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Li Y, Jian Y, Mao Y, Meng F, Shao Z, Wang T, Zheng J, Wang Q, Liu L. "Omics" insights into plastid behavior toward improved carotenoid accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:1001756. [PMID: 36275568 PMCID: PMC9583013 DOI: 10.3389/fpls.2022.1001756] [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: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Jian
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yuanyu Mao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Fanliang Meng
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Tonglin Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jirong Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Lihong Liu
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
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2
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Beshir WF, Tohge T, Watanabe M, Hertog MLATM, Hoefgen R, Fernie AR, Nicolaï BM. Non-aqueous fractionation revealed changing subcellular metabolite distribution during apple fruit development. HORTICULTURE RESEARCH 2019; 6:98. [PMID: 31666959 PMCID: PMC6804870 DOI: 10.1038/s41438-019-0178-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 05/07/2023]
Abstract
In developing apple fruit, metabolic compartmentation is poorly understood due to the lack of experimental data. Distinguishing subcellular compartments in fruit using non-aqueous fractionation has been technically difficult due to the excess amount of sugars present in the different subcellular compartments limiting the resolution of the technique. The work described in this study represents the first attempt to apply non-aqueous fractionation to developing apple fruit, covering the major events occurring during fruit development (cell division, cell expansion, and maturation). Here we describe the non-aqueous fractionation method to study the subcellular compartmentation of metabolites during apple fruit development considering three main cellular compartments (cytosol, plastids, and vacuole). Evidence is presented that most of the sugars and organic acids were predominantly located in the vacuole, whereas some of the amino acids were distributed between the cytosol and the vacuole. The results showed a shift in the plastid marker from the lightest fractions in the early growth stage to the dense fractions in the later fruit growth stages. This implies that the accumulation of starch content with progressing fruit development substantially influenced the distribution of plastidial fragments within the non-aqueous density gradient applied. Results from this study provide substantial baseline information on assessing the subcellular compartmentation of metabolites in apple fruit in general and during fruit growth in particular.
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Affiliation(s)
- Wasiye F. Beshir
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Maarten L. A. T. M. Hertog
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Bart M. Nicolaï
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
- Flanders Centre of Postharvest Technology (VCBT), Leuven, Belgium
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3
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Lestari R, Rio M, Martin F, Leclercq J, Woraathasin N, Roques S, Dessailly F, Clément‐Vidal A, Sanier C, Fabre D, Melliti S, Suharsono S, Montoro P. Overexpression of Hevea brasiliensis ethylene response factor HbERF-IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:322-336. [PMID: 28626940 PMCID: PMC5785357 DOI: 10.1111/pbi.12774] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 05/03/2017] [Accepted: 05/29/2017] [Indexed: 05/20/2023]
Abstract
Ethylene response factor 1 (ERF1) is an essential integrator of the jasmonate and ethylene signalling pathways coordinating a large number of genes involved in plant defences. Its orthologue in Hevea brasiliensis, HbERF-IXc5, has been assumed to play a major role in laticifer metabolism and tolerance to harvesting stress for better latex production. This study sets out to establish and characterize rubber transgenic lines overexpressing HbERF-IXc5. Overexpression of HbERF-IXc5 dramatically enhanced plant growth and enabled plants to maintain some ecophysiological parameters in response to abiotic stress such as water deficit, cold and salt treatments. This study revealed that HbERF-IXc5 has rubber-specific functions compared to Arabidopsis ERF1 as transgenic plants overexpressing HbERF-IXc5 accumulated more starch and differentiated more latex cells at the histological level. The role of HbERF-IXc5 in driving the expression of some target genes involved in laticifer differentiation is discussed.
