Quantitative approaches for analysing fluxes through plant metabolic networks using NMR and stable isotope labelling

The quantitative analysis of metabolic networks is a prerequisite for understanding the integration and regulation of plant metabolism and for devising rational approaches for manipulating resource allocation in plants. The analysis of steady state stable isotope labelling experiments using nuclear magnetic resonance (NMR) spectroscopy has developed into a powerful method for determining these fluxes in micro-organisms and its application to heterotrophic plant metabolism is increasing. After an introductory discussion of the well known role of stable isotopes in pathway delineation, the review considers their application to metabolic flux analysis in plants. These applications are divided into two groups – small scale analyses of fluxes through particular pathways and large scale analyses of multiple fluxes through metabolic networks – and the problems caused by the complexity of intermediary metabolism in plants are discussed. It is concluded that metabolic flux analysis provides a powerful method for defining the metabolic phenotype of wild type, mutant and transgenic plants and that its development should be pursued.     

Changes in elemental and isotopic composition accompanying larval growth and metamorphosis of the moor frog

A variety of early ontogenetic events of anuran species (growth, structural and biochemical diversification, metamorphosis) offers a unique opportunity to evaluate the effectiveness and application limits of mass spectrometry method for the analysis of metabolic and transformation events in developing organisms. The dynamics of relative carbon and nitrogen contents and stable isotopes of these elements during larval development in the period of metamorphosis climax and after its conclusion in moor frog specimens developing in their natural habitat and in vitro on a referent diet are traced. A decrease in C/N ratio and enrichment of the tissues with heavy stable isotopes of carbon and nitrogen during embryonal and larval development (prior to the beginning of independent feeding) indicates the increase in the portion and variety of proteins, accompanied by consumption of yolk lipids. The relative nitrogen content increase and C/N ratio decreases with the growth and development of independently feeding tadpoles, which indicates surpassing increase of the portion of proteins in tissues. In growing tadpoles, the rates of tissue renewal in general and rates of protein metabolism in particular affect the kinetics of changes of tissue isotope composition, which approaches isotope composition of the consumed food. A decrease in С/N ratio in the bodies of metamorphs during mass tissue decomposition is indicative of continuing reconstruction of larval organs and growth of anlage of definitive organs. Significant increase of C/N ratio and depletion of liver samples by heavy carbon isotopes are associated with intensive synthesis and reservation of lipids within the organ. Strong enrichment of metamorphs’ tissues with heavy nitrogen isotope indicates the substitution of ammoniotelic type of nitrogen metabolism by urotelic type. Decrease in C/N ratio and enrichment of tissues by heavy carbon isotope may be connected to intensive oxidation of lipids, which supports the growing energy costs of terrestrial underyearlings. Relative contents of heavy nitrogen isotope in the tissues of underyearlings does not change compared to the tissues of metamorphs.     

Protein-based stable isotope probing

We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d.     

The impact of metabolism on stable isotope dynamics: a theoretical framework

Stable isotope analysis is a powerful tool used for reconstructing individual life histories, identifying food-web structures and tracking flow of elemental matter through ecosystems. The mechanisms determining isotopic incorporation rates and discrimination factors are, however, poorly understood which hinders a reliable interpretation of field data when no experimental data are available. Here, we extend dynamic energy budget (DEB) theory with a limited set of new assumptions and rules in order to study the impact of metabolism on stable isotope dynamics in a mechanistic way. We calculate fluxes of stable isotopes within an organism by following fluxes of molecules involved in a limited number of macrochemical reactions: assimilation, growth but also structure turnover that is here explicitly treated. Two mechanisms are involved in the discrimination of isotopes: (i) selection of molecules occurs at the partitioning of assimilation, growth and turnover into anabolic and catabolic sub-fluxes and (ii) reshuffling of atoms occurs during transformations. Such a framework allows for isotopic routing which is known as a key, but poorly studied, mechanism. As DEB theory specifies the impact of environmental conditions and individual state on molecule fluxes, we discuss how scenario analysis within this framework could help reveal common mechanisms across taxa.     

Stable isotope compounds - production,detection, and application

Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.     

