Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose

Visualizing 13C-Labeled Metabolites in Maize Root Tips with Mass Spectrometry Imaging

Tracing in vivo isotope-labeled metabolites has been used to study metabolic pathways or flux analysis. However, metabolic differences between the cells have been often ignored in these studies due to the limitation of solvent-based extraction. Here we demonstrate that the mass spectrometry imaging of in vivo isotope-labeled metabolites, referred to as MSIi, can provide important insights into metabolic dynamics with cellular resolution that may supplement the traditional metabolomics and flux analysis. Developing maize root tips are adopted as a model system for MSIi by supplementing 200 mM [U-13C]glucose in 0.1x Hoagland medium. MSIi data sets were acquired for longitudinal sections of newly grown maize root tips after growing 5 days in the medium. A total of 56 metabolite features were determined to have been 13C-labeled based on accurate mass and the number of carbon matching with the metabolite databases. Simple sugars and their derivatives were fully labeled, but some small metabolites were partially labeled with a significant amount of fully unlabeled metabolites still present, suggesting the recycling of "old" metabolites in the newly grown tissues. Some distinct localizations were found, including the low abundance of hexose and its derivatives in the meristem, the high abundance of amino acids in the meristem, and the localization to epidermal and endodermal cells for lipids and their intermediates. Fatty acids and lipids were slow in metabolic turnover and showed various isotopologue distributions with intermediate building blocks, which may provide flux information for their biosynthesis.

Metabolic evidence for distinct pyruvate pools inside plant mitochondria

The majority of the pyruvate inside plant mitochondria is either transported into the matrix from the cytosol via the mitochondria pyruvate carrier (MPC) or synthesized in the matrix by alanine aminotransferase (AlaAT) or NAD-malic enzyme (NAD-ME). Pyruvate from these origins could mix into a single pool in the matrix and contribute indistinguishably to respiration via the pyruvate dehydrogenase complex (PDC), or these molecules could maintain a degree of independence in metabolic regulation. Here we demonstrate that feeding isolated mitochondria with uniformly labelled ¹³C-pyruvate and unlabelled malate enables the assessment of pyruvate contribution from different sources to intermediate production in the tricarboxylic acid cycle. Imported pyruvate was the preferred source for citrate production even when the synthesis of NAD-ME-derived pyruvate was optimized. Genetic or pharmacological elimination of MPC activity removed this preference and allowed an equivalent amount of citrate to be generated from the pyruvate produced by NAD-ME. Increasing the mitochondrial pyruvate pool size by exogenous addition affected only metabolites from pyruvate transported by MPC, whereas depleting the pyruvate pool size by transamination to alanine affected only metabolic products derived from NAD-ME. PDC was more membrane-associated than AlaAT and NAD-ME, suggesting that the physical organization of metabolic machinery may influence metabolic rates. Together, these data reveal that the respiratory substrate supply in plants involves distinct pyruvate pools inside the matrix that can be flexibly mixed on the basis of the rate of pyruvate transport from the cytosol. These pools are independently regulated and contribute differentially to organic acid export from plant mitochondria.

Transcriptomic responses to phosphorus in an invasive cyanobacterium, Raphidiopsis raciborskii: Implications for nutrient management

Phosphorus (P) is a vital macronutrient associated with the growth and proliferation of Raphidiopsis raciborskii, an invasive and notorious bloom-forming cyanobacterium. However, the molecular mechanisms involved in P acclimation remain largely unexplored for Raphidiopsis raciborskii. Here, transcriptome sequencing of Raphidiopsis raciborskii was conducted to reveal multifaceted mechanisms involved in mimicking dipotassium phosphate (DIP), β-glycerol phosphate (Gly), 2-aminoethylphosphonic acid (AEP), and P-free conditions (NP). Chlorophyll a fluorescence parameters showed significant differences in the NP and AEP groups compared with the DIP and Gly-groups. Expression levels of genes related to phosphate transportation and uptake, organic P utilization, nitrogen metabolism, urea cycling, carbon fixation, amino acid metabolism, environmental information, the ATP-synthesis process in glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway were remarkably upregulated, while those related to photosynthesis, phycobiliproteins, respiration, oxidative phosphorylation, sulfur metabolism, and genetic information were markedly downregulated in the NP group relative to the DIP group. However, the expression of genes involved in organic P utilization, the urea cycle, and genetic information in the Gly-group, and carbon-phosphorus lyase, genetic information and environmental information in the AEP group were significantly increased compared to the DIP group. Together, these results indicate that Raphidiopsis raciborskii exhibits the evolution of coordination of multiple metabolic pathways and certain key genes to adapt to ambient P changes, which implies that if P is reduced to control Raphidiopsis raciborskii bloom, there is a risk that external nutrients (such as nitrogen, amino acids, and urea) will stimulate the growth or metabolism of Raphidiopsis.

