Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples

Stable isotopes are powerful tools to assess metabolism. 13C labeling is detected using nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS). MS has excellent sensitivity but generally cannot discriminate among different 13C positions (isotopomers), whereas NMR is less sensitive but reports some isotopomers. Here, we develop an MS method that reports all 16 aspartate and 32 glutamate isotopomers while requiring less than 1% of the sample used for NMR. This method discriminates between pathways that result in the same number of 13C labels in aspartate and glutamate, providing enhanced specificity over conventional MS. We demonstrate regional metabolic heterogeneity within human tumors, document the impact of fumarate hydratase (FH) deficiency in human renal cancers, and investigate the contributions of tricarboxylic acid (TCA) cycle turnover and CO2 recycling to isotope labeling in vivo. This method can accompany NMR or standard MS to provide outstanding sensitivity in isotope-labeling experiments, particularly in vivo.

Isotopomer analyses with the tricarboxylic acid cycle intermediates and exchanging metabolites from the rat kidney

Renal metabolism is essential for kidney functions and energy homeostasis in the body. The TCA cycle is the hub of metabolism, but the metabolic activities of the cycle in the kidney have rarely been investigated. This study is to assess metabolic processes at the level of the TCA cycle in the kidney based on isotopomer distributions in multiple metabolites. Isolated rat kidneys were perfused with media containing common substrates including lactate and alanine for an hour. One group of kidneys received [U-13 C3 ]lactate instead of natural abundance lactate while the other group received [U-13 C3 ]alanine instead of natural abundance alanine. Perfused kidneys and effluent were prepared for analysis using NMR spectroscopy. 13 C-labeling patterns in glutamate, fumarate, aspartate and succinate from the kidney extracts showed that pyruvate carboxylase and oxidative metabolism through the TCA cycle were comparably very active, but pyruvate cycling and pyruvate dehydrogenase were relatively less active. Isotopomer analyses with fumarate and malate from effluent, however, indicated that pyruvate carboxylase was much more active than the TCA cycle and other metabolic processes. The reverse equilibrium of oxaloacetate with four-carbon intermediates of the cycle was nearly complete (92%), based on the ratio of [2,3,4-13 C3 ]/[1,2,3-13 C3 ] in aspartate or malate. 13 C enrichment in glucose with 13 C-lactate supply was higher than that with 13 C-alanine. Isotopomer analyses with multiple metabolites (i.e., glutamate, fumarate, aspartate, succinate and malate) allowed us to assess relative metabolic processes in the TCA cycle in the kidney supplied with [U-13 C3 ]lactate. Data from the analytes were generally consistent, indicating highly active pyruvate carboxylase and oxidative metabolism through the TCA cycle. Different 13 C-labeling patterns in analytes from the kidney extracts versus effluent suggested metabolic compartmentalization.

Bonded cumomer analysis of tumor metabolism based on 13 C magnetic resonance spectroscopy

Bonded cumomers are sets of isotopomers of ¹³ C-labeled metabolites containing a particular sequence of contiguously or singly labeled carbon atoms. Only these isotopomers contribute to multiplet structure in the ¹³ C NMR spectrum. We discuss the application of this technique to the study of quantitative tumor metabolism, bioenergetics, and the Warburg effect. The advantages and sensitivity of bonded cumomer analysis over positional enrichment analysis are discussed. When sensitivity requirements are met, bonded cumomer analysis enables the extraction of fluxes through specific metabolic pathways with higher precision. In conjunction with isotopomer control analysis, we evaluate the sensitivity of experimentally measurable metabolite multiplets to determine the robustness of flux analysis in ¹³ C spectra of tumors. This review examines the role of glycolytic and tricarboxylic acid cycle metabolism with special emphasis on flux through the pentose phosphate pathway (PPP). The impact of reversibility of the nonoxidative branch of the PPP with various ¹³ C glucose tracers on fine-structure multiplets is analyzed.