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Affiliation(s)
- Retno Lestari
- CIRADUMR AGAPMontpellierFrance
- Universitas Indonesia (UI)DepokIndonesia
- Bogor Agricultural University (IPB)BogorIndonesia
| | | | | | | | - Natthakorn Woraathasin
- CIRADUMR AGAPMontpellierFrance
- Faculty of Natural ResourcesDepartment of Plant SciencePrince of Songkla University (PSU)Hat YaiSongklaThailand
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4
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Eloundou-Mbebi JMO, Küken A, Omranian N, Kleessen S, Neigenfind J, Basler G, Nikoloski Z. A network property necessary for concentration robustness. Nat Commun 2016; 7:13255. [PMID: 27759015 PMCID: PMC5075777 DOI: 10.1038/ncomms13255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 09/14/2016] [Indexed: 12/15/2022] Open
Abstract
Maintenance of functionality of complex cellular networks and entire organisms exposed to environmental perturbations often depends on concentration robustness of the underlying components. Yet, the reasons and consequences of concentration robustness in large-scale cellular networks remain largely unknown. Here, we derive a necessary condition for concentration robustness based only on the structure of networks endowed with mass action kinetics. The structural condition can be used to design targeted experiments to study concentration robustness. We show that metabolites satisfying the necessary condition are present in metabolic networks from diverse species, suggesting prevalence of this property across kingdoms of life. We also demonstrate that our predictions about concentration robustness of energy-related metabolites are in line with experimental evidence from Escherichia coli. The necessary condition is applicable to mass action biological systems of arbitrary size, and will enable understanding the implications of concentration robustness in genetic engineering strategies and medical applications. Absolute concentration robustness (ACR), independence of the steady-state concentration of a molecule from the environment, is difficult to predict. Here, the authors derive a network structure-based necessary condition for ACR, and suggest that metabolites satisfying the condition are prevalent.
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Affiliation(s)
- Jeanne M O Eloundou-Mbebi
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Muehlenber 1, 14476 Potsdam-Golm, Germany
| | - Anika Küken
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Muehlenber 1, 14476 Potsdam-Golm, Germany
| | - Nooshin Omranian
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Muehlenber 1, 14476 Potsdam-Golm, Germany
| | | | | | - Georg Basler
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Muehlenber 1, 14476 Potsdam-Golm, Germany
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5
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Fürtauer L, Weckwerth W, Nägele T. A Benchtop Fractionation Procedure for Subcellular Analysis of the Plant Metabolome. FRONTIERS IN PLANT SCIENCE 2016; 7:1912. [PMID: 28066469 PMCID: PMC5177628 DOI: 10.3389/fpls.2016.01912] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/02/2016] [Indexed: 05/06/2023]
Abstract
Although compartmentation is a key feature of eukaryotic cells, biological research is frequently limited by methods allowing for the comprehensive subcellular resolution of the metabolome. It has been widely accepted that such a resolution would be necessary in order to approximate cellular biochemistry and metabolic regulation, yet technical challenges still limit both the reproducible subcellular fractionation and the sample throughput being necessary for a statistically robust analysis. Here, we present a method and a detailed protocol which is based on the non-aqueous fractionation technique enabling the assignment of metabolites to their subcellular localization. The presented benchtop method aims at unraveling subcellular metabolome dynamics in a precise and statistically robust manner using a relatively small amount of tissue material. The method is based on the separation of cellular fractions via density gradients consisting of organic, non-aqueous solvents. By determining the relative distribution of compartment-specific marker enzymes together with metabolite profiles over the density gradient it is possible to estimate compartment-specific metabolite concentrations by correlation. To support this correlation analysis, a spreadsheet is provided executing a calculation algorithm to determine the distribution of metabolites over subcellular compartments. The calculation algorithm performs correlation of marker enzyme activity and metabolite abundance accounting for technical errors, reproducibility and the resulting error propagation. The method was developed, tested and validated in three natural accessions of Arabidopsis thaliana showing different ability to acclimate to low temperature. Particularly, amino acids were strongly shuffled between subcellular compartments in a cold-sensitive accession while a cold-tolerant accession was characterized by a stable subcellular metabolic homeostasis. Finally, we conclude that subcellular metabolome analysis is essential to unambiguously unravel regulatory strategies being involved in plant-environment interactions.