Sugar modulation of anaerobic-response networks in maize root tips

Sugar supply is a key component of hypoxia tolerance and acclimation in plants. However, a striking gap remains in our understanding of mechanisms governing sugar impacts on low-oxygen responses. Here, we used a maize (Zea mays) root-tip system for precise control of sugar and oxygen levels. We compared responses to oxygen (21 and 0.2%) in the presence of abundant versus limited glucose supplies (2.0 and 0.2%). Low-oxygen reconfigured the transcriptome with glucose deprivation enhancing the speed and magnitude of gene induction for core anaerobic proteins (ANPs). Sugar supply also altered profiles of hypoxia-responsive genes carrying G4 motifs (sources of regulatory quadruplex structures), revealing a fast, sugar-independent class followed more slowly by feast-or-famine-regulated G4 genes. Metabolite analysis showed that endogenous sugar levels were maintained by exogenous glucose under aerobic conditions and demonstrated a prominent capacity for sucrose re-synthesis that was undetectable under hypoxia. Glucose abundance had distinctive impacts on co-expression networks associated with ANPs, altering network partners and aiding persistence of interacting networks under prolonged hypoxia. Among the ANP networks, two highly interconnected clusters of genes formed around Pyruvate decarboxylase 3 and Glyceraldehyde-3-phosphate dehydrogenase 4. Genes in these clusters shared a small set of cis-regulatory elements, two of which typified glucose induction. Collective results demonstrate specific, previously unrecognized roles of sugars in low-oxygen responses, extending from accelerated onset of initial adaptive phases by starvation stress to maintenance and modulation of co-expression relationships by carbohydrate availability.

Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis

Pennycress (Thlaspi arvense L.) accumulates oil up to 35% of the total seed biomass, and its overall fatty acid composition is suitable for aviation fuel. However, for this plant to become economically viable, its oil production needs to be improved. In vivo culture conditions that resemble the development of pennycress embryos in planta were developed based on the composition of the liquid endosperm. Then, substrate uptake rates and biomass accumulation were measured from cultured pennycress embryos, revealing a biosynthetic efficiency of 93%, which is one of the highest in comparison with other oilseeds to date. Additionally, the ratio of carbon in oil to CO2 indicated that non-conventional pathways are likely to be responsible for such a high carbon conversion efficiency. To identify the reactions enabling this phenomenon, parallel labeling experiments with 13C-labeled substrates were conducted in pennycress embryos. The main findings of these labeling experiments include: (i) the occurrence of the oxidative reactions of the pentose phosphate pathway in the cytosol; (ii) the reversibility of isocitrate dehydrogenase; (iii) the operation of the plastidic NADP-dependent malic enzyme; and (iv) the refixation of CO2 by Rubisco. These reactions are key providers of carbon and reductant for fatty acid synthesis and elongation.

Liquid Chromatography Tandem Mass Spectrometry Quantification of 13C-Labeling in Sugars

Subcellular compartmentation has been challenging in plant ¹³C-metabolic flux analysis. Indeed, plant cells are highly compartmented: they contain vacuoles and plastids in addition to the regular organelles found in other eukaryotes. The distinction of reactions between compartments is possible when metabolites are synthesized in a particular compartment or by a unique pathway. Sucrose is an example of such a metabolite: it is specifically produced in the cytosol from glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). Therefore, determining the ¹³C-labeling in the fructosyl and glucosyl moieties of sucrose directly informs about the labeling of cytosolic F6P and G6P, respectively. To date, the most commonly used method to monitor sucrose labeling is by nuclear magnetic resonance, which requires substantial amounts of biological sample. This study describes a new methodology that accurately measures the labeling in free sugars using liquid chromatography tandem mass spectrometry (LC-MS/MS). For this purpose, maize embryos were pulsed with [U-¹³C]-fructose, intracellular sugars were extracted, and their time-course labeling was analyzed by LC-MS/MS. Additionally, extracts were enzymatically treated with hexokinase to remove the soluble hexoses, and then invertase to cleave sucrose into fructose and glucose. Finally, the labeling in the glucosyl and fructosyl moieties of sucrose was determined by LC-MS/MS.

Plant metabolism as studied by NMR spectroscopy

The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.

Fluxomics links cellular functional analyses to whole-plant phenotyping

Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding.

Genetic and isotope ratio mass spectrometric evidence for the occurrence of starch degradation and cycling in illuminated Arabidopsis leaves

Although there is a great wealth of data supporting the occurrence of simultaneous synthesis and breakdown of storage carbohydrate in many organisms, previous ¹³CO₂ pulse-chase based studies indicated that starch degradation does not operate in illuminated Arabidopsis leaves. Here we show that leaves of gwd, sex4, bam4, bam1/bam3 and amy3/isa3/lda starch breakdown mutants accumulate higher levels of starch than wild type (WT) leaves when cultured under continuous light (CL) conditions. We also show that leaves of CL grown dpe1 plants impaired in the plastidic disproportionating enzyme accumulate higher levels of maltotriose than WT leaves, the overall data providing evidence for the occurrence of extensive starch degradation in illuminated leaves. Moreover, we show that leaves of CL grown mex1/pglct plants impaired in the chloroplastic maltose and glucose transporters display a severe dwarf phenotype and accumulate high levels of maltose, strongly indicating that the MEX1 and pGlcT transporters are involved in the export of starch breakdown products to the cytosol to support growth during illumination. To investigate whether starch breakdown products can be recycled back to starch during illumination through a mechanism involving ADP-glucose pyrophosphorylase (AGP) we conducted kinetic analyses of the stable isotope carbon composition (δ¹³C) in starch of leaves of ¹³CO₂ pulsed-chased WT and AGP lacking aps1 plants. Notably, the rate of increase of δ¹³C in starch of aps1 leaves during the pulse was exceedingly higher than that of WT leaves. Furthermore, δ¹³C decline in starch of aps1 leaves during the chase was much faster than that of WT leaves, which provides strong evidence for the occurrence of AGP-mediated cycling of starch breakdown products in illuminated Arabidopsis leaves.

