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Maciag T, Kozieł E, Otulak-Kozieł K, Jafra S, Czajkowski R. Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia. Int J Mol Sci 2024; 25:3757. [PMID: 38612570 PMCID: PMC11011919 DOI: 10.3390/ijms25073757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.
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Affiliation(s)
- Tomasz Maciag
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
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Díaz-Galiano FJ, Murcia-Morales M, Fernández-Alba AR. From sound check to encore: A journey through high-resolution mass spectrometry-based food analyses and metabolomics. Compr Rev Food Sci Food Saf 2024; 23:e13325. [PMID: 38532695 DOI: 10.1111/1541-4337.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]
Abstract
This manuscript presents a comprehensive review of high-resolution mass spectrometry in the field of food analysis and metabolomics. We have followed the historical evolution of metabolomics, its associated techniques and technologies, and its increasing role in food science and research. The review provides a critical comparison and synthesis of tentative identification guidelines proposed for over 15 years, offering a condensed resource for researchers in the field. We have also examined a wide range of recent metabolomics studies, showcasing various methodologies and highlighting key findings as a testimony of the versatility of the field and the possibilities it offers. In doing so, we have also carefully provided a compilation of the software tools that may be employed in this type of studies. The manuscript also explores the prospects of high-resolution mass spectrometry and metabolomics in food science. By covering the history, guidelines, applications, and tools of metabolomics, this review attempts to become a comprehensive guide for researchers in a rapidly evolving field.
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Affiliation(s)
- Francisco José Díaz-Galiano
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3), University of Almería, Almería, Spain
| | - María Murcia-Morales
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3), University of Almería, Almería, Spain
| | - Amadeo Rodríguez Fernández-Alba
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3), University of Almería, Almería, Spain
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3
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Drapal M, Enfissi EMA, Almeida J, Rapacz E, Nogueira M, Fraser PD. The potential of metabolomics in assessing global compositional changes resulting from the application of CRISPR/Cas9 technologies. Transgenic Res 2023; 32:265-278. [PMID: 37166587 DOI: 10.1007/s11248-023-00347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
Exhaustive analysis of genetically modified crops over multiple decades has increased societal confidence in the technology. New Plant Breeding Techniques are now emerging with improved precision and the ability to generate products containing no foreign DNA and mimic/replicate conventionally bred varieties. In the present study, metabolomic analysis was used to compare (i) tobacco genotypes with and without the CRISPR associated protein 9 (Cas9), (ii) tobacco lines with the edited and non-edited DE-ETIOLATED-1 gene without phenotype and (iii) leaf and fruit tissue from stable non-edited tomato progeny with and without the Cas9. In all cases, multivariate analysis based on the difference test using LC-HRMS/MS and GC-MS data indicated no significant difference in their metabolomes. The variations in metabolome composition that were evident could be associated with the processes of tissue culture regeneration and/or transformation (e.g. interaction with Agrobacterium). Metabolites responsible for the variance included quantitative changes of abundant, well characterised metabolites such as phenolics (e.g. chlorogenic acid) and several common sugars such as fructose. This study provides fundamental data on the characterisation of gene edited crops, that are important for the evaluation of the technology and its assessment. The approach also suggests that metabolomics could contribute to routine product-based analysis of crops/foods generated from New Plant Breeding approaches.
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Affiliation(s)
- Margit Drapal
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Eugenia M A Enfissi
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Elzbieta Rapacz
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Marilise Nogueira
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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Carrillo L, Baroja-Fernández E, Renau-Morata B, Muñoz FJ, Canales J, Ciordia S, Yang L, Sánchez-López ÁM, Nebauer SG, Ceballos MG, Vicente-Carbajosa J, Molina RV, Pozueta-Romero J, Medina J. Ectopic expression of the AtCDF1 transcription factor in potato enhances tuber starch and amino acid contents and yield under open field conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1010669. [PMID: 36937996 PMCID: PMC10014720 DOI: 10.3389/fpls.2023.1010669] [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: 08/03/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cycling Dof transcription factors (CDFs) have been involved in different aspects of plant growth and development. In Arabidopsis and tomato, one member of this family (CDF1) has recently been associated with the regulation of primary metabolism and abiotic stress responses, but their roles in crop production under open field conditions remain unknown. METHODS In this study, we compared the growth, and tuber yield and composition of plants ectopically expressing the CDF1 gene from Arabidopsis under the control of the 35S promoter with wild-type (WT) potato plants cultured in growth chamber and open field conditions. RESULTS In growth chambers, the 35S::AtCDF1 plants showed a greater tuber yield than the WT by increasing the biomass partition for tuber development. Under field conditions, the ectopic expression of CDF1 also promoted the sink strength of the tubers, since 35S::AtCDF1 plants exhibited significant increases in tuber size and weight resulting in higher tuber yield. A metabolomic analysis revealed that tubers of 35S::AtCDF1 plants cultured under open field conditions accumulated higher levels of glucose, starch and amino acids than WT tubers. A comparative proteomic analysis of tubers of 35S::AtCDF1 and WT plants cultured under open field conditions revealed that these changes can be accounted for changes in the expression of proteins involved in energy production and different aspects of C and N metabolism. DISCUSSION The results from this study advance our collective understanding of the role of CDFs and are of great interest for the purposes of improving the yield and breeding of crop plants.
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Affiliation(s)
- Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Mutiloabeti, Nafarroa, Spain
| | - Begoña Renau-Morata
- Departamento de Biología Vegetal, Universitat de València. Vicent Andrés Estellés, Burjassot, Spain
| | - Francisco J. Muñoz
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Mutiloabeti, Nafarroa, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sergio Ciordia
- Unidad Proteomica (CNB), Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Lu Yang
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | | | - Sergio G. Nebauer
- Departamento de Producción Vegetal, Universitat Politècnica de València., València, Spain
| | - Mar G. Ceballos
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | - Rosa V. Molina
- Departamento de Producción Vegetal, Universitat Politècnica de València., València, Spain
| | - Javier Pozueta-Romero
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), CSIC-UMA, Málaga, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
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Gluten proteins: Enzymatic modification, functional and therapeutic properties. J Proteomics 2022; 251:104395. [PMID: 34673267 DOI: 10.1016/j.jprot.2021.104395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/13/2021] [Accepted: 09/27/2021] [Indexed: 01/28/2023]
Abstract
Glutens are potential proteins with multifunctional therapeutic effects. Their covalence network structures with and without protease inhibitors are expected to enhance or to serve further properties and further technological points such as increased bioactive surfaces, gelatinization, gelation and pasting properties. The depletion of the allergic peptide sequences of gluten proteins comprising sometimes protease inhibitors are valid via the enzymatic ingestion using proteolytic enzymes that might enhance these functional and technological processes by producing active peptides having osmoregulation and regular glass transitions, surface activity for coating and encapsulation properties. In addition to further therapeutic functions such as immunoregulatory, antithrombin and opioidal activities, particularly in eradicating most of the free radicals, suppressing diabetes Mellitus II complications and inhibiting angiotensin converting enzyme cardiovascular growth diseases.
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Li D, Gaquerel E. Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:867-891. [PMID: 33781077 DOI: 10.1146/annurev-arplant-071720-114836] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.
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Affiliation(s)
- Dapeng Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 67084 Strasbourg, France;
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A Comprehensive Targeted Metabolomics Assay for Crop Plant Sample Analysis. Metabolites 2021; 11:metabo11050303. [PMID: 34064699 PMCID: PMC8151637 DOI: 10.3390/metabo11050303] [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: 04/14/2021] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 02/01/2023] Open
Abstract
Metabolomics plays an important role in various fields from health to agriculture. However, the comprehensive quantitative metabolomic analysis of plants and plant metabolites has not been widely performed. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based plant metabolomics offers the sensitivity and breadth of coverage for both phenotyping and disease diagnosis of plants. Here, we report a high-coverage and quantitative MS-based assay for plant metabolite analysis. The assay detects and quantifies 206 primary and secondary plant metabolites, including many key plant hormones. In total, it measures 28 amino acids and derivatives, 27 organic acids, 20 biogenic amines and derivatives, 40 acylcarnitines, 90 phospholipids and C-6 sugars. All the analysis methods in this assay are based on LC-MS/MS techniques using both positive and negative-mode multiple reaction monitoring (MRM). The recovery rates of spiked plant samples at three different concentration levels (low, medium and high) ranged from 80% to 120%, with satisfactory precision values of less than 20%. This targeted plant metabolomic assay has been successfully applied to the analysis of large numbers of pine and spruce needle samples, canola root samples, as well as cannabis samples. Moreover, the assay was specifically developed in a 96-well plate format, which enables automated, high-throughput sample analysis. This assay has already been used to analyze over 1500 crop plant samples in less than two months.
