Respirometric 13C flux analysis--Part II: in vivo flux estimation of lysine-producing Corynebacterium glutamicum

A novel method for metabolic flux studies of central metabolism which is based on respirometric (13)C flux analysis, i.e., parallel (13)C tracer studies with online CO(2) labeling measurements is applied to flux quantification of a lysine-producing mutant of Corynebacterium glutamicum. For this purpose, 3 respirometric (13)C labeling experiments with [1-(13)C(1)], [6-(13)C(1)] and [1,6-(13)C(2)] glucose were carried out in parallel. All fluxes comprising the reactions of glycolysis, of TCA cycle, of C3- and C4-metabolite interconversion and of lysine biosynthesis as well as the net reactions in the pentose phosphate pathway could be quantified solely using experimental data obtained from CO(2) labeling and extracellular rate measurements. At key branch points, 68+/-5% of glucose 6-phosphate were observed to be metabolized into pentose phosphate pathway and 48+/-1% of pyruvate into TCA cycle via pyruvate dehydrogenase. The results showed a good agreement with the previous studies using (13)C tracer cultivation and GC/MS analysis of proteinogenic amino acids. Also, respiratory quotient calculated from flux estimates using redox balance showed a high accordance with the value determined directly from the measured specific rates of O(2) consumption and CO(2) production. The results strongly support that the respirometric (13)C metabolic flux analysis is suited as an alternative to the conventional methods to study functional and regulatory activities of cells. The developed method is applicable to study growing or non-growing cells, primary and secondary metabolism and immobilized cells. Due to the non-accumulating nature of CO(2) labeling and instantaneous nature of the resulting fluxes, the method can also be used for dynamic profiling of metabolic activities. Therefore, it is complementary to conventional methods for metabolic flux analysis.     

Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements

Day respiration (R(d)) is an important parameter in leaf ecophysiology. It is difficult to measure directly and is indirectly estimated from gas exchange (GE) measurements of the net photosynthetic rate (A), commonly using the Laisk method or the Kok method. Recently a new method was proposed to estimate R(d) indirectly from combined GE and chlorophyll fluorescence (CF) measurements across a range of low irradiances. Here this method is tested for estimating R(d) in five C(3) and one C(4) crop species. Values estimated by this new method agreed with those by the Laisk method for the C(3) species. The Laisk method, however, is only valid for C(3) species and requires measurements at very low CO(2) levels. In contrast, the new method can be applied to both C(3) and C(4) plants and at any CO(2) level. The R(d) estimates by the new method were consistently somewhat higher than those by the Kok method, because using CF data corrects for errors due to any non-linearity between A and irradiance of the used data range. Like the Kok and Laisk methods, the new method is based on the assumption that R(d) varies little with light intensity, which is still subject to debate. Theoretically, the new method, like the Kok method, works best for non-photorespiratory conditions. As CF information is required, data for the new method are usually collected using a small leaf chamber, whereas the Kok and Laisk methods use only GE data, allowing the use of a larger chamber to reduce the noise-to-signal ratio of GE measurements.     

A Method to Constrain Genome-Scale Models with 13C Labeling Data

Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from ¹³C labeling experiments and genome-scale models. The data from ¹³C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by ¹³C labeling data. A comparison shows that the results of this new method are similar to those found through ¹³C Metabolic Flux Analysis (¹³C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.     

Measuring tree root respiration using (13)C natural abundance: rooting medium matters

Tree root respiration utilizes a major portion of the primary production in forests and is an important process in the global carbon cycle. Because of the lack of ecologically relevant methods, tree root respiration in situ is much less studied compared with above-ground processes such as photosynthesis and leaf respiration. This study introduces a new (13)C natural tracer method for measuring tree root respiration in situ. The method partitions tree root respiration from soil respiration in buried root chambers. Rooting media substantially influenced root respiration rates. Measured in three media, the fine root respiration rates of longleaf pine were 0.78, 0.27 and 0.18 mg CO(2) carbon mg(-1) root nitrogen d(-1) at 25 degrees C in the native soil, tallgrass prairie soil, and sand-vermiculite mixture, respectively. Compared with the root excision method, the root respiration rate of longleaf pine measured by the field chamber method was 18% higher when using the native soil as rooting medium, was similar in the prairie soil, but was 42% lower if in the sand-vermiculite medium. This natural tracer method allows the use of an appropriate rooting medium and is capable of measuring root respiration nondestructively in natural forest conditions.     