Biochemical precursor effects on the fatty acid production in cell suspension cultures of Theobroma cacao L

Cocoa butter (CB) is composed of 96% palmitic, stearic, oleic, linoleic and linolenic fatty acids that are responsible for the hardness, texture and fusion properties of chocolate. Through in vitro plant cell culture it is possible to modify CB lipid profiles and to study the fatty acid biosynthesis pathway on a subcellular level, evaluating fundamental aspects to enhance in vitro fatty acid production in a specific and controlled way. In this research, culture media was supplemented with acetate, biotin, pyruvate, bicarbonate and glycerol at three different concentrations and the effects on the biomass production (g/L), cell viability, and fatty acids profile and production was evaluated in in vitro cell suspensions culture. It was found that biotin stimulated fatty acid synthesis without altering cell viability and cell growth. It was also evident a change in the lipid profile of cell suspensions, increasing middle and long chain fatty acids proportion, which are unusual to those reported in seeds; thus implying that it is possible to modify lipid profiles according to the treatment used. According to the results of sucrose gradients and enzyme assays performed, it is proposed that cacao cells probably use the pentose phosphate pathway, mitochondria being the key organelle in the carbon flux for the synthesis of reductant power and fatty acid precursors.

Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues

Gene expression profiling via quantitative real-time PCR is a robust technique widely used in the life sciences to compare gene expression patterns in, e.g., different tissues, growth conditions, or after specific treatments. In the field of plant science, real-time PCR is the gold standard to study the dynamics of gene expression and is used to validate the results generated with high throughput techniques, e.g., RNA-Seq. An accurate relative quantification of gene expression relies on the identification of appropriate reference genes, that need to be determined for each experimental set-up used and plant tissue studied. Here, we identify suitable reference genes for expression profiling in stems of textile hemp (Cannabis sativa L.), whose tissues (isolated bast fibres and core) are characterized by remarkable differences in cell wall composition. We additionally validate the reference genes by analysing the expression of putative candidates involved in the non-oxidative phase of the pentose phosphate pathway and in the first step of the shikimate pathway. The goal is to describe the possible regulation pattern of some genes involved in the provision of the precursors needed for lignin biosynthesis in the different hemp stem tissues. The results here shown are useful to design future studies focused on gene expression analyses in hemp.

Can stable isotope mass spectrometry replace ‎radiolabelled approaches in metabolic studies?

Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.

Changes and their possible causes in δ13C of dark-respired CO2 and its putative bulk and soluble sources during maize ontogeny

The issues of whether, where, and to what extent carbon isotopic fractionations occur during respiration affect interpretations of plant functions that are important to many disciplines across the natural sciences. Studies of carbon isotopic fractionation during dark respiration in C3 plants have repeatedly shown respired CO2 to be (13)C enriched relative to its bulk leaf sources and (13)C depleted relative to its bulk root sources. Furthermore, two studies showed respired CO2 to become progressively (13)C enriched during leaf ontogeny and (13)C depleted during root ontogeny in C3 legumes. As such data on C4 plants are scarce and contradictory, we investigated apparent respiratory fractionations of carbon and their possible causes in different organs of maize plants during early ontogeny. As in the C3 plants, leaf-respired CO2 was (13)C enriched whereas root-respired CO2 was (13)C depleted relative to their putative sources. In contrast to the findings for C3 plants, however, not only root- but also leaf-respired CO2 became more (13)C depleted during ontogeny. Leaf-respired CO2 was highly (13)C enriched just after light-dark transition but the enrichment rapidly decreased over time in darkness. We conclude that (i) although carbon isotopic fractionations in C4 maize and leguminous C3 crop roots are similar, increasing phosphoenolpyruvate-carboxylase activity during maize ontogeny could have produced the contrast between the progressive (13)C depletion of maize leaf-respired CO2 and (13)C enrichment of C3 leaf-respired CO2 over time, and (ii) in both maize and C3 leaves, highly (13)C enriched leaf-respired CO2 at light-to-dark transition and its rapid decrease during darkness, together with the observed decrease in leaf malate content, may be the result of a transient effect of light-enhanced dark respiration.

Quantifying plant phenotypes with isotopic labeling & metabolic flux analysis

Analyses of metabolic flux using stable isotopes in plants have traditionally been restricted to tissues with presumed homogeneous cell populations and long metabolic steady states such as developing seeds, cell suspensions, or cultured roots and root tips. It is now possible to describe these and other metabolically more dynamic tissues such as leaves in greater detail using novel methods in mass spectrometry, isotope labeling strategies, and transient labeling-based flux analyses. Such studies are necessary for a systems level description of plant function that more closely represents biological reality, and provides insights into the genes that will need to be modified as natural resources become ever more limited and environments change.