Organic fertility inputs synergistically increase denitrification-derived nitrous oxide emissions in agroecosystems

Soil fertility in organic agriculture relies on microbial cycling of nutrient inputs from legume cover crops and animal manure. However, large quantities of labile carbon (C) and nitrogen (N) in these amendments may promote the production and emission of nitrous oxide (N₂ O) from soils. Better ecological understanding of the N₂ O emission controls may lead to new management strategies to reduce these emissions. We measured soil N₂ O emission for two growing seasons in four corn-soybean-winter grain rotations with tillage, cover crop, and manure management variations typical of organic agriculture in temperate and humid North America. To identify N₂ O production pathways and mitigation opportunities, we supplemented N₂ O flux measurements with determinations of N₂ O isotopomer composition and microbiological genomic DNA abundances in microplots where we manipulated cover crop and manure additions. The N input from legume-rich cover crops and manure prior to corn planting made the corn phase the main source of N₂ O emissions, averaging 9.8 kg/ha of N₂ O-N and representing 80% of the 3-yr rotations' total emissions. Nitrous oxide emissions increased sharply when legume cover crop and manure inputs exceeded 1.8 and 4 Mg/ha (dry matter), respectively. Removing the legume aboveground biomass before corn planting to prevent co-location of fresh biomass and manure decreased N₂ O emissions by 60% during the corn phase. The co-occurrence of peak N₂ O emission and high carbon dioxide emission suggests that oxygen (O₂ ) consumption likely caused hypoxia and bacterial denitrification. This interpretation is supported by the N₂ O site preference values trending towards denitrification during peak emissions with limited N₂ O reduction, as revealed by the N₂ O δ¹⁵ N and δ¹⁸ O and the decrease in clade I nosZ gene abundance following incorporation of cover crops and manure. Thus, accelerated microbial O₂ consumption seems to be a critical control of N₂ O emissions in systems with large additions of decomposable C and N substrates. Because many agricultural systems rely on combined fertility inputs from legumes and manures, our research suggests that controlling the rate and timing of organic input additions, as well as preventing the co-location of legume cover crops and manure, could mitigate N₂ O emissions.

Novel Insights into Dietary Phytosterol Utilization and Its Fate in Honey Bees (Apis mellifera L.)

Poor nutrition is an important factor in global bee population declines. A significant gap in knowledge persists regarding the role of various nutrients (especially micronutrients) in honey bees. Sterols are essential micronutrients in insect diets and play a physiologically vital role as precursors of important molting hormones and building blocks of cellular membranes. Sterol requirements and metabolism in honey bees are poorly understood. Among all pollen sterols, 24-methylenecholesterol is considered the key phytosterol required by honey bees. Nurse bees assimilate this sterol from dietary sources and store it in their tissues as endogenous sterol, to be transferred to the growing larvae through brood food. This study examined the duration of replacement of such endogenous sterols in honey bees. The dietary 13C-labeled isotopomer of 24-methylenecholesterol added to artificial bee diet showed differential, progressive in vivo assimilation across various honey bee tissues. Significantly higher survival, diet consumption, head protein content and abdominal lipid content were observed in the dietary sterol-supplemented group than in the control group. These findings provide novel insights into phytosterol utilization and temporal pattern of endogenous 24-methylenecholesterol replacement in honey bees.

Acidification Enhances Hybrid N2O Production Associated with Aquatic Ammonia-Oxidizing Microorganisms

Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N₂O) in aquatic environments. Identifying the impact of pH on N₂O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO₂. We assessed N₂O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with ¹⁵N-labeled ammonium (¹⁵NH4+) and nitrite (¹⁵NO2−), and also measurements of the natural abundance N and O isotopic composition of dissolved N₂O. N₂O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH4+ was the source of most of the N incorporated into N₂O, suggesting that the main N₂O production pathway involved hydroxylamine (NH₂OH) and/or NO2− produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added ¹⁵NO2− was also incorporated into N₂O, but only during the reduced-pH incubations. Mass spectra of this N₂O revealed that NH4+ and ¹⁵NO2− each contributed N equally to N₂O by a “hybrid-N₂O” mechanism consistent with a reaction between NH₂OH and NO2−, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N₂O. Isotopomeric N₂O analyses in Lake Lugano were consistent with incubation results, as ¹⁵N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH₂OH-dependent hybrid-N₂O production. Hybrid-N₂O formation was also observed during incubations of seawater from coastal Namibia with ¹⁵NH4+ and NO2−. However, the site preference of dissolved N₂O here was low (4.9‰), indicating that another mechanism, not captured during the incubations, was important. Multiplex sequencing of 16S rRNA revealed distinct ammonia oxidizer communities: AOB dominated numerically in Lake Lugano, and AOA dominated in the seawater. Potential for hybrid N₂O formation exists among both communities, and at least in AOB-dominated environments, acidification may accelerate this mechanism.