Respirometric 13C flux analysis, Part I: design, construction and validation of a novel multiple reactor system using on-line membrane inlet mass spectrometry

A novel method for (13)C flux analysis based on on-line CO(2) labeling measurements is presented. This so-called respirometric (13)C flux analysis requires multiple parallel (13)C labeling experiments using differently labeled tracer substrates. In Part I of the work, a membrane-inlet mass spectrometry-based measurement system with 6 parallel reactors with each 12 ml liquid volume and associated experimental and computational methods for the respirometric (13)C data acquisition and evaluation are described. Signal dynamics after switching between membrane probes follow exactly first-order allowing extrapolation to steady state. Each measurement cycle involving 3 reactors takes about 2 min. After development of a dynamic calibration method, the suitability and reliability of the analysis was examined with a lysine-producing mutant of Corynebacterium glutamicum using [1-(13)C(1)], [6-(13)C(1)], [1,6-(13)C(2)] glucose. Specific rates of oxygen uptake and CO(2) production were estimated with an error less than +/-0.3 mmol g(-1) h(-1) and had +/-3% to +/-10% deviations between parallel reactors which is primarily caused by inaccuracies in initial biomass concentration. The respiratory quotient could be determined with an uncertainty less than +/-0.02 and varied only +/-3% between reactors. Fractional labeling of CO(2) was estimated with much higher precision of about +/-0.001 to +/-0.005. The detailed statistical analysis suggested that these data should be of sufficient quality to allow physiological interpretation and metabolic flux estimation. The obtained data were applied for the respirometric (13)C metabolic flux analysis in Part II.     

Respiratory carbon metabolism following illumination in intact French bean leaves using (13)C/(12)C isotope labeling

The origin of the carbon atoms in the CO(2) respired by French bean (Phaseolus vulgaris) leaves in the dark has been studied using (13)C/(12)C isotopes as tracers. The stable isotope labeling was achieved through a technical device that uses an open gas-exchange system coupled online to an elemental analyzer and linked to an isotope ratio mass spectrometer. The isotopic analysis of the CO(2) respired in the dark after a light period revealed that the CO(2) was labeled, but the labeling level decreased progressively as the dark period increased. The pattern of disappearance depended on the amount of carbon fixed during the labeling and indicated that there were several pools of respiratory metabolites with distinct turnover rates. We demonstrate that the carbon recently assimilated during photosynthesis accounts for less than 50% of the carbon in the CO(2) lost by dark respiration and that the proportion is not influenced by leaf starvation in darkness before the labeling. Therefore, most of the carbon released by dark respiration after illumination does not come from new photosynthates.     

A simple method for 14CO2 measurement in metabolic experiments]

The determination of the fate of a compound following administration can be performed using the disposition method with 14C-labeled substances, which also allow the measurement of metabolism with CO2 as an expired end product. To substitute the laborious CO2-collection in washing bottles as carbonate a simple instrumentation was built for continuous 14CO2-measurement. The air from the metabolic cage is led in thin layer through a chamber fitted to a foot-monitor, the output of which is online for computation. The instrument is sensitive and calibration is easy.     