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Enfissi EMA, Drapal M, Perez-Fons L, Nogueira M, Berry HM, Almeida J, Fraser PD. New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153378. [PMID: 33631493 DOI: 10.1016/j.jplph.2021.153378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 05/21/2023]
Abstract
Over the previous decades, biotechnological innovations have led to improved agricultural productivity, more nutritious foods and lower chemical usage. Both in western societies and Low Medium Income Countries (LMICs). However, the projected increases in the global population, means the production of nutritious food stuffs must increase dramatically. Building on existing genetic modification technologies a series of New Plant Breeding Technologies (NPBT) has recently emerged. These approaches include, Agro-infiltration, grafting, cis and intragenesis and gene editing technologies. How these new techniques should be regulated has fostered considerable debate. Concerns have also been raised, to ensure over-regulation does not arise, creating administrative and economic burden. In this article the existing landscape of genetically modified crops is reviewed and the potential of several New Plant Breeding Techniques (NPBT) described. Metabolomics is an omic technology that has developed in a concurrent manner with biotechnological advances in plant breeding. There is potentially further opportunities to advance our metabolomic technologies to characterise the outputs of New Plant Breeding Technologies, in a manner that is beneficial both from an academic, biosafety and industrial perspective.
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Affiliation(s)
- Eugenia M A Enfissi
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Margit Drapal
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Laura Perez-Fons
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Marilise Nogueira
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Harriet M Berry
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Juliana Almeida
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Paul D Fraser
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom.
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Burgos E, Belen De Luca M, Diouf I, de Haro LA, Albert E, Sauvage C, Tao ZJ, Bermudez L, Asís R, Nesi AN, Matringe M, Bréhélin C, Guiraud T, Ferrand C, Atienza I, Jorly J, Mauxion JP, Baldet P, Fernie AR, Quadrana L, Rothan C, Causse M, Carrari F. Validated MAGIC and GWAS population mapping reveals the link between vitamin E content and natural variation in chorismate metabolism in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:907-923. [PMID: 33179365 DOI: 10.1111/tpj.15077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 05/21/2023]
Abstract
Tocochromanols constitute the different forms of vitamin E (VTE), essential components of the human diet, and display a high membrane protectant activity. By combining interval mapping and genome-wide association studies (GWAS), we unveiled the genetic determinants of tocochromanol accumulation in tomato (Solanum lycopersicum) fruits. To enhance the nutritional value of this highly consumed vegetable, we dissected the natural intraspecific variability of tocochromanols in tomato fruits and genetically engineered their biosynthetic pathway. These analyses allowed the identification of a total of 25 quantitative trait loci interspersed across the genome pinpointing the chorismate-tyrosine pathway as a regulatory hub controlling the supply of the aromatic head group for tocochromanol biosynthesis. To validate the link between the chorismate-tyrosine pathway and VTE, we engineered tomato plants to bypass the pathway at the arogenate branch point. Transgenic tomatoes showed moderate increments in tocopherols (up to approximately 20%) and a massive accumulation of tocotrienols (up to approximately 3400%). Gene expression analyses of these plants reveal a trade-off between VTE and natural variation in chorismate metabolism explained by transcriptional reprogramming of specific structural genes of the pathway. By restoring the accumulation of alpha-tocotrienols (α-t3) in fruits, the plants produced here are of high pharmacological and nutritional interest.
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Affiliation(s)
- Estanislao Burgos
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
| | - Maria Belen De Luca
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
| | - Isidore Diouf
- INRAE, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, 67 Allée des Chênes, Domaine Saint Maurice CS60094, Montfavet, 84143, France
| | - Luis A de Haro
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
| | - Elise Albert
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Zhao J Tao
- INRAE, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, 67 Allée des Chênes, Domaine Saint Maurice CS60094, Montfavet, 84143, France
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria, and Consejo Nacional de Investigaciones Científicas y Técnicas, PO Box 25, Castelar, B1712WAA, Argentina
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ramon Asís
- CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, CC, 5000, Argentina
| | - Adriano N Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Michel Matringe
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168 CNRS-CEA-INRAE, Université Joseph Fourier, CEA Grenoble, PCV, Grenoble Cedex 9, Grenoble, 38054, France
| | - Claire Bréhélin
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168 CNRS-CEA-INRAE, Université Joseph Fourier, CEA Grenoble, PCV, Grenoble Cedex 9, Grenoble, 38054, France
| | - Thomas Guiraud
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Carine Ferrand
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Isabelle Atienza
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Joana Jorly
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Jean P Mauxion
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Pierre Baldet
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Alisdair R Fernie
- Institute of Molecular Plant Physiology, Max-Planck, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Leandro Quadrana
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France
| | - Christophe Rothan
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Mathilde Causse
- INRAE, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, 67 Allée des Chênes, Domaine Saint Maurice CS60094, Montfavet, 84143, France
| | - Fernando Carrari
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
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Ghatak A, Chaturvedi P, Weckwerth W. Metabolomics in Plant Stress Physiology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 164:187-236. [PMID: 29470599 DOI: 10.1007/10_2017_55] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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11
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Aidoo MK, Sherman T, Lazarovitch N, Fait A, Rachmilevitch S. Physiology and metabolism of grafted bell pepper in response to low root-zone temperature. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:339-349. [PMID: 32172743 DOI: 10.1071/fp18206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/04/2018] [Indexed: 06/10/2023]
Abstract
Low temperature is a prominent limiting factor for tropical originated crops production in temperate regions, particularly during cool-season production. The diverse response of two rootstocks (Canon-sensitive and S103-tolerant to low root-zone temperature) was studied when exposed to aeroponically different temperature regimes at the root zone: constant low temperature of 14°C low root-zone temperature (LRZT), transient exposure to LRZT of 27-14-27°C and control temperature of 27°C. Gas exchange, shoot dry mass, and root morphology were measured. Shifts in central and secondary metabolite levels in the leaves and roots were examined by gas chromatography-mass spectrometry (GC-MS). Low root-zone temperature inhibited photosynthesis and transpiration of both grafted bell pepper plants; however, self-grafted Canon physiology was impeded to a greater extent compared with Canon grafted onto rootstock S103. Rootstock S103 demonstrated higher sink potential contributing to milder reduction of photosynthesis and transpiration during stress compared with self-grafted Canon. This reduction of gas exchange led to a significant reduction of root maximum length and root dry mass in self-grafted Canon in response to the stress at 14°C compared with Canon grafted onto rootstock S103. In response to stress, GC-MS metabolite profiling showed enhance metabolism in both cultivars' leaves, as well as in the roots irrespective of the developmental stage of the plant. This evidence combined indicates enhance gas exchange and carbon assimilation when bell pepper is grafted on S103 under low root-zone temperature.
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Affiliation(s)
- Moses Kwame Aidoo
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | | | - Naftali Lazarovitch
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Aaron Fait
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shimon Rachmilevitch
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel; and Corresponding author.
