PLANT & CELL PHYSIOLOGY 2013; 54:711-727. [PMID: 23509110 DOI: 10.1093/pcp/pct041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.
Collapse
Affiliation(s)
- Shun Ikeda
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara, 630-0192 Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Afendi FM, Ono N, Nakamura Y, Nakamura K, Darusman LK, Kibinge N, Morita AH, Tanaka K, Horai H, Altaf-Ul-Amin M, Kanaya S. Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology. Comput Struct Biotechnol J 2013; 4:e201301010. [PMID: 24688691 PMCID: PMC3962233 DOI: 10.5936/csbj.201301010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/09/2013] [Accepted: 03/09/2013] [Indexed: 01/01/2023] Open
Abstract
Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study. Exploration using Biplot reveals many plants are rarely utilized while some plants are highly utilized toward specific efficacy. Furthermore, the ingredients of Jamu formulas are modeled using Partial Least Squares Discriminant Analysis (PLS-DA) in order to predict their efficacy. The plants used in each Jamu medicine served as the predictors, whereas the efficacy of each Jamu provided the responses. This model produces 71.6% correct classification in predicting efficacy. Permutation test then is used to determine plants that serve as main ingredients in Jamu formula by evaluating the significance of the PLS-DA coefficients. Next, in order to explain the role of plants that serve as main ingredients in Jamu medicines, information of pharmacological activity of the plants is added to the predictor block. Then N-PLS-DA model, multiway version of PLS-DA, is utilized to handle the three-dimensional array of the predictor block. The resulting N-PLS-DA model reveals that the effects of some pharmacological activities are specific for certain efficacy and the other activities are diverse toward many efficacies. Mathematical modeling introduced in the present study can be utilized in global analysis of big data targeting to reveal the underlying biology.
Collapse
Affiliation(s)
- Farit M Afendi
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan ; Department of Statistics, Bogor Agricultural University, Jln. Meranti, Kampus IPB Darmaga, Bogor 16680, Indonesia
| | - Naoaki Ono
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Yukiko Nakamura
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Kensuke Nakamura
- Maebashi Institute of technology, 450-1 Kamisadori, Maebashi-shi, Gunma, 371-0816 Japan
| | - Latifah K Darusman
- Biopharmaca Research Center, Bogor Agricultural University, Kampas IPB Taman Kencana, Jln. Taman Kencana No. 3 Bogor 16151, Indonesia
| | - Nelson Kibinge
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Aki Hirai Morita
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Ken Tanaka
- Department of Medicinal Resources, Institute of Natural Medicine, University of Toyama, 2630 Toyama, 930-0194, Japan
| | - Hisayuki Horai
- Department of Electronic and Computer Engineering, Ibaraki National College of Technology, 866 Nakane, Hitachinaka, Ibaraki 312-8508, Japan
| | - Md Altaf-Ul-Amin
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan
| |
Collapse
|
28
|
Tugizimana F, Piater L, Dubery I. Plant metabolomics: A new frontier in phytochemical analysis. S AFR J SCI 2013. [DOI: 10.1590/sajs.2013/20120005] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
29
|
Houshyani B, Assareh M, Busquets A, Ferrer A, Bouwmeester HJ, Kappers IF. Three-step pathway engineering results in more incidence rate and higher emission of nerolidol and improved attraction of Diadegma semiclausum. Metab Eng 2013; 15:88-97. [DOI: 10.1016/j.ymben.2012.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 10/02/2012] [Accepted: 10/09/2012] [Indexed: 01/20/2023]
|
30
|
Kos M, Houshyani B, Wietsma R, Kabouw P, Vet LEM, van Loon JJA, Dicke M. Effects of glucosinolates on a generalist and specialist leaf-chewing herbivore and an associated parasitoid. PHYTOCHEMISTRY 2012; 77:162-70. [PMID: 22281379 DOI: 10.1016/j.phytochem.2012.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/28/2011] [Accepted: 01/02/2012] [Indexed: 05/07/2023]
Abstract
Glucosinolates (GLS) are secondary plant metabolites that as a result of tissue damage, for example due to herbivory, are hydrolysed into toxic compounds that negatively affect generalist herbivores. Specialist herbivores have evolved specific adaptations to detoxify GLS or inhibit the formation of toxic hydrolytic products. Although rarely studied, GLS and their breakdown products may also affect parasitoids. The objectives were to test the effects of GLS in a multitrophic system consisting of the generalist herbivore Spodoptera exigua, the specialist herbivore Pieris rapae, and the endoparasitoid Hyposoter ebeninus. Three ecotypes of Arabidopsis thaliana that differ in their GLS composition and concentrations and one transformed line that constitutively produces higher concentrations of aliphatic GLS were used, the latter allowing a direct assessment of the effects of aliphatic GLS on insect performance. Feeding by the generalist S. exigua and the specialist P. rapae induced both higher aliphatic and indole GLS concentrations in the A. thaliana ecotypes, although induction was stronger for indole than aliphatic GLS. For both herbivores a negative correlation between performance and aliphatic GLS concentrations was observed. This suggests that the specialist, despite containing a nitrile-specifier protein (NSP) that diverts GLS degradation from toxic isothiocyanates to less toxic nitriles, cannot completely inhibit the formation of toxic GLS hydrolytic products, or that the costs of this mechanism are higher at higher GLS concentrations. Surprisingly, performance of the parasitoid was positively correlated with higher concentrations of aliphatic GLS in the plant, possibly caused by negative effects on host immune responses. Our study indicates that GLS can not only confer resistance against herbivores directly, but also indirectly by increasing the performance of the parasitoids of these herbivores.