(13)C MRS and LC-MS Flux Analysis of Tumor Intermediary Metabolism

We present the first validated metabolic network model for analysis of flux through key pathways of tumor intermediary metabolism, including glycolysis, the oxidative and non-oxidative arms of the pentose pyrophosphate shunt, the TCA cycle as well as its anaplerotic pathways, pyruvate-malate shuttling, glutaminolysis, and fatty acid biosynthesis and oxidation. The model that is called Bonded Cumomer Analysis for application to (13)C magnetic resonance spectroscopy ((13)C MRS) data and Fragmented Cumomer Analysis for mass spectrometric data is a refined and efficient form of isotopomer analysis that can readily be expanded to incorporate glycogen, phospholipid, and other pathways thereby encompassing all the key pathways of tumor intermediary metabolism. Validation was achieved by demonstrating agreement of experimental measurements of the metabolic rates of oxygen consumption, glucose consumption, lactate production, and glutamate pool size with independent measurements of these parameters in cultured human DB-1 melanoma cells. These cumomer models have been applied to studies of DB-1 melanoma and DLCL2 human diffuse large B-cell lymphoma cells in culture and as xenografts in nude mice at 9.4 T. The latter studies demonstrate the potential translation of these methods to in situ studies of human tumor metabolism by MRS with stable (13)C isotopically labeled substrates on instruments operating at high magnetic fields (≥7 T). The melanoma studies indicate that this tumor line obtains 51% of its ATP by mitochondrial metabolism and 49% by glycolytic metabolism under both euglycemic (5 mM glucose) and hyperglycemic conditions (26 mM glucose). While a high level of glutamine uptake is detected corresponding to ~50% of TCA cycle flux under hyperglycemic conditions, and ~100% of TCA cycle flux under euglycemic conditions, glutaminolysis flux and its contributions to ATP synthesis were very small. Studies of human lymphoma cells demonstrated that inhibition of mammalian target of rapamycin (mTOR) signaling produced changes in flux through the glycolytic, pentose shunt, and TCA cycle pathways that were evident within 8 h of treatment and increased at 24 and 48 h. Lactate was demonstrated to be a suitable biomarker of mTOR inhibition that could readily be monitored by (1)H MRS and perhaps also by FDG-PET and hyperpolarized (13)C MRS methods.

Isotopic splitting patterns in the (13) C NMR spectra of some partially deuterated 1-aryl-2-(phenyldiazenyl)butane-1,3-dione and 4-hydroxy-3-(phenyldiazenyl)-2H-chromen-2-one: evidence for elucidation of tautomeric forms

Nuclear magnetic resonance spectra of synthesized azo dyes derived from aniline derivatives in reaction with benzoylacetone and 4-hydroxycoumarin were studied in both CDCl3 and (CD3 )2 SO (two drops of D2 O were added into solutions of dyes). All dyes showed intramolecular hydrogen bonding. Dyes derived from o-nitro aniline in the reaction with benzoylacetone, and 4-hydroxycoumarin showed bifurcated intramolecular hydrogen bonds. The solvent-substrate proton exchange of dyes derived from benzoylacetone and 4-hydroxycoumarin was examined in the presence of two drops of D2 O. Among ten dye samples, two dyes derived from benzoylacetone did not show deuteration, three dyes showed partial deuteration and five dyes showed full deuteration under similar conditions. For the partially deuterated dyes the β-isotope effect in (13) C splitting was investigated and was used for the determination of the predominant tautomeric form.