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12
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Oliveira PMR, Rodrigues MA, Gonçalves AZ, Kerbauy GB. Exposure of Catasetum fimbriatum aerial roots to light coordinates carbon partitioning between source and sink organs in an auxin dependent manner. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:341-347. [PMID: 30605871 DOI: 10.1016/j.plaphy.2018.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
Light energy is essential for carbon metabolism in plants, as well as controlling the transport of metabolites between the organs. While terrestrial plants have a distinct structural and functional separation between the light exposed aerial parts and the non-exposed roots, epiphytic plants, such as orchids, have shoots and roots simultaneously fully exposed to light. The roots of orchids differ mainly from non-orchidaceous plants in their ability to photosynthesize. Since the roots of Catasetum fimbriatum can synthesize auxin which is acropetally transported to the shoot region, we decided to investigate whether: (1) light treatment of C. fimbriatum roots raises the auxin levels in the plant; and (2) distinct auxin concentrations can change the source-sink relationships, altering the amounts of sugars and organic acids in leaves, pseudobulbs and roots. Among the organs studied, the roots accumulated the highest concentrations of indole-3-acetic-acid (IAA); and when roots were exposed to light, IAA accumulated in the leaves. However, when polar auxin transport (PAT) was blocked with N-(1-Naphthyl)phthalamic acid (NPA) treatment, a significant accumulation of sugars and organic acids occurred in the pseudobulbs and leaves, respectively, suggesting that auxin flux from roots to shoots was involved in carbon partitioning of the aerial organs. Considering that C. fimbriatum plants lose all their leaves seasonally, it is possible the roots are a substituting influence on the growth and development of this orchid during its leafless period.
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Affiliation(s)
| | - Maria Aurineide Rodrigues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Ana Zangirolame Gonçalves
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Gilberto Barbante Kerbauy
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
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13
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Kou S, Chen L, Tu W, Scossa F, Wang Y, Liu J, Fernie AR, Song B, Xie C. The arginine decarboxylase gene ADC1, associated to the putrescine pathway, plays an important role in potato cold-acclimated freezing tolerance as revealed by transcriptome and metabolome analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1283-1298. [PMID: 30307077 DOI: 10.1111/tpj.14126] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 05/25/2023]
Abstract
Low temperature severely influences potato production as the cultivated potato (Solanum tuberosum) is frost sensitive, however the mechanism underlying the freezing tolerance of the potato is largely unknown. In the present research, we studied the transcriptome and metabolome of the freezing-tolerant wild species Solanum acaule (Aca) and freezing-sensitive cultivated S. tuberosum (Tub) to identify the main pathways and important factors related to freezing tolerance. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation indicated that polyamine and amino acid metabolic pathways were specifically upregulated in Aca under cold treatment. The transcriptome changes detected in Aca were accompanied by the specific accumulation of putrescine, saccharides, amino acids and other metabolites. The combination of transcriptome and metabolome analyses revealed that putrescine exhibited an accumulative pattern in accordance with the expression of the arginine decarboxylase gene ADC1. The primary role of putrescine was further confirmed by analyzing all three polyamines (putrescine, spermidine, and spermine) and the genes encoding the corresponding enzymes in two sets of potato genotypes with distinct freezing tolerance, implying that only putrescine and ADC1 were uniquely enhanced by cold in the freezing-tolerant genotypes. The function of putrescine was further analyzed by its exogenous application and the overexpression of SaADC1 in S. tuberosum cv. E3, indicating its important role(s) in cold-acclimated freezing tolerance, which was accompanied with the activation of C-repeat binding factor genes (CBFs). The present research has identified that the ADC1-associated putrescine pathway plays an important role in cold-acclimated freezing tolerance of potato, probably by enhancing the expression of CBF genes.
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Affiliation(s)
- Shuang Kou
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Chen
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Tu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Council for Agricultural Research and Economics, Research Center, CREA-OFA, Via di Fioranello 52, 00134, Rome, Italy
| | - Yamei Wang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Liu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Botao Song
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Conghua Xie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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14
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Alseekh S, Fernie AR. Metabolomics 20 years on: what have we learned and what hurdles remain? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:933-942. [PMID: 29734513 DOI: 10.1111/tpj.13950] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 05/11/2023]
Abstract
The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by the use of these approaches, and document the knowledge and technology gaps that are currently constraining its further development. Finally, we detail why we think that the time is ripe to refocus our efforts on the understanding of metabolic function.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Centre of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Centre of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
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15
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Robinson AR, Dauwe R, Mansfield SD. Assessing the between-background stability of metabolic effects arising from lignin-related transgenic modifications, in two Populus hybrids using non-targeted metabolomics. TREE PHYSIOLOGY 2018; 38:378-396. [PMID: 29040774 DOI: 10.1093/treephys/tpx110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/13/2017] [Indexed: 05/24/2023]
Abstract
The advances in 'high-throughput' biology have significantly expanded our fundamental understanding of complex biological processes inherent to tree growth and development. Relative to the significant achievements attained with whole genome re-sequencing and transcriptomics efforts, the development and power of post-transcriptional tools such as proteomics and metabolomics continue to lag behind in tree biology. However, the inclusion of these powerful functional genomics platforms should substantially enable systems biology assessments of tree development, physiology and response(s) to biotic and abiotic stresses. Herein, we employ a non-targeted metabolomics platform to elucidate the metabolic plasticity of xylem lignification in distinct hybrid poplar genetic backgrounds, as well as in transgenic trees in these backgrounds expressing two common constructs: the first construct (C4H::F5H) augments monolignol content (syringyl:guaiacyl (S:G) ratio), while the second construct (C3'H-RNAi) reduces cell wall lignification. The results clearly show that genotype-specific metabolism exists, and provide an appropriate foundation for properly comparing the influence of background on the relationships between metabolic and specific phenotypic traits. Moreover, it was apparent that transgene-induced phenotypic gradients in cell wall chemical wood can be associated with global metabolism of secondary xylem biosynthesis, however in a genotype-specific manner. This result implies that the same may be true for phenotypic gradients arising through natural genetic variation, intensive breeding or environmental factors. It is also apparent that while distinct, at a global level the wood-forming metabolisms of different poplar hybrids can, to some extent, respond similarly to the influences of genetic manipulation of lignin-related genes. This further implies that with the correct approach, it may be possible to associate the emergence of specific wood traits from different genetic backgrounds-be they transgene-induced or otherwise-with stable metabolic signatures.
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Affiliation(s)
- Andrew R Robinson
- Department of Wood Science, Faculty of Forest Sciences, The University of British Columbia, 2424 Main Mall, V6T 1Z4 Vancouver, BC, Canada
| | - Rebecca Dauwe
- Plant Biology & Innovation Research Unit EA3900-UPJV, Université of Picardie Jules Verne, PRES UFECAP, Faculty of Sciences, Ilot des poulies, 33 rue Saint Leu, F-80039 Amiens cedex, France
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forest Sciences, The University of British Columbia, 2424 Main Mall, V6T 1Z4 Vancouver, BC, Canada
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16
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Aidoo MK, Sherman T, Lazarovitch N, Fait A, Rachmilevitch S. A bell pepper cultivar tolerant to chilling enhanced nitrogen allocation and stress-related metabolite accumulation in the roots in response to low root-zone temperature. PHYSIOLOGIA PLANTARUM 2017; 161:196-210. [PMID: 28444904 DOI: 10.1111/ppl.12584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 03/05/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Two bell pepper (Capsicum annuum) cultivars, differing in their response to chilling, were exposed to three levels of root-zone temperatures. Gas exchange, shoot and root phenology, and the pattern of change of the central metabolites and secondary metabolites caffeate and benzoate in the leaves and roots were profiled. Low root-zone temperature significantly inhibited gaseous exchange, with a greater effect on the sensitive commercial pepper hybrid (Canon) than on the new hybrid bred to enhance abiotic stress tolerance (S103). The latter was less affected by the treatment with respect to plant height, shoot dry mass, root maximum length, root projected area, number of root tips and root dry mass. More carbon was allocated to the leaves of S103 than nitrogen at 17°C, while in the roots at 17°C, more nitrogen was allocated and the ratio between C/N decreased. Metabolite profiling showed greater increase in the root than in the leaves. Leaf response between the two cultivars differed significantly. The roots accumulated stress-related metabolites including γ-aminobutyric acid (GABA), proline, galactinol and raffinose and at chilling (7°C) resulted in an increase of sugars in both cultivars. Our results suggest that the enhanced tolerance of S103 to root cold stress, reflected in the relative maintenance of shoot and root growth, is likely linked to a more effective regulation of photosynthesis facilitated by the induction of stress-related metabolism.
