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Dynamic metabolic flux analysis of plant cell wall synthesis. Metab Eng 2013; 18:78-85. [DOI: 10.1016/j.ymben.2013.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/14/2013] [Accepted: 04/16/2013] [Indexed: 11/21/2022]
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52
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Collakova E, Aghamirzaie D, Fang Y, Klumas C, Tabataba F, Kakumanu A, Myers E, Heath LS, Grene R. Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos. Metabolites 2013; 3:347-72. [PMID: 24957996 PMCID: PMC3901275 DOI: 10.3390/metabo3020347] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/16/2013] [Accepted: 05/07/2013] [Indexed: 01/08/2023] Open
Abstract
Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.
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Affiliation(s)
- Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
| | - Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA.
| | - Yihui Fang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
| | - Curtis Klumas
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA.
| | | | - Akshay Kakumanu
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA, USA.
| | - Elijah Myers
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA.
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
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53
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Koubaa M, Cocuron JC, Thomasset B, Alonso AP. Highlighting the tricarboxylic acid cycle: liquid and gas chromatography-mass spectrometry analyses of (13)C-labeled organic acids. Anal Biochem 2013; 436:151-9. [PMID: 23399391 DOI: 10.1016/j.ab.2013.01.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 01/01/2023]
Abstract
The tricarboxylic acid (TCA) cycle is involved in the complete oxidation of organic acids to carbon dioxide in aerobic cells. It not only uses the acetyl-CoA derived from glycolysis but also uses breakdown products of proteins, fatty acids, and nucleic acids. Therefore, the TCA cycle involves numerous carbon fluxes through central metabolism to produce reductant power and transfer the generated electrons to the aerobic electron transport system where energy is formed by oxidative phosphorylation. Although the TCA cycle plays a crucial role in aerobic organisms and tissues, the lack of direct isotopic labeling information in its intermediates (organic acids) makes the quantification of its metabolic fluxes rather approximate. This is the major technical gap that this study intended to fill. In this work, we established and validated liquid and gas chromatography-mass spectrometry methods to determine (13)C labeling in organic acids involved in the TCA cycle using scheduled multiple reaction monitoring and single ion monitoring modes, respectively. Labeled samples were generated using maize embryos cultured with [(13)C]glucose or [(13)C]glutamine. Once steady-state labeling was reached, (13)C-labeled organic acids were extracted and purified. When applying our mass spectrometric methods to those extracts, mass isotopomer abundances of seven major organic acids were successfully determined.
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Affiliation(s)
- Mohamed Koubaa
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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54
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Antoniewicz MR. Tandem mass spectrometry for measuring stable-isotope labeling. Curr Opin Biotechnol 2013; 24:48-53. [DOI: 10.1016/j.copbio.2012.10.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 10/02/2012] [Accepted: 10/16/2012] [Indexed: 12/31/2022]
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Wang Y, Mortimer JC, Davis J, Dupree P, Keegstra K. Identification of an additional protein involved in mannan biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:105-17. [PMID: 22966747 PMCID: PMC3558879 DOI: 10.1111/tpj.12019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/24/2012] [Accepted: 09/07/2012] [Indexed: 05/18/2023]
Abstract
Galactomannans comprise a β-1,4-mannan backbone substituted with α-1,6-galactosyl residues. Genes encoding the enzymes that are primarily responsible for backbone synthesis and side-chain addition of galactomannans were previously identified and characterized. To identify additional genes involved in galactomannan biosynthesis, we previously performed deep EST profiling of fenugreek (Trigonella foenum-graecum L.) seed endosperm, which accumulates large quantities of galactomannans as a reserve carbohydrate during seed development. One of the candidate genes encodes a protein that is likely to be a glycosyltransferase. Because this protein is involved in mannan biosynthesis, we named it 'mannan synthesis-related' (MSR). Here, we report the characterization of a fenugreek MSR gene (TfMSR) and its two Arabidopsis homologs, AtMSR1 and AtMSR2. TfMSR was highly and specifically expressed in the endosperm. TfMSR, AtMSR1 and AtMSR2 proteins were all determined to be localized to the Golgi by fluorescence confocal microscopy. The level of mannosyl residues in stem glucomannans decreased by approximately 40% for Arabidopsis msr1 single T-DNA insertion mutants and by more than 50% for msr1 msr2 double mutants, but remained unchanged for msr2 single mutants. In addition, in vitro mannan synthase activity from the stems of msr1 single and msr1 msr2 double mutants also decreased. Expression of AtMSR1 or AtMSR2 in the msr1 msr2 double mutant completely or partially restored mannosyl levels. From these results, we conclude that the MSR protein is important for mannan biosynthesis, and offer some ideas about its role.