Detecting long-term metabolic shifts using isotopomers: CO2-driven suppression of photorespiration in C3 plants over the 20th century

Terrestrial vegetation currently absorbs approximately a third of anthropogenic CO2 emissions, mitigating the rise of atmospheric CO2. However, terrestrial net primary production is highly sensitive to atmospheric CO2 levels and associated climatic changes. In C3 plants, which dominate terrestrial vegetation, net photosynthesis depends on the ratio between photorespiration and gross photosynthesis. This metabolic flux ratio depends strongly on CO2 levels, but changes in this ratio over the past CO2 rise have not been analyzed experimentally. Combining CO2 manipulation experiments and deuterium NMR, we first establish that the intramolecular deuterium distribution (deuterium isotopomers) of photosynthetic C3 glucose contains a signal of the photorespiration/photosynthesis ratio. By tracing this isotopomer signal in herbarium samples of natural C3 vascular plant species, crops, and a Sphagnum moss species, we detect a consistent reduction in the photorespiration/photosynthesis ratio in response to the ∼100-ppm CO2 increase between ∼1900 and 2013. No difference was detected in the isotopomer trends between beet sugar samples covering the 20th century and CO2 manipulation experiments, suggesting that photosynthetic metabolism in sugar beet has not acclimated to increasing CO2 over >100 y. This provides observational evidence that the reduction of the photorespiration/photosynthesis ratio was ca. 25%. The Sphagnum results are consistent with the observed positive correlations between peat accumulation rates and photosynthetic rates over the Northern Hemisphere. Our results establish that isotopomers of plant archives contain metabolic information covering centuries. Our data provide direct quantitative information on the "CO2 fertilization" effect over decades, thus addressing a major uncertainty in Earth system models.

Flux analysis of cholesterol biosynthesis in vivo reveals multiple tissue and cell-type specific pathways

Two parallel pathways produce cholesterol: the Bloch and Kandutsch-Russell pathways. Here we used stable isotope labeling and isotopomer analysis to trace sterol flux through the two pathways in mice. Surprisingly, no tissue used the canonical K–R pathway. Rather, a hybrid pathway was identified that we call the modified K–R (MK–R) pathway. Proportional flux through the Bloch pathway varied from 8% in preputial gland to 97% in testes, and the tissue-specificity observed in vivo was retained in cultured cells. The distribution of sterol isotopomers in plasma mirrored that of liver. Sterol depletion in cultured cells increased flux through the Bloch pathway, whereas overexpression of 24-dehydrocholesterol reductase (DHCR24) enhanced usage of the MK–R pathway. Thus, relative use of the Bloch and MK–R pathways is highly variable, tissue-specific, flux dependent, and epigenetically fixed. Maintenance of two interdigitated pathways permits production of diverse bioactive sterols that can be regulated independently of cholesterol.

DOI:http://dx.doi.org/10.7554/eLife.07999.001

Cholesterol is important for animals, both as an essential component of the membrane that surrounds cells and as a building block to make hormones and other biologically important molecules. However, cells limit how much cholesterol they make because an excess of this fatty molecule can cause serious health problems, including heart disease and stroke.

Cholesterol is made via a complex process that involves more than 30 different steps, which can be organized into two biochemical pathways (named the Bloch pathway and the Kandutsch–Russell pathway). The enzymes that carry out the steps in these pathways have been characterized in detail. Less is known about which of the two pathways is actually used in different cells and tissues, or how much cholesterol each pathway produces. This is partly because it is difficult to distinguish between the closely related intermediate molecules that are formed in each pathway.

Mitsche et al. have now used mass spectrometry and isotope labeling techniques to analyze the relative contributions of the two cholesterol-making pathways in both cells grown in the laboratory and in mice. The experiments show that many cells use the Bloch pathway. However, no cells were found to use the Kandutsch–Russell pathway as it was originally described. Rather, some of the cells used a hybrid pathway where the production of cholesterol was started using the Bloch pathway and then after a certain number of steps, the process switched to using part of the Kandutsch–Russell pathway. Mitsche et al. referred to this mixed system as the ‘modified Kandutsch–Russell pathway’.

