Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies

O'Grady, John P.; Schwender, Jörg; Shachar‐Hill, Yair; Morgan, John A.

doi:10.1093/jxb/ers032

Cited by 68 publications

(39 citation statements)

References 106 publications

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“…For nonphotosynthetic lipogenesis, the OPPP had to produce all of the reductant. Accordingly, for sunflower and maize (Zea mays) developing embryos, it was estimated that OPPP produces more than 70% of the NADPH required for fatty acid synthesis (O'Grady et al, 2012). However, besides the literature-postulated role of OPPP to be the predominant source of reductant for biosynthetic processes like lipid synthesis or nitrogen assimilation in nonphotosynthetic tissues, in silico constraint-based analysis of central metabolism in oilseed rape developing seeds allows the efficient conversion of sugars into fatty acids and lipids in the dark without any contribution of OPPP (Hay and Schwender, 2011).…”

Section: Oppp Flux Might Be Important But Of Minor Contribution To Famentioning

confidence: 99%

“…Numerous comparative transcriptome studies of oil-accumulating plant tissues have given important additional insights into the regulation of TAG synthesis (Ruuska et al, 2002;Bourgis et al, 2011;Troncoso-Ponce et al, 2011). Metabolic flux studies with developing seeds have added a quantitative understanding of in vivo pathway usage in oilseeds (O'Grady et al, 2012). To modulate seed oil levels or composition, various attempts have been chosen, mostly relying on introducing specific enzymes (Weselake et al, 2008;Kelly et al, 2013) or metabolite transporters (Fuchs et al, 2013;Kim et al, 2013).…”

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Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

et al. 2015

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Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 39,59-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism.Seeds develop by absorbing nutrients from their mother plant and using these to synthesize a combination of starch, protein, and lipid. The size and number of seeds that finally develop determine the crop's yield, while their composition determines the end-use quality of the crop. The conversion of nutrients into storage products involves a complex network of metabolic reactions, many of which are subject to transcriptional, translational, and posttranslational regulation. Attempting to engineer seed composition clearly requires a firm understanding of these regulatory networks.The seed's central metabolism differs markedly from those of both a photosynthesizing leaf and a root. In most species, the immature seed is green for a period during its development, so during this phase it is regarded as being photoheterotrophic. A further level of complexity arises as a result of spatial heterogeneity within the seed (Rolletschek et al., 2011; Borisjuk et al.,

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Section: Oppp Flux Might Be Important But Of Minor Contribution To Famentioning

confidence: 99%

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confidence: 99%

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

et al. 2015

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“…Unfortunately, intracellular fluxes cannot be measured directly but have to be estimated from concentration measurements. 11,12 Various experimental and associated computational methods have been developed to estimate dynamic fluxes through metabolic networks including kinetic models, 13 13 C-metabolic flux analysis (MFA), [14][15][16] and dynamic flux balance analysis (DFBA). 17,18 The development of kinetic models is hampered by limited availability and accuracy of information about condition-specific (in vivo) kinetic parameters, 19 13 C MFA is expensive and tracer availability is limited.…”

Section: Introductionmentioning

confidence: 99%

MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis

et al. 2015

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. (2015). MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Molecular BioSystems, 11(1), 137-145. DOI: 10.1039/c4mb00510d General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Understanding cellular adaptation to environmental changes is one of the major challenges in systems biology. To understand how cellular systems react towards perturbations of their steady state, the metabolic dynamics have to be described. Dynamic properties can be studied with kinetic models but development of such models is hampered by limited in vivo information, especially kinetic parameters.Therefore, there is a need for mathematical frameworks that use a minimal amount of kinetic information. One of these frameworks is dynamic flux balance analysis (DFBA), a method based on the assumption that cellular metabolism has evolved towards optimal changes to perturbations. However, DFBA has some limitations. It is less suitable for larger systems because of the high number of parameters to estimate and the computational complexity. In this paper, we propose MetDFBA, a modification of DFBA, that incorporates measured time series of both intracellular and extracellular metabolite concentrations, in order to reduce both the number of parameters to estimate and the computational complexity. MetDFBA can be used to estimate dynamic flux profiles and, in addition, test hypotheses about metabolic regulation. In a first case study, we demonstrate the validity of our method by comparing our results to flux estimations based on dynamic 13 C MFA measurements, which we considered as experimental reference. For these estimations time-resolved metabolomics data from a feast-famine experiment with Penicillium chrysogenum was used. In a second case study, we used time-resolved metabolomics data from glucose pulse experiments during aerobic growth of Saccharomyces cerevisiae to test various metabolic objectives.

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“…In the case of plants, it is frequently found that metabolite pools exist in more than one location or that the subcellular location of one or more reactions is uncertain [30]. Entire sections of metabolic pathways like glycolysis are duplicated between organelles, particularly the plastid and cytosol, with both being potentially active and carrying flux [31].…”

Section: Introductionmentioning

confidence: 99%

An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing

Sarkar

Shimizu

2015

Bioresour. Bioprocess.

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Biofuel and biochemical production by photosynthetic microorganisms such as cyanobacteria and algae is attractive to improve energy security and to reduce CO 2 emission, contributing to the environmental problems such as global warming. Although biofuel production by photosynthetic microorganisms is called as the third generation biofuels, and significant innovation is necessary for the feasibility in practice, these fuels are attractive due to renewable and potentially carbon neutral resources. Moreover, photosynthetic microorganisms are attractive since they can grow on non-arable land and utilize saline and wastewater streams. Highly versatile and genetically tractable photosynthetic microorganisms need to capture solar energy and convert atmospheric and waste CO 2 to high-energy chemical products. Understanding of the metabolism and the efficient metabolic engineering of the photosynthetic organisms together with cultivation and separation processes as well as increased CO 2 assimilation enables the enhancement of the feasibility of biofuel and biochemical production.

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Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies

Cited by 68 publications

References 106 publications

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis

An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing

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