NMR analysis of plant nitrogen metabolism

The analysis of primary and secondary nitrogen metabolism in plants by nuclear magnetic resonance (NMR) spectroscopy is comprehensively reviewed. NMR is a versatile analytical tool, and the combined use of ¹H, ²H, ¹³C, ¹⁴N and ¹⁵N NMR allows detailed investigation of the acquisition, assimilation and metabolism of nitrogen. The analysis of tissue extracts can be complemented by the in vivo NMR analysis of functioning tissues and cell suspensions, and by the application of solid state NMR techniques. Moreover stable isotope labelling with ²H-, ¹³C- and ¹⁵N-labelled precursors provides direct insight into specific pathways, with the option of both time-course and steady state analysis increasing the potential value of the approach. The scope of the NMR method, and its contribution to studies of plant nitrogen metabolism, are illustrated with a wide range of examples. These include studies of the GS/GOGAT pathway of ammonium assimilation, investigations of the metabolism of glutamate, glycine and other amino acids, and applications to tropane alkaloid metabolism. The continuing development of the NMR technique, together with potential applications in the emerging fields of metabolomics and metabolic flux analysis, leads to the conclusion that NMR will play an increasingly valuable role in the analysis of plant nitrogen metabolism.     

Isotope composition of carbon and nitrogen in tissues and organs of <Emphasis Type="Italic">Betula pendula</Emphasis>

Ratios of ¹³С/¹²C and ¹⁵N/¹⁴N isotopes were identified in different parts and organs of drooping birch (Betula pendula Roth) in preforest-steppe and pine-birch forests of the Middle Urals by mass spectrometry. The data were analyzed and interpreted from the perspective of biochemical processes of carbon and nitrogen metabolism in the leaf, cambial tissue, trunk wood, branches, roots, and in the soil. The lighter isotopic composition of carbon is characteristic for the leaves, trunk cambium as well as fine (<2 mm) roots. The trunk wood is characterized by the basal trend for ¹³C enrichment. The heavier carbon isotopic composition inversely related to metabolic activity of organs and tissues, in addition, ¹³С/¹²C ratio corresponds to the nitrogen content in the organs and tissues, indicating the metabolic control of carbon fractionation in woody plants. The isotopic composition of nitrogen in the aboveground parts of the plant (leaves, trunk cambium, wood) and in the medium and fine roots was significantly depleted in ¹⁵N (δ¹⁵N varies from 0 to–3‰), while main roots (δ¹⁵N = 0.6 ‰) and soil (δ¹⁵N = 2.4–6.7‰) were more enriched. The ratio of stable isotopes of carbon and nitrogen is an integrating index of carbon and nitrogen metabolism in plants.     

(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.     

Enzyme redundancy and the importance of 2-oxoglutarate in plant ammonium assimilation

Ammonium is the reduced nitrogen form available to plants for assimilation into amino acids. This is achieved by the GS/GOGAT pathway that requires carbon skeletons in the form of 2-oxoglutarate. To date, the exact enzymatic origin of this organic acid for plant ammonium assimilation is unknown. Isocitrate dehydrogenases and aspartate aminotransferases have been proposed to carry out this function. Since different (iso)forms located in several subcellular compartments are present within a plant cell, recent efforts have concentrated on evaluating the involvement of these enzymes in ammonium assimilation. Furthermore, several observations indicate that 2-oxoglutarate is a good candidate as a metabolic signal to regulate the co-ordination of C and N metabolism. This will be discussed with respect to recent advances in bacterial signalling processes involving a 2-oxoglutarate binding protein called PII.     

Metabolic origin of δ15N values in nitrogenous compounds from Brassica napus L. leaves

Nitrogen isotope composition (δ¹⁵N) in plant organic matter is currently used as a natural tracer of nitrogen acquisition efficiency. However, the δ¹⁵N value of whole leaf material does not properly reflect the way in which N is assimilated because isotope fractionations along metabolic reactions may cause substantial differences among leaf compounds. In other words, any change in metabolic composition or allocation pattern may cause undesirable variability in leaf δ¹⁵N. Here, we investigated the δ¹⁵N in different leaf fractions and individual metabolites from rapeseed (Brassica napus) leaves. We show that there were substantial differences in δ¹⁵N between nitrogenous compounds (up to 30‰) and the content in (¹⁵N enriched) nitrate had a clear influence on leaf δ¹⁵N. Using a simple steady‐state model of day metabolism, we suggest that the δ¹⁵N value in major amino acids was mostly explained by isotope fractionation associated with isotope effects on enzyme‐catalysed reactions in primary nitrogen metabolism. δ¹⁵N values were further influenced by light versus dark conditions and the probable occurrence of alternative biosynthetic pathways. We conclude that both biochemical pathways (that fractionate between isotopes) and nitrogen sources (used for amino acid production) should be considered when interpreting the δ¹⁵N value of leaf nitrogenous compounds.     