¹⁴C pulse labeling to estimate external fluxes and turnovers in primary metabolism

Steady state (13)C-MFA is classically used to measure fluxes in complex metabolic networks. However, the modeling of steady state labeling allows the quantification of internal fluxes only and requires the estimation, by other methods, of the external fluxes, corresponding to substrate uptake (carbon input into the network) and to the production rate of compounds that accumulate within plant cells (network output). Additionally, it is not always possible to discriminate between different pathways that lead to the same label distribution. Methods to measure fluxes, based on direct measurements of pool size and on (14)C short-time labeling experiments, are described in this chapter. To illustrate this approach, we focus on the quantification of sucrose and starch turnovers.

Steady sucrose degradation is a prerequisite for tolerance to root hypoxia

We investigated the role of glycolysis and sucrolysis in the difference in tolerance to root hypoxia between two Myrtaceae tree species, Melaleuca cajuputi (which shows superior tolerance to root hypoxia) and Eucalyptus camaldulensis (which does not). Analysis of the adenylate energy charge (AEC) in roots subjected to a 4-day hypoxic treatment (HT) in hydroponic culture revealed that the interspecies difference in tolerance corresponds to the ability to maintain energy status under root hypoxia: AEC was reduced by HT in E. camaldulensis, but not in M. cajuputi. The energy status in HT roots of E. camaldulensis was restored by feeding of glucose (Glc) but not sucrose (Suc). These data provide evidence that low substrate availability for glycolysis resulting from an impairment of sucrolysis suppresses ATP production under hypoxic conditions in this species. Measurements of the rates of O2 consumption and CO2 production in roots indicated that E. camaldulensis, but not M. cajuputi, failed to activate fermentation in HT roots. These results cannot be attributed to enzymatic dysfunction, because no inhibition of main glycolytic and fermentative enzymes was observed in both species, and Glc feeding had a beneficial effect on AEC of HT roots of E. camaldulensis. The impairment of sucrolysis was demonstrated by inhibited soluble acid invertase activity in HT roots of E. camaldulensis. In contrast, there was no inhibition in all sucrolytic enzymes tested in HT roots of M. cajuputi, suggesting that steady Suc degradation is essential for maintaining high energy status under root hypoxia. We conclude that root sucrolysis is one of the essential factors that determines the extent of tolerance to root hypoxia.

Opposite carbon isotope discrimination during dark respiration in leaves versus roots - a review

In general, leaves are (13) C-depleted compared with all other organs (e.g. roots, stem/trunk and fruits). Different hypotheses are formulated in the literature to explain this difference. One of these states that CO2 respired by leaves in the dark is (13) C-enriched compared with leaf organic matter, while it is (13) C-depleted in the case of root respiration. The opposite respiratory fractionation between leaves and roots was invoked as an explanation for the widespread between-organ isotopic differences. After summarizing the basics of photosynthetic and post-photosynthetic discrimination, we mainly review the recent findings on the isotopic composition of CO2 respired by leaves (autotrophic organs) and roots (heterotrophic organs) compared with respective plant material (i.e. apparent respiratory fractionation) as well as its metabolic origin. The potential impact of such fractionation on the isotopic signal of organic matter (OM) is discussed. Some perspectives for future studies are also proposed .

Liquid chromatography tandem mass spectrometry for measuring ¹³C-labeling in intermediates of the glycolysis and pentose phosphate pathway

This chapter describes a procedure to analyze (13)C-labeled phosphorylated compounds by liquid chromatography tandem mass spectrometry. Phosphorylated compounds, intermediaries of the glycolysis and pentose phosphate pathway, are separated by anion exchange chromatography and their isotopic labeling is determined by mass spectrometry. A sensitivity in the fmole range is achieved using scheduled multiple reaction monitoring mode.

Metabolic network reconstruction and their topological analysis

This chapter focuses on the way to build a metabolic network and how to analyze its structure. The first part of this chapter describes the methods of the network model reconstruction from biochemical data found in specialized databases and/or literature. The second part deals with metabolic pathway analysis as a useful tool for better understanding the complex architecture of intracellular metabolism. The graph analysis and the stoichiometric network analysis are important approaches for understanding the network topology and consequently the function of metabolic networks. Among the methods presented, the Elementary Flux Modes analysis will be more detailed. Finally, we illustrate in this chapter an example of network reconstruction from heterotrophic plant cells metabolism and its topological analysis leading to a huge number of Elementary Flux Modes.

Application of metabolic flux analysis to plants

This volume compiles a series of chapters that cover the major aspects of plant metabolic flux analysis, such as but not limited to labeling of plant material, acquisition of labeling data, mathematical modeling of metabolic network at the cell, tissue, and plant level. A short revue, including methodological points and applications of flux analysis to plants, is presented in this introductory chapter.