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Affiliation(s)
- Moses Kwame Aidoo
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Sherman
- Zeraim Gedera, Syngenta Seed Company, Kibutz Revadim, Israel
| | - Naftali Lazarovitch
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shimon Rachmilevitch
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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17
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Investigating the Role of the Photorespiratory Pathway in Non-photosynthetic Tissues. Methods Mol Biol 2017. [PMID: 28822136 DOI: 10.1007/978-1-4939-7225-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Whilst photorespiration represents one of the dominant pathway fluxes in photosynthetic tissues there are hints from publically available gene expression data such as that housed in the bioarray resource (BAR; www.bar.utoronto.ca) that several of the constituent enzymes are present in roots and other heterotrophic tissues. Here we describe a protocol based on modification of the gaseous environment surrounding individual tissues of mutant and wild type Arabidopsis and evaluation of the consequences. This method could additionally easily be used for larger plants.
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18
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Josić D, Peršurić Ž, Rešetar D, Martinović T, Saftić L, Kraljević Pavelić S. Use of Foodomics for Control of Food Processing and Assessing of Food Safety. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 81:187-229. [PMID: 28317605 DOI: 10.1016/bs.afnr.2016.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.
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Affiliation(s)
- D Josić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia.
| | - Ž Peršurić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - D Rešetar
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - T Martinović
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - L Saftić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - S Kraljević Pavelić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
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19
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Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas-Oates J, António C. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress. MASS SPECTROMETRY REVIEWS 2016; 35:620-49. [PMID: 25589422 DOI: 10.1002/mas.21449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 05/08/2023]
Abstract
Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.
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Affiliation(s)
- Tiago F Jorge
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
| | - João A Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Camila Caldana
- Max-Planck-partner group at the Brazilian Bioethanol Science and Technology Laboratory/CNPEM, 13083-970, Campinas-SP, Brazil
| | - Romy Schmidt
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Joost T van Dongen
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jane Thomas-Oates
- Jane Thomas-Oates, Centre of Excellence in Mass Spectrometry, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
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20
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Fernie AR, Pichersky E. Focus Issue on Metabolism: Metabolites, Metabolites Everywhere. PLANT PHYSIOLOGY 2015; 169:1421-3. [PMID: 26531677 PMCID: PMC4634105 DOI: 10.1104/pp.15.01499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of MolecularPlant Physiology14476 Potsdam-GolmGermany
| | - Eran Pichersky
- Department of Molecular, Cellular, andDevelopmental BiologyUniversity of MichiganAnn Arbor, MI 48109
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21
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Li QF, Wang JH, Pulkkinen P, Kong LS. Changes in the Metabolome of Picea balfouriana Embryogenic Tissues That Were Linked to Different Levels of 6-BAP by Gas Chromatography-Mass Spectrometry Approach. PLoS One 2015; 10:e0141841. [PMID: 26517840 PMCID: PMC4627733 DOI: 10.1371/journal.pone.0141841] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022] Open
Abstract
Embryogenic cultures of Picea balfouriana, which is an important commercial species for reforestation in Southern China, easily lose their embryogenic ability during long-term culture. Embryogenic tissue that proliferated at lower concentrations (3.6 μM and 2.5 μM) of 6-benzylaminopurine (6-BAP) were more productive, and generated 113 ± 6 and 89 ± 3 mature embryos per 100 mg embryogenic tissue, respectively. A metabolomic approach was used to study the changes in metabolites linked to embryogenic competence related to three different 6-BAP concentrations (2.5 μM, 3.6 μM, and 5 μM). A total of 309 compounds were obtained, among which 123 metabolites mapped to Kyoto Encyclopedia of Genes and genomes (KEGG) pathways. The levels of 35 metabolites were significantly differentially regulated among the three 6-BAP treatments, and 32 metabolites differed between the 2.5 μM and 5 μM treatments. A total of 17 metabolites appeared only once among the three comparisons. The combination of a score plot and a loading plot showed that in the samples with higher embryogenic ability (3.6 μM and 2.5 μM), up-regulated metabolites were mostly amino acids and down-regulated metabolites were mostly primary carbohydrates (especially sugars). These results suggested that 6-BAP may influence embryogenic competence by nitrogen metabolism, which could cause an increase in amino acid levels and higher amounts of aspartate, isoleucine, and leucine in tissues with higher embryogenic ability. Furthermore, we speculated that 6-BAP may affect the amount of tryptophan in tissues, which would change the indole-3-acetic acid levels and influence the embryogenic ability.
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Affiliation(s)
- Q. F. Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation & Utilization, GuangXi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - J. H. Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail:
| | - P. Pulkkinen
- Finnish Forest Research Institute, Haapastensyrjä, Finland
| | - L. S. Kong
- Unit Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, Canada
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22
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Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. BMC Genomics 2015; 16 Suppl 3:S9. [PMID: 25708381 PMCID: PMC4331812 DOI: 10.1186/1471-2164-16-s3-s9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. RESULTS With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. CONCLUSIONS This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Affiliation(s)
- Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Joon-Yong Lee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Wenxu Zhou
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Zhihong Song
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Nick Ransom
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark Westgate
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Vidya Iyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jackie Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Basil Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
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23
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George GM, Ruckle ME, Lloyd JR. Virus-induced gene silencing as a scalable tool to study drought tolerance in plants. Methods Mol Biol 2015; 1287:243-53. [PMID: 25740370 DOI: 10.1007/978-1-4939-2453-0_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Here we describe the methodology of using virus-induced gene silencing (VIGS) as a powerful and scalable tool to screen the function of genes that participate in adaptation to drought. Silencing of endogenous gene expression in Nicotiana benthamiana is achieved by systemic infection of the aerial parts of the plant with a virus engineered to contain homologous fragments of the target gene(s) of interest. Silenced plant material can be consistently produced with little optimization in less than 1 month without specialized equipment, using only simple cloning and transformation techniques. Although maximal silencing is localized to only a few leaves, when whole plants are subjected to water stress, the tissue from these silenced leaves can be characterized for physiological, biochemical, and transcriptional responses to determine the role of the candidate genes in drought tolerance.
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Affiliation(s)
- Gavin M George
- Department of Biology, ETH Zurich, Universitaetsstrasse 2, Zurich, CH-8092, Switzerland
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24
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Kim HW, Kim JB, Cho SM, Cho IK, Li QX, Jang HH, Lee SH, Lee YM, Hwang KA. Characterization and quantification of γ-oryzanol in grains of 16 Korean rice varieties. Int J Food Sci Nutr 2014; 66:166-74. [DOI: 10.3109/09637486.2014.971226] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Heon Woong Kim
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
| | - Jung Bong Kim
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
| | - Soo-Muk Cho
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
| | - Il Kyu Cho
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Hwan-Hee Jang
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
| | - Sung-Hyeon Lee
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
| | - Young-Min Lee
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
| | - Kyung-A. Hwang
- Department of Agro-Food Resources, National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea and
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25
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Corol DI, Harflett C, Beale MH, Ward JL. An efficient high throughput metabotyping platform for screening of biomass willows. Metabolites 2014; 4:946-76. [PMID: 25353313 PMCID: PMC4279154 DOI: 10.3390/metabo4040946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/15/2014] [Accepted: 10/22/2014] [Indexed: 11/16/2022] Open
Abstract
Future improvement of woody biomass crops such as willow and poplar relies on our ability to select for metabolic traits that sequester more atmospheric carbon into biomass, or into useful products to replace petrochemical streams. We describe the development of metabotyping screens for willow, using combined 1D 1H-NMR-MS. A protocol was developed to overcome 1D 1H-NMR spectral alignment problems caused by variable pH and peak broadening arising from high organic acid levels and metal cations. The outcome was a robust method to allow direct statistical comparison of profiles arising from source (leaf) and sink (stem) tissues allowing data to be normalised to a constant weight of the soluble metabolome. We also describe the analysis of two willow biomass varieties, demonstrating how fingerprints from 1D 1H-NMR-MS vary from the top to the bottom of the plant. Automated extraction of quantitative data of 56 primary and secondary metabolites from 1D 1H-NMR spectra was realised by the construction and application of a Salix metabolite spectral library using the Chenomx software suite. The optimised metabotyping screen in conjunction with automated quantitation will enable high-throughput screening of genetic collections. It also provides genotype and tissue specific data for future modelling of carbon flow in metabolic networks.