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Affiliation(s)
- Lisa Fürtauer
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Thomas Nägele
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6
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Rojas-González JA, Soto-Súarez M, García-Díaz Á, Romero-Puertas MC, Sandalio LM, Mérida Á, Thormählen I, Geigenberger P, Serrato AJ, Sahrawy M. Disruption of both chloroplastic and cytosolic FBPase genes results in a dwarf phenotype and important starch and metabolite changes in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2673-89. [PMID: 25743161 PMCID: PMC4986871 DOI: 10.1093/jxb/erv062] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In this study, evidence is provided for the role of fructose-1,6-bisphosphatases (FBPases) in plant development and carbohydrate synthesis and distribution by analysing two Arabidopsis thaliana T-DNA knockout mutant lines, cyfbp and cfbp1, and one double mutant cyfbp cfbp1 which affect each FBPase isoform, cytosolic and chloroplastic, respectively. cyFBP is involved in sucrose synthesis, whilst cFBP1 is a key enzyme in the Calvin-Benson cycle. In addition to the smaller rosette size and lower rate of photosynthesis, the lack of cFBP1 in the mutants cfbp1 and cyfbp cfbp1 leads to a lower content of soluble sugars, less starch accumulation, and a greater superoxide dismutase (SOD) activity. The mutants also had some developmental alterations, including stomatal opening defects and increased numbers of root vascular layers. Complementation also confirmed that the mutant phenotypes were caused by disruption of the cFBP1 gene. cyfbp mutant plants without cyFBP showed a higher starch content in the chloroplasts, but this did not greatly affect the phenotype. Notably, the sucrose content in cyfbp was close to that found in the wild type. The cyfbp cfbp1 double mutant displayed features of both parental lines but had the cfbp1 phenotype. All the mutants accumulated fructose-1,6-bisphosphate and triose-phosphate during the light period. These results prove that while the lack of cFBP1 induces important changes in a wide range of metabolites such as amino acids, sugars, and organic acids, the lack of cyFBP activity in Arabidopsis essentially provokes a carbon metabolism imbalance which does not compromise the viability of the double mutant cyfbp cfbp1.
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Affiliation(s)
- José A Rojas-González
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
| | - Mauricio Soto-Súarez
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
| | - Ángel García-Díaz
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
| | - María C Romero-Puertas
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
| | - Luisa M Sandalio
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
| | - Ángel Mérida
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-US, Avda Américo Vespucio, 49, 41092, Sevilla, Spain
| | - Ina Thormählen
- Ludwig Maximilians University of Munich, Biology Department I, Plant Metabolism, Grosshaderner Str. 2-4, D-82152 Planegg, Germany
| | - Peter Geigenberger
- Ludwig Maximilians University of Munich, Biology Department I, Plant Metabolism, Grosshaderner Str. 2-4, D-82152 Planegg, Germany
| | - Antonio J Serrato
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
| | - Mariam Sahrawy
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008, Granada, Spain
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7
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García-Flores M, Juárez-Colunga S, García-Casarrubias A, Trachsel S, Winkler R, Tiessen A. Metabolic profiling of plant extracts using direct-injection electrospray ionization mass spectrometry allows for high-throughput phenotypic characterization according to genetic and environmental effects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:1042-52. [PMID: 25588121 DOI: 10.1021/jf504853w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In comparison to the exponential increase of genotyping methods, phenotyping strategies are lagging behind in agricultural sciences. Genetic improvement depends upon the abundance of quantitative phenotypic data and the statistical partitioning of variance into environmental, genetic, and random effects. A metabolic phenotyping strategy was adapted to increase sample throughput while saving reagents, reducing cost, and simplifying data analysis. The chemical profiles of stem extracts from maize plants grown under low nitrogen (LN) or control trial (CT) were analyzed using optimized protocols for direct-injection electrospray ionization mass spectrometry (DIESI-MS). Specific ions significantly decreased or increased because of environmental (LN versus CT) or genotypic effects. Biochemical profiling with DIESI-MS had a superior cost-benefit compared to other standard analytical technologies (e.g., ultraviolet, near-infrared reflectance spectroscopy, high-performance liquid chromatography, and gas chromatography with flame ionization detection) routinely used for plant breeding. The method can be successfully applied in maize, strawberry, coffee, and other crop species.