Analysis of metabolic flux using dynamic labelling and metabolic modelling

Metabolic fluxes and the capacity to modulate them are a crucial component of the ability of the plant cell to react to environmental perturbations. Our ability to quantify them and to attain information concerning the regulatory mechanisms that control them is therefore essential to understand and influence metabolic networks. For all but the simplest of flux measurements labelling methods have proven to be the most informative. Both steady-state and dynamic labelling approaches have been adopted in the study of plant metabolism. Here the conceptual basis of these complementary approaches, as well as their historical application in microbial, mammalian and plant sciences, is reviewed, and an update on technical developments in label distribution analyses is provided. This is supported by illustrative cases studies involving the kinetic modelling of secondary metabolism. One issue that is particularly complex in the analysis of plant fluxes is the extensive compartmentation of the plant cell. This problem is discussed from both theoretical and experimental perspectives, and the current approaches used to address it are assessed. Finally, current limitations and future perspectives of kinetic modelling of plant metabolism are discussed.

The futile cycling of hexose phosphates could account for the fact that hexokinase exerts a high control on glucose phosphorylation but not on glycolytic rate in transgenic potato (Solanum tuberosum) roots

The metabolism of potato (Solanum tuberosum) roots constitutively over- and underexpressing hexokinase (HK, EC 2.7.1.1) was examined. An 11-fold variation in HK activity resulted in altered root growth, with antisense roots growing better than sense roots. Quantification of sugars, organic acids and amino acids in transgenic roots demonstrated that the manipulation of HK activity had very little effect on the intracellular pools of these metabolites. However, adenylate and free Pi levels were negatively affected by an increase in HK activity. The flux control coefficient of HK over the phosphorylation of glucose was measured for the first time in plants. Its value varied with HK level. It reached 1.71 at or below normal HK activity value and was much lower (0.32) at very high HK levels. Measurements of glycolytic flux and O₂ uptake rates demonstrated that the differences in glucose phosphorylation did not affect significantly glycolytic and respiratory metabolism. We hypothesized that these results could be explained by the existence of a futile cycle between the pools of hexose-Ps and carbohydrates. This view is supported by several lines of evidence. Firstly, activities of enzymes capable of catalyzing these reactions were detected in roots, including a hexose-P phosphatase. Secondly, metabolic tracer experiments using ¹⁴C-glucose as precursor showed the formation of ¹⁴C-fructose and ¹⁴C-sucrose. We conclude that futile cycling of hexose-P could be partially responsible for the differences in energetic status in roots with high and low HK activity and possibly cause the observed alterations in growth in transgenic roots. The involvement of HK and futile cycles in the control of glucose-6P metabolism is discussed.

Gas chromatography-mass spectrometry analysis of 13C labeling in sugars for metabolic flux analysis

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.

Insights into metabolic efficiency from flux analysis

The efficiency of carbon and energy flows throughout metabolism defines the potential for growth and reproductive success of plants. Understanding the basis for metabolic efficiency requires relevant definitions of efficiency as well as measurements of biochemical functions through metabolism. Here insights into the basis of efficiency provided by (13)C-based metabolic flux analysis (MFA) as well as the uses and limitations of efficiency in predictive flux balance analysis (FBA) are highlighted. (13)C-MFA studies have revealed unusual features of central metabolism in developing green seeds for the efficient use of light to conserve carbon and identified metabolic inefficiencies in plant metabolism due to dissipation of ATP by substrate cycling. Constraints-based FBA has used efficiency to guide the prediction of the growth and actual internal flux distribution of plant systems. Comparisons in a few cases have been made between flux maps measured by (13)C-based MFA and those predicted by FBA assuming one or more maximal efficiency parameters. These studies suggest that developing plant seeds and photoautotrophic microorganisms may indeed have patterns of metabolic flux that maximize efficiency. MFA and FBA are synergistic toolsets for uncovering and explaining the metabolic basis of efficiencies and inefficiencies in plant systems.

Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems

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.

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

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.

Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues

The tricarboxylic acid (TCA) cycle is a crucial component of respiratory metabolism in both photosynthetic and heterotrophic plant organs. All of the major genes of the tomato TCA cycle have been cloned recently, allowing the generation of a suite of transgenic plants in which the majority of the enzymes in the pathway are progressively decreased. Investigations of these plants have provided an almost complete view of the distribution of control in this important pathway. Our studies suggest that citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA ligase, succinate dehydrogenase, fumarase and malate dehydrogenase have control coefficients flux for respiration of -0.4, 0.964, -0.123, 0.0008, 0.289, 0.601 and 1.76, respectively; while 2-oxoglutarate dehydrogenase is estimated to have a control coefficient of 0.786 in potato tubers. These results thus indicate that the control of this pathway is distributed among malate dehydrogenase, aconitase, fumarase, succinate dehydrogenase and 2-oxoglutarate dehydrogenase. The unusual distribution of control estimated here is consistent with specific non-cyclic flux mode and cytosolic bypasses that operate in illuminated leaves. These observations are discussed in the context of known regulatory properties of the enzymes and some illustrative examples of how the pathway responds to environmental change are given.

