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      Metabolite pools and carbon flow during C 4 photosynthesis in maize: 13CO 2 labeling kinetics and cell type fractionation

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          Abstract

          Analysis of labeling kinetics, pool sizes, and concentration gradients of metabolites reveals the operation of multiple decarboxylation pathways and rapid movement of carbon between the Calvin–Benson cycle and the CO 2-concentrating shuttles in maize.

          Abstract

          Worldwide efforts to engineer C 4 photosynthesis into C 3 crops require a deep understanding of how this complex pathway operates. CO 2 is incorporated into four-carbon metabolites in the mesophyll, which move to the bundle sheath where they are decarboxylated to concentrate CO 2 around RuBisCO. We performed dynamic 13CO 2 labeling in maize to analyze C flow in C 4 photosynthesis. The overall labeling kinetics reflected the topology of C 4 photosynthesis. Analyses of cell-specific labeling patterns after fractionation to enrich bundle sheath and mesophyll cells revealed concentration gradients to drive intercellular diffusion of malate, but not pyruvate, in the major CO 2-concentrating shuttle. They also revealed intercellular concentration gradients of aspartate, alanine, and phosph enolpyruvate to drive a second phospho enolpyruvate carboxykinase (PEPCK)-type shuttle, which carries 10–14% of the carbon into the bundle sheath. Gradients also exist to drive intercellular exchange of 3-phosphoglycerate and triose-phosphate. There is rapid carbon exchange between the Calvin–Benson cycle and the CO 2-concentrating shuttle, equivalent to ~10% of carbon gain. In contrast, very little C leaks from the large pools of metabolites in the C concentration shuttle into respiratory metabolism. We postulate that the presence of multiple shuttles, alongside carbon transfer between them and the Calvin–Benson cycle, confers great flexibility in C 4 photosynthesis.

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          Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements.

          Metabolic fluxes, estimated from stable isotope studies, provide a key to quantifying physiology in fields ranging from metabolic engineering to the analysis of human metabolic diseases. A serious drawback of the flux estimation method in current use is that it does not produce confidence limits for the estimated fluxes. Without this information it is difficult to interpret flux results and expand the physiological significance of flux studies. To address this shortcoming we derived analytical expressions of flux sensitivities with respect to isotope measurements and measurement errors. These tools allow the determination of local statistical properties of fluxes and relative importance of measurements. Furthermore, we developed an efficient algorithm to determine accurate flux confidence intervals and demonstrated that confidence intervals obtained with this method closely approximate true flux uncertainty. In contrast, confidence intervals approximated from local estimates of standard deviations are inappropriate due to inherent system nonlinearities. We applied these methods to analyze the statistical significance and confidence of estimated gluconeogenesis fluxes from human studies with [U-13C]glucose as tracer and found true limits for flux estimation in specific human isotopic protocols.
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            A Robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness.

            A platform has been developed to measure the activity of 23 enzymes that are involved in central carbon and nitrogen metabolism in Arabidopsis thaliana. Activities are assayed in optimized stopped assays and the product then determined using a suite of enzyme cycling assays. The platform requires inexpensive equipment, is organized in a modular manner to optimize logistics, calculates results automatically, combines high sensitivity with throughput, can be robotized, and has a throughput of three to four activities in 100 samples per person/day. Several of the assays, including those for sucrose phosphate synthase, ADP glucose pyrophosphorylase (AGPase), ferredoxin-dependent glutamate synthase, glycerokinase, and shikimate dehydrogenase, provide large advantages over previous approaches. This platform was used to analyze the diurnal changes of enzyme activities in wild-type Columbia-0 (Col-0) and the starchless plastid phosphoglucomutase (pgm) mutant, and in Col-0 during a prolongation of the night. The changes of enzyme activities were compared with the changes of transcript levels determined with the Affymetrix ATH1 array. Changes of transcript levels typically led to strongly damped changes of enzyme activity. There was no relation between the amplitudes of the diurnal changes of transcript and enzyme activity. The largest diurnal changes in activity were found for AGPase and nitrate reductase. Examination of the data and comparison with the literature indicated that these are mainly because of posttranslational regulation. The changes of enzyme activity are also strongly delayed, with the delay varying from enzyme to enzyme. It is proposed that enzyme activities provide a quasi-stable integration of regulation at several levels and provide useful data for the characterization and diagnosis of different physiological states. As an illustration, a decision tree constructed using data from Col-0 during diurnal changes and a prolonged dark treatment was used to show that, irrespective of the time of harvest during the diurnal cycle, the pgm mutant resembles a wild-type plant that has been exposed to a 3 d prolongation of the night.
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              Metabolic fluxes in an illuminated Arabidopsis rosette.

              Photosynthesis is the basis for life, and its optimization is a key biotechnological aim given the problems of population explosion and environmental deterioration. We describe a method to resolve intracellular fluxes in intact Arabidopsis thaliana rosettes based on time-dependent labeling patterns in the metabolome. Plants photosynthesizing under limiting irradiance and ambient CO2 in a custom-built chamber were transferred into a (13)CO2-enriched environment. The isotope labeling patterns of 40 metabolites were obtained using liquid or gas chromatography coupled to mass spectrometry. Labeling kinetics revealed striking differences between metabolites. At a qualitative level, they matched expectations in terms of pathway topology and stoichiometry, but some unexpected features point to the complexity of subcellular and cellular compartmentation. To achieve quantitative insights, the data set was used for estimating fluxes in the framework of kinetic flux profiling. We benchmarked flux estimates to four classically determined flux signatures of photosynthesis and assessed the robustness of the estimates with respect to different features of the underlying metabolic model and the time-resolved data set.
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                Author and article information

                Journal
                J Exp Bot
                J. Exp. Bot
                exbotj
                Journal of Experimental Botany
                Oxford University Press (UK )
                0022-0957
                1460-2431
                21 January 2017
                07 November 2016
                07 November 2016
                : 68
                : 2 , Special Issue: C4 Photosynthesis: 50 Years of Discovery and Innovation
                : 283-298
                Affiliations
                Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
                Author notes

                These authors contributed equally to this work.

                Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.

                Article
                erw414
                10.1093/jxb/erw414
                5853532
                27834209
                7b15ae56-413c-4fd5-834f-933bdecebcd0
                © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 24 June 2016
                : 18 October 2016
                Page count
                Pages: 16
                Funding
                Funded by: European Commission 10.13039/501100000780
                Award ID: 289582
                Categories
                Research Paper

                Plant science & Botany
                13c labeling,c4 photosynthesis,carbon flow,co2-concentrating shuttle,maize
                Plant science & Botany
                13c labeling, c4 photosynthesis, carbon flow, co2-concentrating shuttle, maize

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