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Affiliation(s)
- Delia I Corol
- Department of Plant Biology and Crop Sciences, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, UK.
| | - Claudia Harflett
- Department of Plant Biology and Crop Sciences, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, UK.
| | - Michael H Beale
- Department of Plant Biology and Crop Sciences, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, UK.
| | - Jane L Ward
- Department of Plant Biology and Crop Sciences, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, UK.
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26
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Simó C, Ibáñez C, Valdés A, Cifuentes A, García-Cañas V. Metabolomics of genetically modified crops. Int J Mol Sci 2014; 15:18941-66. [PMID: 25334064 PMCID: PMC4227254 DOI: 10.3390/ijms151018941] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 01/03/2023] Open
Abstract
Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade.
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Affiliation(s)
- Carolina Simó
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Nicolas Cabrera 9, Cantoblanco Campus, Madrid 28049, Spain.
| | - Clara Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Nicolas Cabrera 9, Cantoblanco Campus, Madrid 28049, Spain.
| | - Alberto Valdés
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Nicolas Cabrera 9, Cantoblanco Campus, Madrid 28049, Spain.
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Nicolas Cabrera 9, Cantoblanco Campus, Madrid 28049, Spain.
| | - Virginia García-Cañas
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Nicolas Cabrera 9, Cantoblanco Campus, Madrid 28049, Spain.
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27
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Field Phenotyping and Long-Term Platforms to Characterise How Crop Genotypes Interact with Soil Processes and the Environment. AGRONOMY-BASEL 2014. [DOI: 10.3390/agronomy4020242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Valdés A, Simó C, Ibáñez C, García-Cañas V. Foodomics strategies for the analysis of transgenic foods. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.05.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Nardozza S, Boldingh HL, Osorio S, Höhne M, Wohlers M, Gleave AP, MacRae EA, Richardson AC, Atkinson RG, Sulpice R, Fernie AR, Clearwater MJ. Metabolic analysis of kiwifruit (Actinidia deliciosa) berries from extreme genotypes reveals hallmarks for fruit starch metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5049-63. [PMID: 24058160 PMCID: PMC3830485 DOI: 10.1093/jxb/ert293] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Tomato, melon, grape, peach, and strawberry primarily accumulate soluble sugars during fruit development. In contrast, kiwifruit (Actinidia Lindl. spp.) and banana store a large amount of starch that is released as soluble sugars only after the fruit has reached maturity. By integrating metabolites measured by gas chromatography-mass spectrometry, enzyme activities measured by a robot-based platform, and transcript data sets during fruit development of Actinidia deliciosa genotypes contrasting in starch concentration and size, this study identified the metabolic changes occurring during kiwifruit development, including the metabolic hallmarks of starch accumulation and turnover. At cell division, a rise in glucose (Glc) concentration was associated with neutral invertase (NI) activity, and the decline of both Glc and NI activity defined the transition to the cell expansion and starch accumulation phase. The high transcript levels of β-amylase 9 (BAM9) during cell division, prior to net starch accumulation, and the correlation between sucrose phosphate synthase (SPS) activity and sucrose suggest the occurrence of sucrose cycling and starch turnover. ADP-Glc pyrophosphorylase (AGPase) is identified as a key enzyme for starch accumulation in kiwifruit berries, as high-starch genotypes had 2- to 5-fold higher AGPase activity, which was maintained over a longer period of time and was also associated with enhanced and extended transcription of the AGPase large subunit 4 (APL4). The data also revealed that SPS and galactinol might affect kiwifruit starch accumulation, and suggest that phloem unloading into kiwifruit is symplastic. These results are relevant to the genetic improvement of quality traits such as sweetness and sugar/acid balance in a range of fruit species.
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Affiliation(s)
- Simona Nardozza
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Helen L. Boldingh
- PFR, Ruakura Research Centre, Private Bag 3230, Hamilton, New Zealand
| | - Sonia Osorio
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Wohlers
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Andrew P. Gleave
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Elspeth A. MacRae
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | | | - Ross G. Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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30
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Gunning TK, Conlan XA, Parker RM, Dyson GA, Adams MJ, Barnett NW, Cahill DM. Profiling of secondary metabolites in blue lupin inoculated with Phytophthora cinnamomi following phosphite treatment. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1089-1097. [PMID: 32481177 DOI: 10.1071/fp13023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/19/2013] [Indexed: 06/11/2023]
Abstract
In order to discover phytochemicals that are potentially bioactive against Phytophthora cinnamomi, (a soil-borne plant pathogen) a metabolite profiling protocol for investigation of metabolic changes in Lupinus angustifolius L. plant roots in response to pathogen challenge has been established. Analysis of the metabolic profiles from healthy and P. cinnamomi-inoculated root tissue with high resolution mass spectrometry and nuclear magnetic resonance spectroscopy confirmed that although susceptible, L. angustifolius upregulated a defence associated genistein and 2'-hydroxygenistein-based isoflavonoid and a soyasapogenol saponin at 12h post inoculation which increased in concentration at 72h post inoculation. In contrast to the typical susceptible interaction, the application of a phosphorous-based treatment to L. angustifolius foliage 48h before P. cinnamomi challenge negated the ability of the pathogen to colonise the root tissue and cause disease. Importantly, although the root profiles of water-treated and phosphite-treated plants post pathogen inoculation contained the same secondary metabolites, concentration variations were observed. Accumulation of secondary metabolites within the P. cinnamomi-inoculated plants confirms that pathogen ingress of the root interstitially occurs in phosphite-treated plants, confirming a direct mode of action against the pathogen upon breaching the root cells.
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Affiliation(s)
- Tiffany K Gunning
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic. 3217, Australia
| | - Xavier A Conlan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic. 3217, Australia
| | - Rhiannon M Parker
- Applied Chemistry, School of Applied Sciences, RMIT University, Melbourne, Vic. 3001, Australia
| | - Gail A Dyson
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic. 3217, Australia
| | - Mike J Adams
- Applied Chemistry, School of Applied Sciences, RMIT University, Melbourne, Vic. 3001, Australia
| | - Neil W Barnett
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic. 3217, Australia
| | - David M Cahill
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic. 3217, Australia
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31
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Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N, Chakraborty S. Comparative Proteomics Reveals a Role for Seed Storage Protein AmA1 in Cellular Growth, Development, and Nutrient Accumulation. J Proteome Res 2013; 12:4904-30. [DOI: 10.1021/pr4007987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lalit Agrawal
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Kanika Narula
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Swaraj Basu
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Shubhendu Shekhar
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Sudip Ghosh
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Asis Datta
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
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32
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Pal D, Khozin-Goldberg I, Didi-Cohen S, Solovchenko A, Batushansky A, Kaye Y, Sikron N, Samani T, Fait A, Boussiba S. Growth, lipid production and metabolic adjustments in the euryhaline eustigmatophyte Nannochloropsis oceanica CCALA 804 in response to osmotic downshift. Appl Microbiol Biotechnol 2013; 97:8291-306. [DOI: 10.1007/s00253-013-5092-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/24/2022]
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33
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Du X, Zeisel SH. Spectral deconvolution for gas chromatography mass spectrometry-based metabolomics: current status and future perspectives. Comput Struct Biotechnol J 2013; 4:e201301013. [PMID: 24688694 PMCID: PMC3962095 DOI: 10.5936/csbj.201301013] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 06/20/2013] [Accepted: 06/23/2013] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry coupled to gas chromatography (GC-MS) has been widely applied in the field of metabolomics. Success of this application has benefited greatly from computational workflows that process the complex raw mass spectrometry data and extract the qualitative and quantitative information of metabolites. Among the computational algorithms within a workflow, deconvolution is critical since it reconstructs a pure mass spectrum for each component that the mass spectrometer observes. Based on the pure spectrum, the corresponding component can be eventually identified and quantified. Deconvolution is challenging due to the existence of co-elution. In this review, we focus on progress that has been made in the development of deconvolution algorithms and provide thoughts on future developments that will expand the application of GC-MS in metabolomics.