(12)C/(13)C fractionations in plant primary metabolism

Natural (13)C abundance is now an unavoidable tool to study ecosystem and plant carbon economies. A growing number of studies take advantage of isotopic fractionation between carbon pools or (13)C abundance in respiratory CO(2) to examine the carbon source of respiration, plant biomass production or organic matter sequestration in soils. (12)C/(13)C isotope effects associated with plant metabolism are thus essential to understand natural isotopic signals. However, isotope effects of enzymes do not influence metabolites separately, but combine to yield a (12)C/(13)C isotopologue redistribution orchestrated by metabolic flux patterns. In this review, we summarise key metabolic isotope effects and integrate them into the corpus of plant primary carbon metabolism.

Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells

BACKGROUND

(13)C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explore feasible metabolic behaviours and to define the boundaries of steady state flux distributions. Elementary flux mode analysis is one of the most efficient methods for performing this analysis. In this context, recent approaches have tended to compare experimental flux measurements with topological network analysis.

RESULTS

Metabolic networks describing the main pathways of central carbon metabolism were set up for a bacteria species (Corynebacterium glutamicum) and a plant species (Brassica napus) for which experimental flux maps were available. The structural properties of each network were then studied using the concept of elementary flux modes. To do this, coefficients of flux efficiency were calculated for each reaction within the networks by using selected sets of elementary flux modes. Then the relative differences - reflecting the change of substrate i.e. a sugar source for C. glutamicum and a nitrogen source for B. napus - of both flux efficiency and flux measured experimentally were compared. For both organisms, there is a clear relationship between these parameters, thus indicating that the network structure described by the elementary flux modes had captured a significant part of the metabolic activity in both biological systems. In B. napus, the extension of the elementary flux mode analysis to an enlarged metabolic network still resulted in a clear relationship between the change in the coefficients and that of the measured fluxes. Nevertheless, the limitations of the method to fit some particular fluxes are discussed.

CONCLUSION

This consistency between EFM analysis and experimental flux measurements, validated on two metabolic systems allows us to conclude that elementary flux mode analysis could be a useful tool to complement (13)C metabolic flux analysis, by allowing the prediction of changes in internal fluxes before carbon labelling experiments.

Seasonal dynamics in the stable carbon isotope composition δ¹³C from non-leafy branch, trunk and coarse root CO₂ efflux of adult deciduous (Fagus sylvatica) and evergreen (Picea abies) trees

Respiration is a substantial driver of carbon (C) flux in forest ecosystems and stable C isotopes provide an excellent tool for its investigation. We studied seasonal dynamics in δ¹³C of CO₂ efflux (δ¹³C(E)) from non-leafy branches, upper and lower trunks and coarse roots of adult trees, comparing deciduous Fagus sylvatica (European beech) with evergreen Picea abies (Norway spruce). In both species, we observed strong and similar seasonal dynamics in the δ¹³C(E) of above-ground plant components, whereas δ¹³C(E) of coarse roots was rather stable. During summer, δ¹³C(E) of trunks was about -28.2‰ (Beech) and -26.8‰ (Spruce). During winter dormancy, δ¹³C(E) increased by 5.6-9.1‰. The observed dynamics are likely related to a switch from growth to starch accumulation during fall and remobilization of starch, low TCA cycle activity and accumulation of malate by PEPc during winter. The seasonal δ¹³C(E) pattern of branches of Beech and upper trunks of Spruce was less variable, probably because these organs were additionally supplied by winter photosynthesis. In view of our results and pervious studies, we conclude that the pronounced increases in δ¹³C(E) of trunks during the winter results from interrupted access to recent photosynthates.

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli

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.

Central metabolic fluxes in the endosperm of developing maize seeds and their implications for metabolic engineering

¹⁴C labeling experiments performed with kernel cultures showed that developing maize endosperm is more efficient than other non-photosynthetic tissues such as sunflower and maize embryos at converting maternally supplied substrates into biomass. To characterize the metabolic fluxes in endosperm, maize kernels were labeled to isotopic steady state using ¹³C-labeled glucose. The resultant labeling in free metabolites and biomass was analyzed by NMR and GC-MS. After taking into account the labeling of substrates supplied by the metabolically active cob, the fluxes through central metabolism were quantified by computer-aided modeling. The flux map indicates that 51-69% of the ATP produced is used for biomass synthesis and up to 47% is expended in substrate cycling. These findings point to potential engineering targets for improving yield and increasing oil contents by, respectively, reducing substrate cycling and increasing the commitment of plastidic carbon into fatty acid synthesis at the level of pyruvate kinase.

Photosynthetic carbon isotope discrimination and its relationship to the carbon isotope signals of stem, soil and ecosystem respiration

• Photosynthetic carbon (C) isotope discrimination (Δ(Α)) labels photosynthates (δ(A) ) and atmospheric CO(2) (δ(a)) with variable C isotope compositions during fluctuating environmental conditions. In this context, the C isotope composition of respired CO(2) within ecosystems is often hypothesized to vary temporally with Δ(Α). • We investigated the relationship between Δ(Α) and the C isotope signals from stem (δ(W)), soil (δ(S)) and ecosystem (δ(E)) respired CO(2) to environmental fluctuations, using novel tuneable diode laser absorption spectrometer instrumentation in a mature maritime pine forest. • Broad seasonal changes in Δ(Α) were reflected in δ(W,) δ(S) and δ(E). However, respired CO(2) signals had smaller short-term variations than Δ(A) and were offset and delayed by 2-10 d, indicating fractionation and isotopic mixing in a large C pool. Variations in δ(S) did not follow Δ(A) at all times, especially during rainy periods and when there is a strong demand for C allocation above ground. • It is likely that future isotope-enabled vegetation models will need to develop transfer functions that can account for these phenomena in order to interpret and predict the isotopic impact of biosphere gas exchange on the C isotope composition of atmospheric CO(2).