Mitsche et al. next examined the flow of molecules through these two pathways in different tissues and observed that the Bloch pathway is exclusively used in the testes and adrenal glands, which produce high levels of cholesterol. In contrast, the skin and brain use the modified Kandutsch–Russell pathway. In some tissues, a fraction of the building blocks that can be used to make cholesterol were instead diverted to make other products. This suggests that animals have maintained the two pathways over the course of evolution to enable them to generate a variety of products, which can be used to carry out different biological processes. One challenge following this work will be to use the newly developed methods to analyze other complex biochemical pathways.

DOI:http://dx.doi.org/10.7554/eLife.07999.002

Recognition of hydrogen isotopomers by an open-cage fullerene

We present our study on the recognition of hydrogen isotopes by an open-cage fullerene through determination of binding affinity of isotopes H₂/HD/D₂ with the open-cage fullerene and comparison of their relative molecular sizes through kinetic-isotope-release experiments. We took advantage of isotope H₂/D₂ exchange that generated an equilibrium mixture of H₂/HD/D₂ in a stainless steel autoclave to conduct high-pressure hydrogen insertion into an open-cage fullerene. The equilibrium constants of three isotopes with the open-cage fullerene were determined at various pressures and temperatures. Our results show a higher equilibrium constant for HD into open-cage fullerene than the other two isotopomers, which is consistent with its dipolar nature. D₂ molecule generally binds stronger than H₂ because of its heavier mass; however, the affinity for H₂ becomes larger than D₂ at lower temperature, when size effect becomes dominant. We further investigated the kinetics of H₂/HD/D₂ release from open-cage fullerene, proving their relative escaping rates. D₂ was found to be the smallest and H₂ the largest molecule. This notion has not only supported the observed inversion of relative binding affinities between H₂ and D₂, but also demonstrated that comparison of size difference of single molecules through non-convalent kinetic-isotope effect was applicable.

Synthesis of enantiomerically enriched (R)-C-labelled 2-aminoisobutyric acid (Aib) by conformational memory in the alkylation of a derivative of L-alanine

The method of Kouklovsky and coworkers for the enantioselective alkylation of cyclic N-naphthoyl derivatives of amino acids was used to introduce a ¹³C label into one of the two enantiotopic methyl groups of 2-aminoisobutyric acid (Aib) by retentive alkylation of L-alanine with ¹³CH₃I. Conditions were identified for optimization of yield and enantiomeric purity, and the absolute configuration of the labelled product was established.

Global metabolic effects of glycerol kinase overexpression in rat hepatoma cells

Glycerol kinase has several diverse activities in mammalian cells. Glycerol kinase deficiency is a complex, single-gene, inborn error of metabolism wherein no genotype-phenotype correlation has been established. Since glycerol kinase has been suggested to exhibit additional activities than glycerol phosphorylation, expression level perturbation in this enzyme may affect cellular physiology globally. To investigate this possibility, we conducted metabolic investigations of wild-type and two glycerol kinase-overexpressing H4IIE rat hepatoma cell lines constructed in this study. The glycerol kinase-overexpressing cell lines exhibited a significantly higher consumption of carbon sources per cell, suggesting excess carbon expenditure. Furthermore, we quantified intracellular metabolic fluxes by employing stable isotope 13C labeling with a mathematically designed substrate mixture, gas chromatography-mass spectrometry, and comprehensive isotopomer balancing. This flux analysis revealed that the pentose phosphate pathway flux in the glycerol kinase-overexpressing cell lines was 2-fold higher than that in the wild-type, in addition to subtler flux changes in other pathways of carbohydrate metabolism. Furthermore, the activity and transcript level of the lipogenic enzyme glucose-6-phosphate dehydrogenase, the rate-limiting enzyme of the pentose phosphate pathway, were also about 2-fold higher than that of the wild-type; these data corroborate the flux analysis results. This study shows that glycerol kinase affects carbon metabolism globally, possibly through its additional functions, and highlights glycerol kinase's multifaceted role in cellular physiology.