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Affiliation(s)
- Xiuxia Du
- Department of Bioinformatics, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Steven H Zeisel
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
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de Godoy F, Bermúdez L, Lira BS, de Souza AP, Elbl P, Demarco D, Alseekh S, Insani M, Buckeridge M, Almeida J, Grigioni G, Fernie AR, Carrari F, Rossi M. Galacturonosyltransferase 4 silencing alters pectin composition and carbon partitioning in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2449-66. [PMID: 23599271 PMCID: PMC3654432 DOI: 10.1093/jxb/ert106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pectin is a main component of the plant cell wall and is the most complex family of polysaccharides in nature. Its composition is essential for the normal growth and morphology pattern, as demonstrated by pectin-defective mutant phenotypes. Besides this basic role in plant physiology, in tomato, pectin structure contributes to very important quality traits such as fruit firmness. Sixty-seven different enzymatic activities have been suggested to be required for pectin biosynthesis, but only a few genes have been identified and studied so far. This study characterized the tomato galacturonosyltransferase (GAUT) family and performed a detailed functional study of the GAUT4 gene. The tomato genome harbours all genes orthologous to those described previously in Arabidopsis thaliana, and a transcriptional profile revealed that the GAUT4 gene was expressed at higher levels in developing organs. GAUT4-silenced tomato plants exhibited an increment in vegetative biomass associated with palisade parenchyma enlargement. Silenced fruits showed an altered pectin composition and accumulated less starch along with a reduced amount of pectin, which coincided with an increase in firmness. Moreover, the harvest index was dramatically reduced as a consequence of the reduction in the fruit weight and number. Altogether, these results suggest that, beyond its role in pectin biosynthesis, GAUT4 interferes with carbon metabolism, partitioning, and allocation. Hence, this cell-wall-related gene seems to be key in determining plant growth and fruit production in tomato.
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Affiliation(s)
- Fabiana de Godoy
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
- * These authors contributed equally to this work
| | - Luisa Bermúdez
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
- * These authors contributed equally to this work
| | | | | | - Paula Elbl
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
| | - Diego Demarco
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam-Golm, D-14 476, Germany
| | - Marina Insani
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, PO Box 25, B1712WAA Castelar, Argentina
| | - Marcos Buckeridge
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
| | - Juliana Almeida
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
| | - Gabriela Grigioni
- Instituto de Tecnología de Alimentos, Instituto Nacional de Tecnología Agropecuaría, PO Box 25, B1712WAA Castelar, Argentina
| | - Alisdair Robert Fernie
- Max Planck Institute for Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam-Golm, D-14 476, Germany
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, PO Box 25, B1712WAA Castelar, Argentina
| | - Magdalena Rossi
- Departamento de Botânica-IB-USP, 277, 05508-900, São Paulo, SP, Brazil
- † To whom correspondence should be addressed.
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Kabir AH, Paltridge NG, Roessner U, Stangoulis JCR. Mechanisms associated with Fe-deficiency tolerance and signaling in shoots of Pisum sativum. PHYSIOLOGIA PLANTARUM 2013; 147:381-95. [PMID: 22913816 DOI: 10.1111/j.1399-3054.2012.01682.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/13/2012] [Indexed: 05/23/2023]
Abstract
Mechanisms of Fe-deficiency tolerance and signaling were investigated in shoots of Santi (deficiency tolerant) and Parafield (deficiency intolerant) pea genotypes using metabolomic and physiological approaches. From metabolomic studies, Fe deficiency induced significant increases in N-, S- and tricarboxylic acid cycle metabolites in Santi but not in Parafield. Elevated N metabolites reflect an increase in N-recycling processes. Increased glutathione and S-metabolites suggest better protection of pea plants from Fe-deficiency-induced oxidative stress. Furthermore, Fe-deficiency induced increases in citrate and malate in leaves of Santi suggests long-distance transport of Fe is promoted by better xylem unloading. Supporting a role of citrate in the deficiency tolerance mechanism, physiological experiments showed higher Fe and citrate in the xylem of Santi. Reciprocal-grafting experiments confirm that the Fe-deficiency signal driving root Fe reductase and proton extrusion activity is generated in the shoot. Finally, our studies show that auxin can induce increased Fe-reductase activity and proton extrusion in roots. This article identifies several mechanisms in shoots associated with the differential Fe-deficiency tolerance of genotypes within a species, and provides essential background for future efforts to improve the Fe content and deficiency tolerance in peas.
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Affiliation(s)
- Ahmad H Kabir
- School of Biological Sciences, Flinders University, Bedford Park, 5042, SA, Australia.
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Szecowka M, Osorio S, Obata T, Araújo WL, Rohrmann J, Nunes-Nesi A, Fernie AR. Decreasing the mitochondrial synthesis of malate in potato tubers does not affect plastidial starch synthesis, suggesting that the physiological regulation of ADPglucose pyrophosphorylase is context dependent. PLANT PHYSIOLOGY 2012; 160:2227-38. [PMID: 23064409 PMCID: PMC3510143 DOI: 10.1104/pp.112.204826] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/11/2012] [Indexed: 05/21/2023]
Abstract
Modulation of the malate content of tomato (Solanum lycopersicum) fruit by altering the expression of mitochondrially localized enzymes of the tricarboxylic acid cycle resulted in enhanced transitory starch accumulation and subsequent effects on postharvest fruit physiology. In this study, we assessed whether such a manipulation would similarly affect starch biosynthesis in an organ that displays a linear, as opposed to a transient, kinetic of starch accumulation. For this purpose, we used RNA interference to down-regulate the expression of fumarase in potato (Solanum tuberosum) under the control of the tuber-specific B33 promoter. Despite displaying similar reductions in both fumarase activity and malate content as observed in tomato fruit expressing the same construct, the resultant transformants were neither characterized by an increased flux to, or accumulation of, starch, nor by alteration in yield parameters. Since the effect in tomato was mechanistically linked to derepression of the reaction catalyzed by ADP-glucose pyrophosphorylase, we evaluated whether the lack of effect on starch biosynthesis was due to differences in enzymatic properties of the enzyme from potato and tomato or rather due to differential subcellular compartmentation of reductant in the different organs. The results are discussed in the context both of current models of metabolic compartmentation and engineering.
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37
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Toubiana D, Semel Y, Tohge T, Beleggia R, Cattivelli L, Rosental L, Nikoloski Z, Zamir D, Fernie AR, Fait A. Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations. PLoS Genet 2012; 8:e1002612. [PMID: 22479206 PMCID: PMC3315483 DOI: 10.1371/journal.pgen.1002612] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 02/07/2012] [Indexed: 01/20/2023] Open
Abstract
To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs) grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL). Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i) reflect the extensive redundancy of the regulation underlying seed metabolism, (ii) demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii) emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study highlights the added value of integrating metabolic network analysis with mQTL mapping. Seeds represent 70% of the food source for man and livestock. However, as a result of millennia of domestication, crop plants have undergone major genetic deterioration, leading to a loss of important quality traits. Thus, the reintroduction of these quality traits is the key to the improvement of crops in modern agriculture. Seed quality traits include nutritional components, such as proteins and amino acids, and seed germination and storability, which are, in turn, inherently related to metabolism. To understand the genetic basis of seed metabolism—a strategic need in the improvement of seed crops—we studied a collection of offspring plants stemming from the cross between a domesticated tomato cultivar Solanum lycopersicum cv M82 and its distant wild relative S. pennellii. We monitored the changes in metabolism and studied the mode of regulation of the concentration of metabolites in the seeds as a result of genetic introgression, by taking advantage of state-of-the-art technologies and methods of data elaboration such as network-based analysis. We identified a number of candidate genes that may be useful in manipulations to enhance nutritional values in seeds. Finally, in an effort to study the relation among the seed, the fruit, and the mother plant, we determined potential yield-associated metabolic markers.