Use of 13C substrates for metabolic studies in exercise: methodological considerations

The purpose of this study is to outline a common mistake made when the rate of oxidation of exogenous substrates during prolonged exercise is computed using 13C naturally labeled substrates. The equation proposed and commonly used in the computation does not take into account that exercise and/or exogenous substrate ingestion modifies the composition of the mixture of endogenous substrates oxidized and, consequently, the isotopic composition of CO2 arising from oxidation of endogenous substrates. The recovery of 13C and the amount of exogenous substrate oxidized are thus overestimated. An adequate procedure for the computation of exogenous substrate oxidation taking into account changes in isotopic composition of CO2 arising from oxidation of endogenous substrates is suggested. Results from a pilot experiment (4 subjects) using this procedure indicate that over 2 h of exercise (66% of maximal O2 uptake), with ingestion of 60 g of glucose, 39 +/- 4 g of glucose were oxidized. Estimates made without taking into account changes in isotopic composition of CO2 arising from oxidation of endogenous substrates range between 70 +/- 8 and 44 +/- 3 g depending on 1) the isotopic composition of exogenous glucose and 2) the isotopic composition of expired CO2 taken as reference (rest or exercise without glucose ingestion). These observations suggest that results from previous studies of exogenous substrate oxidation during exercise using 13C labeling should be used with caution.     

Validation of manometric microrespirometers for measuring oxygen consumption in small arthropods

Scientists have used numerous techniques to measure organismal metabolic rate, including assays of oxygen (O(2)) consumption and carbon dioxide (CO(2)) production. Relatively few studies have directly compared estimates of metabolic rate on the same groups of animals as determined by different assay methods. This study directly compared measures of the metabolic rate of three lines of Drosophila simulans as determined either from direct measures of CO(2) production using infrared gas analysis (IRGA), or from estimates of O(2) consumption based on manometeric techniques. Determinations of metabolic rate of the same cohorts of flies using these two methods produced results that often differed widely. Typically metabolic rate as determined by the manometric method was significantly greater than that determined by CO(2) output. These differences are difficult to explain by simple biotic or abiotic factor(s). Because of the idiosyncratic nature of these differences it is not possible to use a simple factor to convert from metabolic rate measurements done using manometric techniques to those expected from direct measures of CO(2) output or O(2) consumption. Although manometric devices are simple to construct and use, measurements of metabolic rate made with this method can vary significantly from measurements made by directly assaying CO(2) production or O(2) consumption.     

Use of 13C-labeled glucose for estimating glucose oxidation: some design considerations

Use of 13C-labeled glucose for estimating in vivo rates of glucose oxidation faces several difficulties, particularly the accurate determination of the output of 13C in expired air. In an investigation of wholebody glucose metabolism in healthy adult humans, using a continuous intravenous infusion of D-[U-13C]glucose, we found that a precise estimate of the rate of glucose oxidation was difficult to achieve when the study included infusions with unlabeled glucose. Problems arose 1) as a result of the slow rate at which the 13CO2 released by glucose oxidation reaches an equilibrium in expired air CO2 and 2) due to the contribution to 13CO2 output by the natural 13C in the unlabeled glucose that was infused. In a subsequent series of experiments in healthy young adults, we found that the entry of 13CO2 released by the tissues into the bicarbonate pool and into the expired air is relatively slow and a tracer infusion protocol of approximately 6 h is required for determination of glucose oxidation. This applies when metabolic states are changed acutely during the experiment or when unlabeled glucose is infused. However, for resting subjects in the basal postabsorptive state we confirmed that the time required to achieve a steady state in the 13C enrichment of expired air can be shortened significantly by the use of a NaH13CO3 priming dose, even when this dose varies from the ideal.     