Collapse
Affiliation(s)
- Martine Kos
- Laboratory of Entomology, Wageningen University, 6700 EH Wageningen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
31
|
Plischke A, Choi YH, Brakefield PM, Klinkhamer PGL, Bruinsma M. Metabolomic plasticity in GM and non-GM potato leaves in response to aphid herbivory and virus infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:1488-93. [PMID: 22243672 PMCID: PMC3279958 DOI: 10.1021/jf204864y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 01/13/2012] [Indexed: 05/19/2023]
Abstract
An important aspect of ecological safety of genetically modified (GM) plants is the evaluation of unintended effects on plant-insect interactions. These interactions are to a large extent influenced by the chemical composition of plants. This study uses NMR-based metabolomics to establish a baseline of chemical variation to which differences between a GM potato line and its parent cultivar are compared. The effects of leaf age, virus infection, and aphid herbivory on plant metabolomes were studied. The metabolome of the GM line differed from its parent only in young leaves of noninfected plants. This effect was small when compared to the baseline. Consistently, aphid performance on excised leaves was influenced by leaf age, while no difference in performance was found between GM and non-GM plants. The metabolomic baseline approach is concluded to be a useful tool in ecological safety assessment.
Collapse
Affiliation(s)
- Andreas Plischke
- Ecology and Phytochemistry, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | | | | | | | | |
Collapse
|
32
|
Kos M, Houshyani B, Achhami BB, Wietsma R, Gols R, Weldegergis BT, Kabouw P, Bouwmeester HJ, Vet LEM, Dicke M, van Loon JJA. Herbivore-mediated effects of glucosinolates on different natural enemies of a specialist aphid. J Chem Ecol 2012. [PMID: 22258357 DOI: 10.1007/s10886-012-0065-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The cabbage aphid Brevicoryne brassicae is a specialist herbivore that sequesters glucosinolates from its host plant as a defense against its predators. It is unknown to what extent parasitoids are affected by this sequestration. We investigated herbivore-mediated effects of glucosinolates on the parasitoid wasp Diaeretiella rapae and the predator Episyrphus balteatus. We reared B. brassicae on three ecotypes of Arabidopsis thaliana that differ in glucosinolate content and on one genetically transformed line with modified concentrations of aliphatic glucosinolates. We tested aphid performance and the performance and behavior of both natural enemies. We correlated this with phloem and aphid glucosinolate concentrations and emission of volatiles. Brevicoryne brassicae performance correlated positively with concentrations of both aliphatic and indole glucosinolates in the phloem. Aphids selectively sequestered glucosinolates. Glucosinolate concentration in B. brassicae correlated negatively with performance of the predator, but positively with performance of the parasitoid, possibly because the aphids with the highest glucosinolate concentrations had a higher body weight. Both natural enemies showed a positive performance-preference correlation. The predator preferred the ecotype with the lowest emission of volatile glucosinolate breakdown products in each test combination, whereas the parasitoid wasp preferred the A. thaliana ecotype with the highest emission of these volatiles. The study shows that there are differential herbivore-mediated effects of glucosinolates on a predator and a parasitoid of a specialist aphid that selectively sequesters glucosinolates from its host plant.
Collapse
Affiliation(s)
- Martine Kos
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Kos M, Houshyani B, Achhami BB, Wietsma R, Gols R, Weldegergis BT, Kabouw P, Bouwmeester HJ, Vet LEM, Dicke M, van Loon JJA. Herbivore-mediated effects of glucosinolates on different natural enemies of a specialist aphid. J Chem Ecol 2012; 38:100-15. [PMID: 22258357 PMCID: PMC3268984 DOI: 10.1007/s10886-012-0065-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/22/2011] [Accepted: 12/28/2011] [Indexed: 01/07/2023]
Abstract
The cabbage aphid Brevicoryne brassicae is a specialist herbivore that sequesters glucosinolates from its host plant as a defense against its predators. It is unknown to what extent parasitoids are affected by this sequestration. We investigated herbivore-mediated effects of glucosinolates on the parasitoid wasp Diaeretiella rapae and the predator Episyrphus balteatus. We reared B. brassicae on three ecotypes of Arabidopsis thaliana that differ in glucosinolate content and on one genetically transformed line with modified concentrations of aliphatic glucosinolates. We tested aphid performance and the performance and behavior of both natural enemies. We correlated this with phloem and aphid glucosinolate concentrations and emission of volatiles. Brevicoryne brassicae performance correlated positively with concentrations of both aliphatic and indole glucosinolates in the phloem. Aphids selectively sequestered glucosinolates. Glucosinolate concentration in B. brassicae correlated negatively with performance of the predator, but positively with performance of the parasitoid, possibly because the aphids with the highest glucosinolate concentrations had a higher body weight. Both natural enemies showed a positive performance-preference correlation. The predator preferred the ecotype with the lowest emission of volatile glucosinolate breakdown products in each test combination, whereas the parasitoid wasp preferred the A. thaliana ecotype with the highest emission of these volatiles. The study shows that there are differential herbivore-mediated effects of glucosinolates on a predator and a parasitoid of a specialist aphid that selectively sequesters glucosinolates from its host plant.
Collapse
Affiliation(s)
- Martine Kos
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|