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Affiliation(s)
- David Toubiana
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
| | - Yaniv Semel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Faculty of Agriculture, Rehovot, Israel
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Leah Rosental
- French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Dani Zamir
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Faculty of Agriculture, Rehovot, Israel
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail: (AF); (ARF)
| | - Aaron Fait
- French Associates Institute for Agriculture and Biotechnology of Drylands (FAAB), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, Israel
- * E-mail: (AF); (ARF)
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Herrero M, Simó C, García-Cañas V, Ibáñez E, Cifuentes A. Foodomics: MS-based strategies in modern food science and nutrition. MASS SPECTROMETRY REVIEWS 2012; 31:49-69. [PMID: 21374694 DOI: 10.1002/mas.20335] [Citation(s) in RCA: 205] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 02/02/2011] [Accepted: 02/02/2011] [Indexed: 05/23/2023]
Abstract
Modern research in food science and nutrition is moving from classical methodologies to advanced analytical strategies in which MS-based techniques play a crucial role. In this context, Foodomics has been recently defined as a new discipline that studies food and nutrition domains through the application of advanced omics technologies in which MS techniques are considered indispensable. Applications of Foodomics include the genomic, transcriptomic, proteomic, and/or metabolomic study of foods for compound profiling, authenticity, and/or biomarker-detection related to food quality or safety; the development of new transgenic foods, food contaminants, and whole toxicity studies; new investigations on food bioactivity, food effects on human health, etc. This review work does not intend to provide an exhaustive revision of the many works published so far on food analysis using MS techniques. The aim of the present work is to provide an overview of the different MS-based strategies that have been (or can be) applied in the new field of Foodomics, discussing their advantages and drawbacks. Besides, some ideas about the foreseen development and applications of MS-techniques in this new discipline are also provided.
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Affiliation(s)
- Miguel Herrero
- Institute of Food Science Research (CIAL), CSIC, Nicolas Cabrera 9, Campus de Cantoblanco, 28049 Madrid, Spain
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Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D, Schellenberg M, Willmitzer L, Persson S, Martinoia E, Fernie AR. Toward the storage metabolome: profiling the barley vacuole. PLANT PHYSIOLOGY 2011; 157:1469-82. [PMID: 21949213 PMCID: PMC3252150 DOI: 10.1104/pp.111.185710] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 09/21/2011] [Indexed: 05/18/2023]
Abstract
While recent years have witnessed dramatic advances in our capacity to identify and quantify an ever-increasing number of plant metabolites, our understanding of how metabolism is spatially regulated is still far from complete. In an attempt to partially address this question, we studied the storage metabolome of the barley (Hordeum vulgare) vacuole. For this purpose, we used highly purified vacuoles isolated by silicon oil centrifugation and compared their metabolome with that found in the mesophyll protoplast from which they were derived. Using a combination of gas chromatography-mass spectrometry and Fourier transform-mass spectrometry, we were able to detect 59 (primary) metabolites for which we know the exact chemical structure and a further 200 (secondary) metabolites for which we have strong predicted chemical formulae. Taken together, these metabolites comprise amino acids, organic acids, sugars, sugar alcohols, shikimate pathway intermediates, vitamins, phenylpropanoids, and flavonoids. Of the 259 putative metabolites, some 12 were found exclusively in the vacuole and 34 were found exclusively in the protoplast, while 213 were common in both samples. When analyzed on a quantitative basis, however, there is even more variance, with more than 60 of these compounds being present above the detection limit of our protocols. The combined data were also analyzed with respect to the tonoplast proteome in an attempt to infer specificities of the transporter proteins embedded in this membrane. Following comparison with recent observations made using nonaqueous fractionation of Arabidopsis (Arabidopsis thaliana), we discuss these data in the context of current models of metabolic compartmentation in plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Alisdair R. Fernie
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.T., A.N.-N., M.M., P.G., D.S., L.W., S.P., A.R.F.); Institute of Plant Biology, University of Zürich, 8008 Zurich, Switzerland (M.S.R., M.S., E.M.); Institut des Sciences du Végétal, CNRS, 91198 Gif-sur-Yvette, France (M.S.R.); King Abdulaziz University, Jeddah 21589, Saudi Arabia (L.W.)
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Koek MM, Jellema RH, van der Greef J, Tas AC, Hankemeier T. Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives. Metabolomics 2011; 7:307-328. [PMID: 21949491 PMCID: PMC3155681 DOI: 10.1007/s11306-010-0254-3] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Accepted: 10/25/2010] [Indexed: 01/17/2023]
Abstract
Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites relevant to a specific phenotypic characteristic can be identified. However, the reliability of the analytical data is a prerequisite for correct biological interpretation in metabolomics analysis. In this review the challenges in quantitative metabolomics analysis with regards to analytical as well as data preprocessing steps are discussed. Recommendations are given on how to optimize and validate comprehensive silylation-based methods from sample extraction and derivatization up to data preprocessing and how to perform quality control during metabolomics studies. The current state of method validation and data preprocessing methods used in published literature are discussed and a perspective on the future research necessary to obtain accurate quantitative data from comprehensive GC-MS data is provided.
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Affiliation(s)
- Maud M. Koek
- Analytical Research Department, TNO Quality of Life, Utrechtseweg 48, P.O. Box 360, 3700 AJ Zeist, The Netherlands
| | - Renger H. Jellema
- DSM Biotechnology Center, Alexander Fleminglaan 1, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Jan van der Greef
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- SU BioMedicine and TNO Quality of Life, Utrechtseweg 48, P.O. Box 360, 3700 AJ Zeist, The Netherlands
| | - Albert C. Tas
- Analytical Research Department, TNO Quality of Life, Utrechtseweg 48, P.O. Box 360, 3700 AJ Zeist, The Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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García-Cañas V, Simó C, León C, Ibáñez E, Cifuentes A. MS-based analytical methodologies to characterize genetically modified crops. MASS SPECTROMETRY REVIEWS 2011; 30:396-416. [PMID: 21500243 DOI: 10.1002/mas.20286] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 05/09/2023]
Abstract
The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart.
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Affiliation(s)
- Virginia García-Cañas
- Institute of Industrial Fermentations (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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Allwood JW, De Vos RC, Moing A, Deborde C, Erban A, Kopka J, Goodacre R, Hall RD. Plant Metabolomics and Its Potential for Systems Biology Research. Methods Enzymol 2011; 500:299-336. [DOI: 10.1016/b978-0-12-385118-5.00016-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Tohge T, Mettler T, Arrivault S, Carroll AJ, Stitt M, Fernie AR. From models to crop species: caveats and solutions for translational metabolomics. FRONTIERS IN PLANT SCIENCE 2011; 2:61. [PMID: 22639601 PMCID: PMC3355600 DOI: 10.3389/fpls.2011.00061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 09/13/2011] [Indexed: 05/04/2023]
Abstract
Although plant metabolomics is largely carried out on Arabidopsis it is essentially genome-independent, and thus potentially applicable to a wide range of species. However, transfer between species, or even between different tissues of the same species, is not facile. This is because the reliability of protocols for harvesting, handling and analysis depends on the biological features and chemical composition of the plant tissue. In parallel with the diversification of model species it is important to establish good handling and analytic practice, in order to augment computational comparisons between tissues and species. Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is one of the powerful approaches for metabolite profiling. By using a combination of different extraction methods, separation columns, and ion detection, a very wide range of metabolites can be analyzed. However, its application requires careful attention to exclude potential pitfalls, including artifactual changes in metabolite levels during sample preparation under variations of light or temperature and analytic errors due to ion suppression. Here we provide case studies with two different LC-MS-based metabolomics platforms and four species (Arabidopsis thaliana, Chlamydomonas reinhardtii, Solanum lycopersicum, and Oryza sativa) that illustrate how such dangers can be detected and circumvented.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
- *Correspondence: Takayuki Tohge, Max-Planck-Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
| | - Tabea Mettler
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
| | | | - Adam James Carroll
- Australian Research Council Centre of Excellence in Plant Energy Biology, The Australian National UniversityCanberra, ACT, Australia
| | - Mark Stitt
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institute for Molecular Plant PhysiologyPotsdam-Golm, Germany
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44
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Developmental changes of carbohydrates, organic acids, amino acids, and phenolic compounds in ‘Honeycrisp’ apple flesh. Food Chem 2010. [DOI: 10.1016/j.foodchem.2010.05.053] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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George GM, van der Merwe MJ, Nunes-Nesi A, Bauer R, Fernie AR, Kossmann J, Lloyd JR. Virus-induced gene silencing of plastidial soluble inorganic pyrophosphatase impairs essential leaf anabolic pathways and reduces drought stress tolerance in Nicotiana benthamiana. PLANT PHYSIOLOGY 2010; 154:55-66. [PMID: 20605913 PMCID: PMC2938153 DOI: 10.1104/pp.110.157776] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 07/02/2010] [Indexed: 05/18/2023]
Abstract
The role of pyrophosphate in primary metabolism is poorly understood. Here, we report on the transient down-regulation of plastid-targeted soluble inorganic pyrophosphatase in Nicotiana benthamiana source leaves. Physiological and metabolic perturbations were particularly evident in chloroplastic central metabolism, which is reliant on fast and efficient pyrophosphate dissipation. Plants lacking plastidial soluble inorganic pyrophosphatase (psPPase) were characterized by increased pyrophosphate levels, decreased starch content, and alterations in chlorophyll and carotenoid biosynthesis, while constituents like amino acids (except for histidine, serine, and tryptophan) and soluble sugars and organic acids (except for malate and citrate) remained invariable from the control. Furthermore, translation of Rubisco was significantly affected, as observed for the amounts of the respective subunits as well as total soluble protein content. These changes were concurrent with the fact that plants with reduced psPPase were unable to assimilate carbon to the same extent as the controls. Furthermore, plants with lowered psPPase exposed to mild drought stress showed a moderate wilting phenotype and reduced vitality, which could be correlated to reduced abscisic acid levels limiting stomatal closure. Taken together, the results suggest that plastidial pyrophosphate dissipation through psPPase is indispensable for vital plant processes.