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Affiliation(s)
- Yan Wang
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
| | | | - Jonathan Davis
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Paul Dupree
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Kenneth Keegstra
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- *For correspondence (e-mail )
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56
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Neveling DP, Endo A, Dicks LMT. Fructophilic Lactobacillus kunkeei and Lactobacillus brevis isolated from fresh flowers, bees and bee-hives. Curr Microbiol 2012; 65:507-15. [PMID: 22797888 DOI: 10.1007/s00284-012-0186-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/26/2012] [Indexed: 11/26/2022]
Abstract
Two-hundred-and-thirty-six isolates were collected from fresh flowers, bees and bee-hives. Of these, 20 isolates preferred D-fructose as carbon source, produced lactic acid and acetic acid but trace amounts of ethanol and were classified as fructophilic. Poor growth was recorded when strains were incubated anaerobically in the presence of D-glucose as sole carbon source. Good growth was, however, recorded when D-glucose was metabolized in the presence of external electron acceptors such as fructose, pyruvate and oxygen. Nineteen of the strains were classified as Lactobacillus kunkeei and one as Lactobacillus brevis based on phenotypic characteristics, 16S rRNA sequences, recA sequences and DNA homology. This is the first description of a fructophilic strain of L. brevis.
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Affiliation(s)
- Deon P Neveling
- Department of Microbiology, University of Stellenbosch, Matieland, Stellenbosch 7602, South Africa
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57
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Farré EM, Weise SE. The interactions between the circadian clock and primary metabolism. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:293-300. [PMID: 22305520 DOI: 10.1016/j.pbi.2012.01.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/11/2012] [Accepted: 01/11/2012] [Indexed: 05/26/2023]
Abstract
Primary metabolism in plants is tightly regulated by environmental factors such as light and nutrient availability at multiple levels. The circadian clock is a self-sustained endogenous oscillator that enables organisms to predict daily and seasonal changes. The regulation of primary metabolism by the circadian clock has been proposed to explain the importance of circadian rhythms in plant growth and survival. Recent transcriptomic and metabolomic analyses indicate a wide spread circadian regulation of different metabolic processes. We review evidence of circadian regulation of pathways in primary metabolism, discuss the challenges faced for discerning the mechanisms regulating circadian metabolic oscillations and present recent evidence of regulation of the circadian clock by metabolites.
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Affiliation(s)
- Eva M Farré
- Michigan State University, Department of Plant Biology, East Lansing, MI 48824, USA.