氮代谢参与植物逆境抵抗的作用机理研究进展

近年来,植物所受到的诸如干旱、盐、高温、低氧、重金属胁迫和营养元素缺乏等环境胁迫越来越多,严重影响了植物的生长发育及作物的质量和产量。氮素是植物生长发育所需的必需营养元素,同时也是核酸、蛋白质和叶绿素的重要组成成分,其代谢过程与植物抵抗逆境的能力息息相关。氮代谢是指植物对氮素的吸收、同化和利用的全过程,是植物体内基础代谢途径之一。氮代谢主要从氮素吸收、同化及氨基酸代谢等方面参与植物的抗逆性,并通过调节离子吸收和转运、稳定细胞形态和蛋白质结构、维持激素平衡和细胞代谢水平、减少体内活性氧(reactive oxygen species,ROS)生成以及促进叶绿素合成等生理机制来影响植物抵抗非生物胁迫的能力。因此,提高植物在逆境下的氮代谢水平是减轻外界胁迫对其损伤的一种潜在途径。该文从氮素同化的基本途径出发,分别阐述了氮代谢在干旱胁迫、盐胁迫和高温胁迫等多个方面的逆境抵抗过程中的作用机理,为氮代谢参与植物抗逆性研究提供了有利参考。     

The use of stable carbon isotopes to decipher global change effects on soil organic carbon: present status,limitations, and future prospects

Major global change factors, including carbon dioxide (CO₂) fertilization, warming, change in precipitation, nitrogen deposition, and land-use change have the potential to significantly affect future stocks of soil organic carbon (SOC). These factors, individually or by interacting with each other, can also trigger positive or negative feedback to the processes affecting the rate of SOC formation or loss. Despite rapid progress in the understanding of carbon (C) cycling processes in the last few decades, much uncertainty remains in our ability to precisely forecast potential changes in SOC stocks in the rapidly changing future world. Stable C isotopes have been extensively used in natural observational studies as well as in laboratory and field experiments that manipulate CO₂ concentration, temperature, moisture, nitrogen fertilization, and vegetation type to understand the complex interactions and feedbacks that result from changing climate, plants and their herbivores, as well as soil microorganisms. Newly developed tools such as compound-specific isotope analysis, nano-SIMS (secondary ion mass spectroscopy), and stable isotope probing (SIP) permit isotope tracing in a specific ecosystem pool into specific C compounds and processes, thus providing in-depth insights into many processes affecting C biogeochemistry. The recent availability of affordable and reliable field-deployable optical isotope monitoring devices has provided researchers with a new set of tools for continuously tracking the ¹³C-CO₂ fluxes at the ecosystem level, enabling deeper insights into C biogeochemistry under changing environmental conditions. Despite these great strides, there is a scarcity of review studies that have comprehensively examined the use of C isotopes in studying SOC responses under global change factors. This review highlights recent progress in understanding the effect of major global change factors on SOC fluxes and stocks using selected examples covering scales from plant rhizospheres to geographic regions. Moreover, we discuss the strengths and limitations of current approaches and recent scientific advancements to highlight the new prospects evolving from the exceptional temporal and spatial resolution of stable isotope analysis in studying how global change affects SOC. Finally, we suggest that studies using stable C isotopes are well-poised to focus on identifying how dominant SOC cycling processes respond to environment-specific limiting factors and any thresholds and tipping points that define those relationships.

     

The in vivo nitrogen isotope discrimination among organic plant compounds

The bulk delta 15 N-value of plant (leaf) biomass is determined by that of the inorganic primary nitrogen sources NO(3)(-), NH(4)(+) and N(2), and by isotope discriminations on their uptake or assimilation. NH(4)(+) from these is transferred into "organic N" mainly by the glutamine synthetase reaction. The involved kinetic nitrogen isotope effect does not become manifest, because the turnover is quantitative. From the product glutamine any further conversion proceeds in a "closed system", where kinetic isotope effects become only efficient in connection with metabolic branching. The central and most important corresponding process is the GOGAT-reaction, involved in the de novo nitrogen binding and in recycling processes like the phenylpropanoid biosynthesis and photorespiration. The reaction yields relatively 15N-depleted glutamate and remaining glutamine, source of 15N-enriched amide-N in heteroaromatic compounds. Glutamate provides nitrogen for all amino acids and some other compounds with different 15N-abundances. An isotope equilibration is not connected to transamination; the relative delta 15 N-value of individual amino acids is determined by their metabolic tasks. Relative to the bulk delta 15 N-value of the plant cell, proteins are generally 15N-enriched, secondary products like chlorophyll, lipids, amino sugars and alkaloids are depleted in 15N. Global delta 15 N-values and 15N-patterns of compounds with several N-atoms can be calculated from those of their precursors and isotope discriminations in their biosyntheses.     