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Affiliation(s)
- Martín García-Flores
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Unidad Irapuato , Km 9.6 Libramiento Norte, 36821 Irapuato, Guanajuato, Mexico
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8
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Arrivault S, Guenther M, Florian A, Encke B, Feil R, Vosloh D, Lunn JE, Sulpice R, Fernie AR, Stitt M, Schulze WX. Dissecting the subcellular compartmentation of proteins and metabolites in arabidopsis leaves using non-aqueous fractionation. Mol Cell Proteomics 2014; 13:2246-59. [PMID: 24866124 DOI: 10.1074/mcp.m114.038190] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-aqueous fractionation is a technique for the enrichment of different subcellular compartments derived from lyophilized material. It was developed to study the subcellular distribution of metabolites. Here we analyzed the distribution of about 1,000 proteins and 70 metabolites, including 22 phosphorylated intermediates in wild-type Arabidopsis rosette leaves, using non-aqueous gradients divided into 12 fractions. Good separation of plastidial, cytosolic, and vacuolar metabolites and proteins was achieved, but cytosolic, mitochondrial, and peroxisomal proteins clustered together. There was considerable heterogeneity in the fractional distribution of transcription factors, ribosomal proteins, and subunits of the vacuolar-ATPase, indicating diverse compartmental location. Within the plastid, sub-organellar separation of thylakoids and stromal proteins was observed. Metabolites from the Calvin-Benson cycle, photorespiration, starch and sucrose synthesis, glycolysis, and the tricarboxylic acid cycle grouped with their associated proteins of the respective compartment. Non-aqueous fractionation thus proved to be a powerful method for the study of the organellar, and in some cases sub-organellar, distribution of proteins and their association with metabolites. It remains the technique of choice for the assignment of subcellular location to metabolites in intact plant tissues, and thus the technique of choice for doing combined metabolite-protein analysis on a single tissue sample.
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Affiliation(s)
- Stéphanie Arrivault
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Manuela Guenther
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexandra Florian
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beatrice Encke
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Regina Feil
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Daniel Vosloh
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; §Stellenbosch University, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - John E Lunn
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ronan Sulpice
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; ¶National University of Ireland, University Rd., Galway, Ireland
| | - Alisdair R Fernie
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Waltraud X Schulze
- From the ‡Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; ‖Department of Plant Systems Biology, Universität Hohenheim, 70593 Stuttgart, Germany
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9
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Allen DK, Evans BS, Libourel IGL. Analysis of isotopic labeling in peptide fragments by tandem mass spectrometry. PLoS One 2014; 9:e91537. [PMID: 24626471 PMCID: PMC3953442 DOI: 10.1371/journal.pone.0091537] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/13/2014] [Indexed: 01/18/2023] Open
Abstract
Phenotype in multicellular organisms is the consequence of dynamic metabolic events that occur in a spatially dependent fashion. This spatial and temporal complexity presents challenges for investigating metabolism; creating a need for improved methods that effectively probe biochemical events such as amino acid biosynthesis. Isotopic labeling can provide a temporal-spatial recording of metabolic events through, for example, the description of enriched amino acids in the protein pool. Proteins are therefore an important readout of metabolism and can be assessed with modern mass spectrometers. We compared the measurement of isotopic labeling in MS2 spectra obtained from tandem mass spectrometry under either higher energy collision dissociation (HCD) or collision induced dissociation (CID) at varied energy levels. Developing soybean embryos cultured with or without 13C-labeled substrates, and Escherichia coli MG1655 enriched by feeding 7% uniformly labeled glucose served as a source of biological material for protein evaluation. CID with low energies resulted in a disproportionate amount of heavier isotopologues remaining in the precursor isotopic distribution. HCD resulted in fewer quantifiable products; however deviation from predicted distributions were small relative to the CID-based comparisons. Fragment ions have the potential to provide information on the labeling of amino acids in peptides, but our results indicate that without further development the use of this readout in quantitative methods such as metabolic flux analysis is limited.
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Affiliation(s)
- Doug K. Allen
- United States Department of Agriculture, Agricultural Research Service, Plant Genetic Research Unit, St. Louis, Missouri, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Bradley S. Evans
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Igor G. L. Libourel
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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10
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Jazmin LJ, O'Grady JP, Ma F, Allen DK, Morgan JA, Young JD. Isotopically nonstationary MFA (INST-MFA) of autotrophic metabolism. Methods Mol Biol 2014; 1090:181-210. [PMID: 24222417 DOI: 10.1007/978-1-62703-688-7_12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Metabolic flux analysis (MFA) is a powerful approach for quantifying plant central carbon metabolism based upon a combination of extracellular flux measurements and intracellular isotope labeling measurements. In this chapter, we present the method of isotopically nonstationary (13)C MFA (INST-MFA), which is applicable to autotrophic systems that are at metabolic steady state but are sampled during the transient period prior to achieving isotopic steady state following the introduction of (13)CO2. We describe protocols for performing the necessary isotope labeling experiments, sample collection and quenching, nonaqueous fractionation and extraction of intracellular metabolites, and mass spectrometry (MS) analysis of metabolite labeling. We also outline the steps required to perform computational flux estimation using INST-MFA. By combining several recently developed experimental and computational techniques, INST-MFA provides an important new platform for mapping carbon fluxes that is especially applicable to autotrophic organisms, which are not amenable to steady-state (13)C MFA experiments.