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58
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Wang Y, Alonso AP, Wilkerson CG, Keegstra K. Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation. PLANT MOLECULAR BIOLOGY 2012; 79:243-58. [PMID: 22527750 PMCID: PMC3349874 DOI: 10.1007/s11103-012-9909-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 03/28/2012] [Indexed: 05/23/2023]
Abstract
Galactomannans are hemicellulosic polysaccharides composed of a (1 → 4)-linked β-D-mannan backbone substituted with single-unit (1 → 6)-α-linked D-galactosyl residues. Developing fenugreek (Trigonella foenum-graecum) seeds are known to accumulate large quantities of galactomannans in the endosperm, and were thus used here as a model system to better understand galactomannan biosynthesis and its regulation. We first verified the specific deposition of galactomannans in developing endosperms and determined that active accumulation occurred from 25 to 38 days post anthesis (DPA) under our growth conditions. We then examined the expression levels during seed development of ManS and GMGT, two genes encoding backbone and side chain synthetic enzymes. Based on transcript accumulation dynamics for ManS and GMGT, cDNA libraries were constructed using RNA isolated from endosperms at four ages corresponding to before, at the beginning of, and during active galactomannan deposition. DNA from these libraries was sequenced using the 454 sequencing technology to yield a total of 1.5 million expressed sequence tags (ESTs). Through analysis of the EST profiling data, we identified genes known to be involved in galactomannan biosynthesis, as well as new genes that may be involved in this process, and proposed a model for the flow of carbon from sucrose to galactomannans. Measurement of in vitro ManS and GMGT activities and analysis of sugar phosphate and nucleotide sugar levels in the endosperms of developing fenugreek seeds provided data consistent with this model. In vitro enzymatic assays also revealed that the ManS enzyme from fenugreek endosperm preferentially used GDP-mannose as the substrate for the backbone synthesis.
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Affiliation(s)
- Yan Wang
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Ana P. Alonso
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Present Address: Department of Molecular Genetics, Ohio State University, Columbus, OH 43210 USA
| | - Curtis G. Wilkerson
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Kenneth Keegstra
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
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59
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Yang Z, Drew DP, Jørgensen B, Mandel U, Bach SS, Ulvskov P, Levery SB, Bennett EP, Clausen H, Petersen BL. Engineering mammalian mucin-type O-glycosylation in plants. J Biol Chem 2012; 287:11911-23. [PMID: 22334671 PMCID: PMC3320939 DOI: 10.1074/jbc.m111.312918] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/16/2012] [Indexed: 11/06/2022] Open
Abstract
Mucin-type O-glycosylation is an important post-translational modification that confers a variety of biological properties and functions to proteins. This post-translational modification has a particularly complex and differentially regulated biosynthesis rendering prediction and control of where O-glycans are attached to proteins, and which structures are formed, difficult. Because plants are devoid of GalNAc-type O-glycosylation, we have assessed requirements for establishing human GalNAc O-glycosylation de novo in plants with the aim of developing cell systems with custom-designed O-glycosylation capacity. Transient expression of a Pseudomonas aeruginosa Glc(NAc) C4-epimerase and a human polypeptide GalNAc-transferase in leaves of Nicotiana benthamiana resulted in GalNAc O-glycosylation of co-expressed human O-glycoprotein substrates. A chimeric YFP construct containing a 3.5 tandem repeat sequence of MUC1 was glycosylated with up to three and five GalNAc residues when co-expressed with GalNAc-T2 and a combination of GalNAc-T2 and GalNAc-T4, respectively, as determined by mass spectrometry. O-Glycosylation was furthermore demonstrated on a tandem repeat of MUC16 and interferon α2b. In plants, prolines in certain classes of proteins are hydroxylated and further substituted with plant-specific O-glycosylation; unsubstituted hydroxyprolines were identified in our MUC1 construct. In summary, this study demonstrates that mammalian type O-glycosylation can be established in plants and that plants may serve as a host cell for production of recombinant O-glycoproteins with custom-designed O-glycosylation. The observed hydroxyproline modifications, however, call for additional future engineering efforts.