Whole‐plant and organ‐level nitrogen isotope discrimination indicates modification of partitioning of assimilation,fluxes and allocation of nitrogen in knockout lines of Arabidopsis thaliana

The nitrogen isotope composition (δ¹⁵N) of plants has potential to provide time‐integrated information on nitrogen uptake, assimilation and allocation. Here, we take advantage of existing T‐DNA and γ‐ray mutant lines of Arabidopsis thaliana to modify whole‐plant and organ‐level nitrogen isotope composition. Nitrate reductase 2 (nia2), nitrate reductase 1 (nia1) and nitrate transporter (nrt2) mutant lines and the Col‐0 wild type were grown hydroponically under steady‐state NO₃^– conditions at either 100 or 1000 μM NO₃^– for 35 days. There were no significant effects on whole‐plant discrimination and growth in the assimilatory mutants (nia2 and nia1). Pronounced root vs leaf differences in δ¹⁵N, however, indicated that nia2 had an increased proportion of nitrogen assimilation of NO₃^– in leaves while nia1 had an increased proportion of assimilation in roots. These observations are consistent with reported ratios of nia1 and nia2 gene expression levels in leaves and roots. Greater whole‐plant discrimination in nrt2 indicated an increase in efflux of unassimilated NO₃^– back to the rooting medium. This phenotype was associated with an overall reduction in NO₃^– uptake, assimilation and decreased partitioning of NO₃^– assimilation to the leaves, presumably because of decreased symplastic intercellular movement of NO₃^– in the root. Although the results were more varied than expected, they are interpretable within the context of expected mechanisms of whole‐plant and organ‐level nitrogen isotope discrimination that indicate variation in nitrogen fluxes, assimilation and allocation between lines.     

Experimental evidence for diel δ15N‐patterns in different tissues,xylem and phloem saps of castor bean (Ricinus communis L.)

Nitrogen isotope signatures in plants might give insights in the metabolism and allocation of nitrogen. To obtain a deeper understanding of the modifications of the nitrogen isotope signatures, we determined δ¹⁵N in transport saps and in different fractions of leaves, axes and roots during a diel course along the plant axis. The most significant diel variations were observed in xylem and phloem saps where δ¹⁵N was significantly higher during the day compared with during the night. However in xylem saps, this was observed only in the canopy, but not at the hypocotyl positions. In the canopy, δ¹⁵N was correlated fairly well between phloem and xylem saps. These variations in δ¹⁵N in transport saps can be attributed to nitrate reduction in leaves during the photoperiod as well as to ¹⁵N‐enriched glutamine acting as transport form of N. δ¹⁵N of the water soluble fraction of roots and leaves partially affected δ¹⁵N of phloem and xylems saps. δ¹⁵N patterns are likely the result of a complex set of interactions and N‐fluxes between plant organs. Furthermore, the natural nitrogen isotope abundance in plant tissue is not constant during the diel course – a fact that needs to be taken into account when sampling for isotopic studies.     

Stable isotopes of carbon and nitrogen in soil ecological studies

The development of stable isotope techniques is one of the main methodological advances in ecology of the last decades of the 20th century. Many biogeochemical processes are accompanied by changes in the ratio between stable isotopes of carbon and nitrogen (¹²C/¹³C and ¹⁴N/¹⁵N), which allows different ecosystem components and different ecosystems to be distinguished by their isotopic composition. Analysis of isotopic composition makes it possible to trace matter and energy flows through biological systems and to evaluate the rate of many ecological processes. The main concepts and methods of stable isotope ecology and patterns of stable isotope fractionation during organic matter decomposition are considered with special emphasis on the fractionation of isotopes in food chains and the use of stable isotope studies of trophic relationships between soil animals in the field.     