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Affiliation(s)
- Lara J Jazmin
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
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11
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Lintala M, Schuck N, Thormählen I, Jungfer A, Weber KL, Weber APM, Geigenberger P, Soll J, Bölter B, Mulo P. Arabidopsis tic62 trol mutant lacking thylakoid-bound ferredoxin-NADP+ oxidoreductase shows distinct metabolic phenotype. MOLECULAR PLANT 2014; 7:45-57. [PMID: 24043709 DOI: 10.1093/mp/sst129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ferredoxin-NADP+ oxidoreductase (FNR), functioning in the last step of the photosynthetic electron transfer chain, exists both as a soluble protein in the chloroplast stroma and tightly attached to chloroplast membranes. Surface plasmon resonance assays showed that the two FNR isoforms, LFNR1 and LFNR2, are bound to the thylakoid membrane via the C-terminal domains of Tic62 and TROL proteins in a pH-dependent manner. The tic62 trol double mutants contained a reduced level of FNR, exclusively found in the soluble stroma. Although the mutant plants showed no visual phenotype or defects in the function of photosystems under any conditions studied, a low ratio of NADPH/NADP+ was detected. Since the CO₂ fixation capacity did not differ between the tic62 trol plants and wild-type, it seems that the plants are able to funnel reducing power to most crucial reactions to ensure survival and fitness of the plants. However, the activity of malate dehydrogenase was down-regulated in the mutant plants. Apparently, the plastid metabolism is able to cope with substantial changes in directing the electrons from the light reactions to stromal metabolism and thus only few differences are visible in steady-state metabolite pool sizes of the tic62 trol plants.
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Affiliation(s)
- Minna Lintala
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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12
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Allen DK, Laclair RW, Ohlrogge JB, Shachar-Hill Y. Isotope labelling of Rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments. PLANT, CELL & ENVIRONMENT 2012; 35:1232-44. [PMID: 22292468 PMCID: PMC3556518 DOI: 10.1111/j.1365-3040.2012.02485.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 01/19/2012] [Accepted: 01/22/2012] [Indexed: 05/18/2023]
Abstract
The architecture of plant metabolism includes substantial duplication of metabolite pools and enzyme catalyzed reactions in different subcellular compartments. This poses challenges for understanding the regulation of metabolism particularly in primary metabolism and amino acid biosynthesis. To explore the extent to which amino acids are made in single compartments and to gain insight into the metabolic precursors from which they derive, we used steady state (13) C labelling and analysed labelling in protein amino acids from plastid and cytosol. Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major component of green tissues and its large and small subunits are synthesized from different pools of amino acids in the plastid and cytosol, respectively. Developing Brassica napus embryos were cultured in the presence of [U-(13) C]-sucrose, [U-(13) C]-glucose, [U-(13) C]-glutamine or [U-(13) C]-alanine to generate proteins. The large subunits (LSU) and small subunits (SSU) of Rubisco were isolated and the labelling in their constituent amino acids was analysed by gas chromatography-mass spectrometry. Amino acids including alanine, glycine and serine exhibited different (13) C enrichment in the LSU and SSU, demonstrating that these pools have different metabolic origins and are not isotopically equilibrated between the plastid and cytosol on the time scale of cellular growth. Potential extensions of this novel approach to other macromolecules, organelles and cell types of eukaryotes are discussed.
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Affiliation(s)
- Doug K Allen
- USDA-ARS, Plant Genetics Research Unit, St Louis, MO 63132, USA Donald Danforth Plant Science Center, St Louis, MO 63132, USA.