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Affiliation(s)
- Zhang Yang
- From the Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | | | - Bodil Jørgensen
- Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark, and
| | - Ulla Mandel
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Søren S. Bach
- the Department of Plant Biology and Biotechnology and
| | - Peter Ulvskov
- the Department of Plant Biology and Biotechnology and
| | - Steven B. Levery
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Eric P. Bennett
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
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60
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Koubaa M, Mghaieth S, Thomasset B, Roscher A. Gas chromatography-mass spectrometry analysis of 13C labeling in sugars for metabolic flux analysis. Anal Biochem 2012; 425:183-8. [PMID: 22475504 DOI: 10.1016/j.ab.2012.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 03/25/2012] [Accepted: 03/26/2012] [Indexed: 01/29/2023]
Abstract
Metabolic flux analysis, using 13C labeled substrates, has become a powerful methodology for quantifying intracellular fluxes. Most often, analysis is restricted to nuclear magnetic resonance or mass spectrometry measurement of 13C label incorporation into protein amino acids. However, amino acid isotopomer distribution insufficiently covers the entire network of central metabolism, especially in plant cells with highly compartmented metabolism, and analysis of other metabolites is required. Analysis of label in saccharides provides complementary data to better define fluxes around hexose, pentose, and triose phosphate pools. Here, we propose a gas chromatography-mass spectrometry (GC-MS) method to analyze 13C labeling in glucose and fructose moieties of sucrose, free glucose, fructose, maltose, inositol, and starch. Our results show that saccharide labeling for isotopomer quantification is better analyzed by chemical ionization than by electron ionization. The structure of the generated fragments was simulated and validated using labeled standards. The method is illustrated by analysis of saccharides extracted from developing rapeseed (Brassica napus L.) embryos. It is shown that glucose 6-phosphate isomerase and plastidial glucose 6-phosphate transport reactions are not at equilibrium, and light is shed on the pathways leading to fructose, maltose, and inositol synthesis.
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Affiliation(s)
- Mohamed Koubaa
- Génie Enzymatique et Cellulaire, UMR CNRS 6022, Université de Technologie de Compiègne, 60205 Compiègne Cedex, France
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61
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Kruger NJ, Masakapalli SK, Ratcliffe RG. Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2309-23. [PMID: 22140245 DOI: 10.1093/jxb/err382] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Steady-state (13)C metabolic flux analysis (MFA) is currently the experimental method of choice for generating flux maps of the compartmented network of primary metabolism in heterotrophic and mixotrophic plant tissues. While statistically robust protocols for the application of steady-state MFA to plant tissues have been developed by several research groups, the implementation of the method is still far from routine. The effort required to produce a flux map is more than justified by the information that it contains about the metabolic phenotype of the system, but it remains the case that steady-state MFA is both analytically and computationally demanding. This article provides an overview of principles that underpin the implementation of steady-state MFA, focusing on the definition of the metabolic network responsible for redistribution of the label, experimental considerations relating to data collection, the modelling process that allows a set of metabolic fluxes to be deduced from the labelling data, and the interpretation of flux maps. The article draws on published studies of Arabidopsis cell cultures and other systems, including developing oilseeds, with the aim of providing practical guidance and strategies for handling the issues that arise when applying steady-state MFA to the complex metabolic networks encountered in plants.
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Affiliation(s)
- N J Kruger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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62
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O'Grady J, Schwender J, Shachar-Hill Y, Morgan JA. Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2293-308. [PMID: 22371075 DOI: 10.1093/jxb/ers032] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (13)CO(2) dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.