Equations for Lipid Normalization of Carbon Stable Isotope Ratios in Aquatic Bird Eggs

Stable isotope ratios are biogeochemical tracers that can be used to determine the source of nutrients and contaminants in avian eggs. However, the interpretation of stable carbon ratios in lipid-rich eggs is complicated because ¹³C is depleted in lipids. Variation in ¹³C abundance can therefore be obscured by variation in percent lipids. Past attempts to establish an algebraic equation to correct carbon isotope ratios for lipid content in eggs have been unsuccessful, possibly because they relied partly on data from coastal or migratory species that may obtain egg lipids from different habitats than egg protein. We measured carbon, nitrogen and sulphur stable isotope ratios in 175 eggs from eight species of aquatic birds. Carbon, nitrogen and sulphur isotopes were enriched in lipid-extracted egg samples compared with non extracted egg samples. A logarithmic equation using the C∶N ratio and carbon isotope ratio from the non extracted egg tissue calculated 90% of the lipid-extracted carbon isotope ratios within ±0.5‰. Calculating separate equations for eggs laid by species in different habitats (pelagic, offshore and terrestrial-influenced) improved the fit. A logarithmic equation, rather than a linear equation as often used for muscle, was necessary to accurately correct for lipid content because the relatively high lipid content of eggs compared with muscle meant that a linear relationship did not accurately approximate the relationship between percent lipids and the C∶N ratio. Because lipid extraction alters sulphur and nitrogen isotope ratios (and cannot be corrected algebraically), we suggest that isotopic measurement on bulk tissue followed by algebraic lipid normalization of carbon stable isotope ratio is often a good solution for homogenated eggs, at least when it is not possible to complete separate chemical analyses for each isotope.     

15N自然丰度法在生态系统氮素循环研究中的应用

稳定性同位素技术是现代生态学研究中的一门新兴技术,在生态学研究的诸多领域都展示了广阔的应用前景,其中,稳定性同位素＾１５Ｎ自然丰度法近年来在生态系统氮素循环研究中发挥了正在发挥着极为重要的作用,首先简述了自然生态系统氮素循环诸过程中的＾１５Ｎ同位素分馏机制,然后,在此基础上,综述了＾１５Ｎ自然丰度法的基本原理与方法,列举了近年 来此法在生物固氮及氮素转化过程研究中的一些应用实例,并预测了该方法在国     

Environmental and species‐specific controls on δ13C and δ15N in dominant woody plants from central‐western Argentinian drylands

Spatial variation in mean annual precipitation is the principal driver of plant water and nitrogen status in drylands. The natural abundance of carbon stable isotopes (δ¹³C) in photosynthetic tissues of C3 plants is an indicator of time‐integrated behaviour of stomatal conductance; while that of nitrogen stable isotopes (δ¹⁵N) is an indicator of the main source of plant N (soil N vs. atmospheric N₂). Previous studies in drylands have documented that plant δ¹³C and δ¹⁵N values increase with decreasing mean annual precipitation due to reductions in stomatal conductance, and soil enriched in ¹⁵N, respectively. However, evidence for this comes from studies focused on stable isotopes measurements integrated at the plant community level or on dominant plants at the site level, but little effort has been made to study C and N isotope variations within a species growing along rainfall gradients. We analysed plant δ¹³C, δ¹⁵N and C/N values of three woody species having different phenological leaf traits (deciduous, perennial and aphyllous) along a regional mean annual precipitation gradient from the central‐western Argentinian drylands. Noticeably, plant δ¹³C and δ¹⁵N values in the three woody species did not increase towards sites with low precipitation or at the start of the growing season (drier period), as we expected. These results suggest that environmental factors other than mean annual precipitation may be affecting plant δ¹³C and δ¹⁵N. The short‐term environmental conditions may interact with species‐specific plant traits related to water and nitrogen use strategies and override the predictive influence of the mean annual precipitation on plant δ¹³C and δ¹⁵N widely reported in drylands.     

Strategies for metabolic flux analysis in plants using isotope labelling

Flux measurements through metabolic pathways generate insights into the integration of metabolism, and there is increasing interest in using such measurements to quantify the metabolic effects of mutation and genetic manipulation. Isotope labelling provides a powerful approach for measuring metabolic fluxes, and it gives rise to several distinct methods based on either dynamic or steady-state experiments. We discuss the application of these methods to photosynthetic and non-photosynthetic plant tissues, and we illustrate the different approaches with an analysis of the pathways interconverting hexose phosphates and triose phosphates. The complicating effects of the pentose phosphate pathway and the problems arising from the extensive compartmentation of plant cell metabolism are considered. The non-trivial nature of the analysis is emphasised by reference to invalid deductions in earlier work. It is concluded that steady-state isotopic labelling experiments can provide important information on the fluxes through primary metabolism in plants, and that the combination of stable isotope labelling with detection by nuclear magnetic resonance is particularly informative.