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Tiessen A, Nerlich A, Faix B, Hümmer C, Fox S, Trafford K, Weber H, Weschke W, Geigenberger P. Subcellular analysis of starch metabolism in developing barley seeds using a non-aqueous fractionation method. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2071-87. [PMID: 22200665 PMCID: PMC3295393 DOI: 10.1093/jxb/err408] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 05/20/2023]
Abstract
Compartmentation of metabolism in developing seeds is poorly understood due to the lack of data on metabolite distributions at the subcellular level. In this report, a non-aqueous fractionation method is described that allows subcellular concentrations of metabolites in developing barley endosperm to be calculated. (i) Analysis of subcellular volumes in developing endosperm using micrographs shows that plastids and cytosol occupy 50.5% and 49.9% of the total cell volume, respectively, while vacuoles and mitochondria can be neglected. (ii) By using non-aqueous fractionation, subcellular distribution between the cytosol and plastid of the levels of metabolites involved in sucrose degradation, starch synthesis, and respiration were determined. With the exception of ADP and AMP which were mainly located in the plastid, most other metabolites of carbon and energy metabolism were mainly located outside the plastid in the cytosolic compartment. (iii) In developing barley endosperm, the ultimate precursor of starch, ADPglucose (ADPGlc), was mainly located in the cytosol (80-90%), which was opposite to the situation in growing potato tubers where ADPGlc was almost exclusively located in the plastid (98%). This reflects the different subcellular distribution of ADPGlc pyrophosphorylase (AGPase) in these tissues. (iv) Cytosolic concentrations of ADPGlc were found to be close to the published K(m) values of AGPase and the ADPGlc/ADP transporter at the plastid envelope. Also the concentrations of the reaction partners glucose-1-phosphate, ATP, and inorganic pyrophosphate were close to the respective K(m) values of AGPase. (v) Knock-out of cytosolic AGPase in Riso16 mutants led to a strong decrease in ADPGlc level, in both the cytosol and plastid, whereas knock-down of the ADPGlc/ADP transporter led to a large shift in the intracellular distribution of ADPGlc. (v) The thermodynamic structure of the pathway of sucrose to starch was determined by calculating the mass-action ratios of all the steps in the pathway. The data show that AGPase is close to equilibrium, in both the cytosol and plastid, whereas the ADPGlc/ADP transporter is strongly displaced from equilibrium in vivo. This is in contrast to most other tissues, including leaves and potato tubers. (vi) Results indicate transport rather than synthesis of ADPGlc to be the major regulatory site of starch synthesis in barley endosperm. The reversibility of AGPase in the plastid has important implications for the regulation of carbon partitioning between different biosynthetic pathways.
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Affiliation(s)
- Axel Tiessen
- Departamento de Ingeniería Genética, CINVESTAV, Campus Guanajuato, 36821 Irapuato, México
- Ludwig-Maximilians-Universität München, Department Biologie I, Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
| | - Annika Nerlich
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Golm, Germany
| | - Benjamin Faix
- Ludwig-Maximilians-Universität München, Department Biologie I, Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
| | - Christine Hümmer
- Ludwig-Maximilians-Universität München, Department Biologie I, Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
| | - Simon Fox
- John Innes Centre, Norwich Research Park, Colney, Norwich, UK
| | - Kay Trafford
- John Innes Centre, Norwich Research Park, Colney, Norwich, UK
| | - Hans Weber
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), D-06466 Gatersleben, Germany
| | - Winfriede Weschke
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), D-06466 Gatersleben, Germany
| | - Peter Geigenberger
- Ludwig-Maximilians-Universität München, Department Biologie I, Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
- To whom correspondence should be addressed. E-mail:
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Schudoma C, Steinfath M, Sprenger H, van Dongen JT, Hincha D, Zuther E, Geigenberger P, Kopka J, Köhl K, Walther D. Conducting molecular biomarker discovery studies in plants. Methods Mol Biol 2012; 918:127-150. [PMID: 22893290 DOI: 10.1007/978-1-61779-995-2_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Molecular biomarkers are molecules whose concentrations in a biological system inform about the current phenotypical state and, more importantly, may also be predictive of future phenotypic trait endpoints. The identification of biomarkers has gained much attention in targeted plant breeding since technologies have become available that measure many molecules across different levels of molecular organization and at decreasing costs. In this chapter, we outline the general strategy and workflow of conducting biomarker discovery studies. Critical aspects of study design as well as the statistical data analysis and model building will be highlighted.
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Affiliation(s)
- Christian Schudoma
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
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