Not just a circle: flux modes in the plant TCA cycle

The tricarboxylic acid (TCA) cycle is one of the iconic pathways in metabolism. The cycle is commonly thought of in terms of energy metabolism, being responsible for the oxidation of respiratory substrates to drive ATP synthesis. However, the reactions of carboxylic acid metabolism are embedded in a larger metabolic network and the conventional TCA cycle is only one way in which the component reactions can be organised. Recent evidence from labelling studies and metabolic network models suggest that the organisation of carboxylic acid metabolism in plants is highly dependent on the metabolic and physiological demands of the cell. Thus, alternative, non-cyclic flux modes occur in leaves in the light, in some developing oilseeds, and under specific physiological circumstances such as anoxia.

Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks

Now that complete genome sequences are available for a variety of organisms, the elucidation of gene functions involved in metabolism necessarily includes a better understanding of cellular responses upon mutations on all levels of gene products, mRNA, proteins, and metabolites. Such progress is essential since the observable properties of organisms – the phenotypes – are produced by the genotype in juxtaposition with the environment. Whereas much has been done to make mRNA and protein profiling possible, considerably less effort has been put into profiling the end products of gene expression, metabolites. To date, analytical approaches have been aimed primarily at the accurate quantification of a number of pre-defined target metabolites, or at producing fingerprints of metabolic changes without individually determining metabolite identities. Neither of these approaches allows the formation of an in-depth understanding of the biochemical behaviour within metabolic networks. Yet, by carefully choosing protocols for sample preparation and analytical techniques, a number of chemically different classes of compounds can be quantified simultaneously to enable such understanding. In this review, the terms describing various metabolite-oriented approaches are given, and the differences among these approaches are outlined. Metabolite target analysis, metabolite profiling, metabolomics, and metabolic fingerprinting are considered. For each approach, a number of examples are given, and potential applications are discussed.

Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis

The efficiency with which developing maize embryos convert substrates into seed storage reserves was determined to be 57-71%, by incubating developing maize embryos with uniformly labeled 14C substrates and measuring their conversion to CO2 and biomass products. To map the pattern of metabolic fluxes underlying this efficiency, maize embryos were labeled to isotopic steady state using a combination of labeled 13C-substrates. Intermediary metabolic fluxes were estimated by computer-aided modeling of the central metabolic network using the labeling data collected by NMR and GC-MS and the biomass composition. The resultant flux map reveals that even though 36% of the entering carbon goes through the oxidative pentose-phosphate pathway, this does not fully meet the NADPH demands for fatty acid synthesis. Metabolic flux analysis and enzyme activities highlight the importance of plastidic NADP-dependent malic enzyme, which provides one-third of the carbon and NADPH required for fatty acid synthesis in developing maize embryos.

Subcellular flux analysis of central metabolism in a heterotrophic Arabidopsis cell suspension using steady-state stable isotope labeling

The presence of cytosolic and plastidic pathways of carbohydrate oxidation is a characteristic feature of plant cell metabolism. Ideally, steady-state metabolic flux analysis, an emerging tool for creating flux maps of heterotrophic plant metabolism, would capture this feature of the metabolic phenotype, but the extent to which this can be achieved is uncertain. To address this question, fluxes through the pathways of central metabolism in a heterotrophic Arabidopsis (Arabidopsis thaliana) cell suspension culture were deduced from the redistribution of label in steady-state (13)C-labeling experiments using [1-(13)C]-, [2-(13)C]-, and [U-(13)C(6)]glucose. Focusing on the pentose phosphate pathway (PPP), multiple data sets were fitted simultaneously to models in which the subcellular compartmentation of the PPP was altered. The observed redistribution of the label could be explained by any one of three models of the subcellular compartmentation of the oxidative PPP, but other biochemical evidence favored the model in which the oxidative steps of the PPP were duplicated in the cytosol and plastids, with flux through these reactions occurring largely in the cytosol. The analysis emphasizes the inherent difficulty of analyzing the PPP without predefining the extent of its compartmentation and the importance of obtaining high-quality data that report directly on specific subcellular processes. The Arabidopsis flux map also shows that the potential ATP yield of respiration in heterotrophic plant cells can greatly exceed the direct metabolic requirements for biosynthesis, highlighting the need for caution when predicting flux through metabolic networks using assumptions based on the energetics of resource utilization.