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Affiliation(s)
- John O'Grady
- School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
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63
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Tjellström H, Yang Z, Allen DK, Ohlrogge JB. Rapid kinetic labeling of Arabidopsis cell suspension cultures: implications for models of lipid export from plastids. PLANT PHYSIOLOGY 2012; 158:601-11. [PMID: 22128138 PMCID: PMC3271753 DOI: 10.1104/pp.111.186122] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/22/2011] [Indexed: 05/18/2023]
Abstract
Cell cultures allow rapid kinetic labeling experiments that can provide information on precursor-product relationships and intermediate pools. T-87 suspension cells are increasingly used in Arabidopsis (Arabidopsis thaliana) research, but there are no reports describing their lipid composition or biosynthesis. To facilitate application of T-87 cells for analysis of glycerolipid metabolism, including tests of gene functions, we determined composition and accumulation of lipids of light- and dark-grown cultures. Fatty acid synthesis in T-87 cells was 7- to 8-fold higher than in leaves. Similar to other plant tissues, phosphatidylcholine (PC) and phosphatidylethanolamine were major phospholipids, but galactolipid levels were 3- to 4-fold lower than Arabidopsis leaves. Triacylglycerol represented 10% of total acyl chains, a greater percentage than in most nonseed tissues. The initial steps in T-87 cell lipid assembly were evaluated by pulse labeling cultures with [(14)C]acetate and [(14)C]glycerol. [(14)C]acetate was very rapidly incorporated into PC, preferentially at sn-2 and without an apparent precursor-product relationship to diacylglycerol (DAG). By contrast, [(14)C]glycerol most rapidly labeled DAG. These results indicate that acyl editing of PC is the major pathway for initial incorporation of fatty acids into glycerolipids of cells derived from a 16:3 plant. A very short lag time (5.4 s) for [(14)C]acetate labeling of PC implied channeled incorporation of acyl chains without mixing with the bulk acyl-CoA pool. Subcellular fractionation of pea (Pisum sativum) leaf protoplasts indicated that 30% of lysophosphatidylcholine acyltransferase activity colocalized with chloroplasts. Together, these data support a model in which PC participates in trafficking of newly synthesized acyl chains from plastids to the endoplasmic reticulum.
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64
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Reboul R, Tenhaken R. An emerging role of pectic rhamnogalacturonanII for cell wall integrity. PLANT SIGNALING & BEHAVIOR 2012; 7:298-9. [PMID: 22353862 PMCID: PMC3405716 DOI: 10.4161/psb.18894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The plant cell wall is a complex network of different polysaccharides and glycoproteins, showing high diversity in nature. The essential components, tethering cell wall are under debate, as novel mutants challenge established models. The mutant ugd2,3 with a reduced supply of the important wall precursor UDP-glucuronic acid reveals the critical role of the pectic compound rhamnogalacturonanII for cell wall stability. This polymer seems to be more important for cell wall integrity than the previously favored xyloglucan.
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65
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Araújo WL, Nunes-Nesi A, Williams TCR. Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions. FRONTIERS IN PLANT SCIENCE 2012; 3:210. [PMID: 22973288 PMCID: PMC3434416 DOI: 10.3389/fpls.2012.00210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/20/2012] [Indexed: 05/10/2023]
Abstract
The application of post-genomic techniques in plant respiration studies has greatly improved our ability to assign functions to gene products. In addition it has also revealed previously unappreciated interactions between distal elements of metabolism. Such results have reinforced the need to consider plant respiratory metabolism as part of a complex network and making sense of such interactions will ultimately require the construction of predictive and mechanistic models. Transcriptomics, proteomics, metabolomics, and the quantification of metabolic flux will be of great value in creating such models both by facilitating the annotation of complex gene function, determining their structure and by furnishing the quantitative data required to test them. In this review, we highlight how these experimental approaches have contributed to our current understanding of plant respiratory metabolism and its interplay with associated process (e.g., photosynthesis, photorespiration, and nitrogen metabolism). We also discuss how data from these techniques may be integrated, with the ultimate aim of identifying mechanisms that control and regulate plant respiration and discovering novel gene functions with potential biotechnological implications.
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Affiliation(s)
- Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, ViçosaBrazil
- *Correspondence: Wagner L. Araújo, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, Brazil. e-mail:
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, ViçosaBrazil
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, ViçosaBrazil
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66
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Strasser R. Challenges in O-glycan engineering of plants. FRONTIERS IN PLANT SCIENCE 2012; 3:218. [PMID: 23015807 PMCID: PMC3449291 DOI: 10.3389/fpls.2012.00218] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/02/2012] [Indexed: 05/20/2023]
Abstract
Plants are attractive alternative expression hosts for the production of recombinant proteins. Many therapeutic proteins are glycosylated with N- and O-glycosylation being the most prevalent forms of protein glycosylation. While N-glycans have already been modified in plants toward the formation of homogenous mammalian-type glycoforms with equal or improved biological function compared to mammalian-cell culture produced glycoproteins little attention has been paid to the modification of O-linked glycans. Recently, the first step of mammalian O-glycan biosynthesis has been accomplished in plants. However, as outlined in this short review there are important issues that have to be addressed in the future. These include: (i) elimination of potentially immunogenic or allergenic carbohydrate epitopes containing arabinosides or arabinogalactans, (ii) a detailed investigation of the interplay between engineered N- and O-glycosylation pathways to avoid competition for common metabolites like UDP-GlcNAc, and (iii) a deeper understanding of signals and mechanisms for distribution of glycan processing enzymes, which is a prerequisite for complete and homogenous glycosylation of recombinant proteins.