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Affiliation(s)
| | | | | | | | | | | | - James R. Lloyd
- Institute of Plant Biotechnology, University of Stellenbosch, Matieland 7602, Stellenbosch, South Africa (G.M.G., M.J.v.d.M., R.B., J.K., J.R.L.); Max Planck Institute of Molecular Plant Physiology, D–14476 Potsdam-Golm, Germany (A.N.-N., A.R.F.)
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van der Merwe MJ, Groenewald JH, Stitt M, Kossmann J, Botha FC. Downregulation of pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase activity in sugarcane culms enhances sucrose accumulation due to elevated hexose-phosphate levels. PLANTA 2010; 231:595-608. [PMID: 19957089 PMCID: PMC2806535 DOI: 10.1007/s00425-009-1069-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 11/09/2009] [Indexed: 05/19/2023]
Abstract
Analyses of transgenic sugarcane clones with 45-95% reduced cytosolic pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase (PFP, EC 2.7.1.90) activity displayed no visual phenotypical change, but significant changes were evident in in vivo metabolite levels and fluxes during internode development. In three independent transgenic lines, sucrose concentrations increased between three- and sixfold in immature internodes, compared to the levels in the wildtype control. There was an eightfold increase in the hexose-phosphate:triose-phosphate ratio in immature internodes, a significant restriction in the triose phosphate to hexose phosphate cycle and significant increase in sucrose cycling as monitored by (13)C nuclear magnetic resonance. This suggests that an increase in the hexose-phosphate concentrations resulting from a restriction in the conversion of hexose phosphates to triose phosphates drive sucrose synthesis in the young internodes. These effects became less pronounced as the tissue matured. Decreased expression of PFP also resulted in an increase of the ATP/ADP and UTP/UDP ratios, and an increase of the total uridine nucleotide and, at a later stage, the total adenine nucleotide pool, revealing strong interactions between PPi metabolism and general energy metabolism. Finally, decreased PFP leads to a reduction of PPi levels in older internodes indicating that in these developmental stages PFP acts in the gluconeogenic direction. The lowered PPi levels might also contribute to the absence of increases in sucrose contents in the more mature tissues of transgenic sugarcane with reduced PFP activity.
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Affiliation(s)
- Margaretha J van der Merwe
- Institute of Plant Biotechnology, University of Stellenbosch, Merriman Avenue, Stellenbosch 7602, South Africa.
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47
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Llorach-Asunción R, Jauregui O, Urpi-Sarda M, Andres-Lacueva C. Methodological aspects for metabolome visualization and characterization. J Pharm Biomed Anal 2010; 51:373-81. [DOI: 10.1016/j.jpba.2009.06.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 06/16/2009] [Accepted: 06/18/2009] [Indexed: 10/20/2022]
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48
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Brown NJ, Palmer BG, Stanley S, Hajaji H, Janacek SH, Astley HM, Parsley K, Kajala K, Quick WP, Trenkamp S, Fernie AR, Maurino VG, Hibberd JM. C acid decarboxylases required for C photosynthesis are active in the mid-vein of the C species Arabidopsis thaliana, and are important in sugar and amino acid metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:122-33. [PMID: 19807880 DOI: 10.1111/j.1365-313x.2009.04040.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cells associated with veins of petioles of C(3) tobacco possess high activities of the decarboxylase enzymes required in C(4) photosynthesis. It is not clear whether this is the case in other C(3) species, nor whether these enzymes provide precursors for specific biosynthetic pathways. Here, we investigate the activity of C(4) acid decarboxylases in the mid-vein of Arabidopsis, identify regulatory regions sufficient for this activity, and determine the impact of removing individual isoforms of each protein on mid-vein metabolite profiles. This showed that radiolabelled malate and bicarbonate fed to the xylem stream were incorporated into soluble and insoluble material in the mid-vein of Arabidopsis leaves. Compared with the leaf lamina, mid-veins possessed high activities of NADP-dependent malic enzyme (NADP-ME), NAD-dependent malic enzyme (NAD-ME) and phosphoenolpyruvate carboxykinase (PEPCK). Transcripts derived from both NAD-ME, one PCK and two of the four NADP-ME genes were detectable in these veinal cells. The promoters of each decarboxylase gene were sufficient for expression in mid-veins. Analysis of insertional mutants revealed that cytosolic NADP-ME2 is responsible for 80% of NADP-ME activity in mid-veins. Removing individual decarboxylases affected the abundance of amino acids derived from pyruvate and phosphoenolpyruvate. Reducing cytosolic NADP-ME activity preferentially affected the sugar content, whereas abolishing NAD-ME affected both the amino acid and the glucosamine content of mid-veins.
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Affiliation(s)
- Naomi J Brown
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, CB2 3EA, UK
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Robinson AR, Dauwe R, Ukrainetz NK, Cullis IF, White R, Mansfield SD. Predicting the regenerative capacity of conifer somatic embryogenic cultures by metabolomics. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:952-963. [PMID: 19906246 DOI: 10.1111/j.1467-7652.2009.00456.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Somatic embryogenesis in gymnosperms is an effective approach to clonally propagating germplasm. However, embryogenic cultures frequently lose regenerative capacity. The interactions between metabolic composition, physiological state, genotype and embryogenic capacity in Pinus taeda (loblolly pine) somatic embryogenic cultures were explored using metabolomics. A stepwise modelling procedure, using the Bayesian information criterion, generated a 47 metabolite predictive model that could explain culture productivity. The model performed extremely well in cross-validation, achieving a correlation coefficient of 0.98 between actual and predicted mature embryo production. The metabolic composition and structure of the model implied that variation in culture regenerative capacity was closely linked to the physiological transition of cultures from the proliferation phase to the maturation phase of development. The propensity of cultures to advance into this transition appears to relate to nutrient uptake and allocation in vivo, and to be associated with the tolerance and response of cultures to stress, during the proliferation phase.
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Affiliation(s)
- Andrew R Robinson
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada
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50
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Feldberg L, Venger I, Malitsky S, Rogachev I, Aharoni A. Dual Labeling of Metabolites for Metabolome Analysis (DLEMMA): A New Approach for the Identification and Relative Quantification of Metabolites by Means of Dual Isotope Labeling and Liquid Chromatography−Mass Spectrometry. Anal Chem 2009; 81:9257-66. [DOI: 10.1021/ac901495a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Liron Feldberg
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Venger
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
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