In folio respiratory fluxomics revealed by 13C isotopic labeling and H/D isotope effects highlight the noncyclic nature of the tricarboxylic acid "cycle" in illuminated leaves

While the possible importance of the tricarboxylic acid (TCA) cycle reactions for leaf photosynthesis operation has been recognized, many uncertainties remain on whether TCA cycle biochemistry is similar in the light compared with the dark. It is widely accepted that leaf day respiration and the metabolic commitment to TCA decarboxylation are down-regulated in illuminated leaves. However, the metabolic basis (i.e. the limiting steps involved in such a down-regulation) is not well known. Here, we investigated the in vivo metabolic fluxes of individual reactions of the TCA cycle by developing two isotopic methods, (13)C tracing and fluxomics and the use of H/D isotope effects, with Xanthium strumarium leaves. We provide evidence that the TCA "cycle" does not work in the forward direction like a proper cycle but, rather, operates in both the reverse and forward directions to produce fumarate and glutamate, respectively. Such a functional division of the cycle plausibly reflects the compromise between two contrasted forces: (1) the feedback inhibition by NADH and ATP on TCA enzymes in the light, and (2) the need to provide pH-buffering organic acids and carbon skeletons for nitrate absorption and assimilation.

Metabolic flux analysis in plants: coping with complexity

Theory and experience in metabolic engineering both show that metabolism operates at the network level. In plants, this complexity is compounded by a high degree of compartmentation and the synthesis of a very wide array of secondary metabolic products. A further challenge to understanding and predicting plant metabolic function is posed by our ignorance about the structure of metabolic networks even in well-studied systems. Metabolic flux analysis (MFA) provides tools to measure and model the functioning of metabolism, and is making significant contributions to coping with their complexity. This review gives an overview of different MFA approaches, the measurements required to implement them and the information they yield. The application of MFA methods to plant systems is then illustrated by several examples from the recent literature. Next, the challenges that plant metabolism poses for MFA are discussed together with ways that these can be addressed. Lastly, new developments in MFA are described that can be expected to improve the range and reliability of plant MFA in the coming years.

A single-substrate model to interpret intra-annual stable isotope signals in tree-ring cellulose

The carbon and oxygen stable isotope composition of wood cellulose (delta(13)C(cellulose) and delta(18)O(cellulose), respectively) reveal well-defined seasonal variations that contain valuable records of past climate, leaf gas exchange and carbon allocation dynamics within the trees. Here, we present a single-substrate model for wood growth to interpret seasonal isotopic signals collected in an even-aged maritime pine plantation growing in South-west France, where climate, soil and flux variables were also monitored. Observed seasonal patterns in delta(13)C(cellulose) and delta(18)O(cellulose) were different between years and individuals, and mostly captured by the model, suggesting that the single-substrate hypothesis is a good approximation for tree ring studies on Pinus pinaster, at least for the environmental conditions covered by this study. A sensitivity analysis revealed that the model was mostly affected by five isotopic discrimination factors and two leaf gas-exchange parameters. Modelled early wood signals were also very sensitive to the date when cell wall thickening begins (t(wt)). Our model could therefore be used to reconstruct t(wt) time series and improve our understanding of how climate influences this key parameter of xylogenesis.

Tracing metabolic pathways of lipid biosynthesis in ectomycorrhizal fungi from position-specific 13C-labelling in glucose

Six position-specific (13)C-labelled isotopomers of glucose were supplied to the ectomycorrhizal fungi Suillus pungens and Tricholoma flavovirens. From the resulting distribution of (13)C among fungal PLFAs, the overall order and contribution of each glucose atom to fatty acid (13)C enrichment was: C6 (approximately 31%) > C5 (approximately 25%) > C1 (approximately 18%) > C2 (approximately 18%) > C3 (approximately 8%) > C4 (approximately 1%). These data were used to parameterize a metabolic model of the relative fluxes from glucose degradation to lipid synthesis. Our data revealed that a higher amount of carbon is directed to glycolysis than to the oxidative pentose phosphate pathway (60% and 40% respectively) and that a significant part flows through these pathways more than once (73%) due to the reversibility of some glycolysis reactions. Surprisingly, 95% of carbon cycled through glyoxylate prior to incorporation into lipids, possibly to consume the excess of acetyl-CoA produced during fatty acid turnover. Our approach provides a rigorous framework for analysing lipid biosynthesis in fungi. In addition, this approach could ultimately improve the interpretation of isotopic patterns at natural abundance in field studies.

Co-localization of carbonic anhydrase and phosphoenol-pyruvate carboxylase and localization of pyruvate kinase in roots and hypocotyls of etiolated Glycine max seedlings

We investigated the presence of carbonic anhydrase in root and hypocotyl of etiolated soybean using enzymatic, histochemical, immunohistochemical and in situ hybridization approaches. In parallel, we used in situ hybridization and immunolocalization to determine the expression pattern and localization of phosphoenolpyruvate carboxylase. Their co-localization in the root tip as well as in the central cylinder, suggests that a large fraction of the CO(2) may be re-introduced into C4 compounds. GmPK3 expression, coding for a cytoplasmic isoform of pyruvate kinase, was detected in all different root cell types, suggesting that both phosphoenolpyruvate-utilizing enzymes are involved in phosphoenolpyruvate metabolism in etiolated soybean roots; a case indicative of the necessary flexibility plant metabolism has to adopt in order to compensate various physiological conditions.