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Affiliation(s)
- Richard Strasser
- *Correspondence: Richard Strasser, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria. e-mail:
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Bar-Peled M, O'Neill MA. Plant nucleotide sugar formation, interconversion, and salvage by sugar recycling. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:127-55. [PMID: 21370975 DOI: 10.1146/annurev-arplant-042110-103918] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleotide sugars are the universal sugar donors for the formation of polysaccharides, glycoproteins, proteoglycans, glycolipids, and glycosylated secondary metabolites. At least 100 genes encode proteins involved in the formation of nucleotide sugars. These nucleotide sugars are formed using the carbohydrate derived from photosynthesis, the sugar generated by hydrolyzing translocated sucrose, the sugars released from storage carbohydrates, the salvage of sugars from glycoproteins and glycolipids, the recycling of sugars released during primary and secondary cell wall restructuring, and the sugar generated during plant-microbe interactions. Here we emphasize the importance of the salvage of sugars released from glycans for the formation of nucleotide sugars. We also outline how recent studies combining biochemical, genetic, molecular and cellular approaches have led to an increased appreciation of the role nucleotide sugars in all aspects of plant growth and development. Nevertheless, our understanding of these pathways at the single cell level is far from complete.
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Affiliation(s)
- Maor Bar-Peled
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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Chen X, Alonso AP, Allen DK, Reed JL, Shachar-Hill Y. Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. Metab Eng 2010; 13:38-48. [PMID: 21129495 DOI: 10.1016/j.ymben.2010.11.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 10/20/2010] [Accepted: 11/16/2010] [Indexed: 01/28/2023]
Abstract
Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and ¹³C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes.
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Affiliation(s)
- Xuewen Chen
- Department of Plant Biology, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis. Biochem J 2010; 430:275-84. [PMID: 20557289 DOI: 10.1042/bj20100315] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
UDP-GlcNAc is an essential precursor for glycoprotein and glycolipid synthesis. In the present study, a functional nucleotidyltransferase gene from Arabidopsis encoding a 58.3 kDa GlcNAc1pUT-1 (N-acetylglucosamine-1-phosphate uridylyltransferase) was identified. In the forward reaction the enzyme catalyses the formation of UDP-N-acetylglucosamine and PPi from the respective monosaccharide 1-phosphate and UTP. The enzyme can utilize the 4-epimer UDP-GalNAc as a substrate as well. The enzyme requires divalent ions (Mg2+ or Mn2+) for activity and is highly active between pH 6.5 and 8.0, and at 30-37 degrees C. The apparent Km values for the forward reaction were 337 microM (GlcNAc-1-P) and 295 microM (UTP) respectively. Another GlcNAc1pUT-2, which shares 86% amino acid sequence identity with GlcNAc1pUT-1, was found to convert, in addition to GlcNAc-1-P and GalNAc-1-P, Glc-1-P into corresponding UDP-sugars, suggesting that subtle changes in the UT family cause different substrate specificities. A three-dimensional protein structure model using the human AGX1 as template showed a conserved catalytic fold and helped identify key conserved motifs, despite the high sequence divergence. The identification of these strict and promiscuous gene products open a window to identify new roles of amino sugar metabolism in plants and specifically their role as signalling molecules. The ability of GlcNAc1pUT-2 to utilize three different substrates may provide further understanding as to why biological systems have plasticity.
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