碳同位素示踪技术及其在陆地生态系统碳循环研究中的应用与展望

碳同位素示踪技术具有高度的专一性和灵敏度, 经过几十年的发展, 形成了一系列成熟的标记方法, 在陆地生态系统碳循环过程的研究中已得到广泛应用。目前, 自然丰度法、与¹³C贫化示踪技术结合的自由空气中气体浓度增加(FACE)实验、脉冲与连续标记法以及碳同位素高丰度底物富集标记法是研究陆地生态系统碳循环过程常用的碳同位素示踪方法; 通过将长期定位实验和室内模拟实验结合, 量化光合碳在植物-土壤系统的传输与分配特征, 明确植物光合碳对土壤有机质的来源、稳定化过程的影响及其微生物驱动机制; 阐明土壤碳动态变化(迁移与转化)和新碳与老碳对土壤碳库储量的相对贡献, 评估有机碳输入、转化与稳定的生物与非生物微观界面过程机制。然而, 生态系统碳循环受气候、植被、人为活动等多因素影响, 碳同位素技术需要结合质谱、光谱技术实现原位示踪, 结合分子生物学技术阐明其微生物驱动机制, 从而构建灵敏、准确、多尺度、多方位的同位素示踪技术体系。因此, 该文以稳定碳同位素为主, 综述了碳同位素示踪技术的原理、分析方法和在陆地生态系统碳循环过程中的应用进展, 归纳总结了碳同位素示踪技术结合原位检测技术和分子生物学技术的研究进展和应用前景, 并对碳同位素示踪技术存在的问题进行了分析和展望。     

CO2浓度升高对红松和长白松土壤呼吸作用的影响

以开顶箱法研究了CO₂浓度升高对红松和长白松土壤呼吸作用的影响.结果表明,500 μmol CO₂·mol^-1使红松和长白松土壤呼吸速率明显降低,土壤表面CO₂浓度升高导致CO₂扩散受阻可能是土壤呼吸受到抑制的主要原因.500 μmol CO₂·mol^-1下两树种土壤表面CO₂浓度明显高于对照箱和裸地条件下的CO₂浓度,增加幅度在40～150 μmol·mol^-1之间;对照箱内长白松土壤表面CO₂浓度略高于裸地,差异不显著,红松差异显著500 μmol CO₂·mol^-1下的长白松土壤全氮及总有机碳含量略高于对照组,差异不显著,红松裸地的碳氮含量明显低于500 μmol CO₂·mol^-1 及对照箱内土壤碳氮含量;500 μmol CO₂·mol^-1 及开顶箱的微环境对地下3 cm处土壤温度没有明显影响.     

Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A new methodology for quantitative analysis of proteins is described, applying stable-isotope labeling by small organic molecules combined with one- or two-dimensional electrophoresis and MALDI-TOF-MS, also allowing concurrent protein identification by peptide mass fingerprinting. Our method eliminates fundamental problems in other existing isotope-tagging methods requiring liquid chromatography and MS/MS, such as isotope effects, fragmentation, and solubility. It is also anticipated to be more practical and accessible than those LC-dependent methods.     

Carbon Dioxide Output as an Index of Circadian Timing in Lemna Photoperiodism

Previous work on flowering suggested that photoperiodism in Lemna perpusilla 6746 involves an endogenous circadian "clock," but direct evidence requires study of an overt rhythm in the same plant. The CO(2) output rate of axenic cultures supplied with sucrose has been studied in a system using infrared analysis and monitoring four sets of cultures at once. Alternations of (1/4) to 21 hours of dim red light with darkness in 24-hour cycles can entrain the CO(2) output. In darkness following either continuous dim red light or entrainment to a 12(12) light (dark) schedule, the rate oscillates through two maxima and two minima, with a circadian periodicity, before apparently damping. In continuous red light, the rate is linear. The skeleton photoperiodic schedule (1/4)(5(1/2))(1/4)(18), with its two portions highly unequal, rapidly entrains the CO(2) output in a phase relationship which is the same irrespective of which dark period is given first. The schedules (1/4)(13)(1/4)(10(1/2)) and its inverse, however, with two portions more nearly equal in length, differ markedly from each other with respect to manner of entrainment, as they do in their effects on flowering. These and other results strongly support the concept that a circadian clock is an important component of photoperiodism, and they provide a new experimental system in which to study its action.     

Metabolic interactions between glucose, glycerol, alanine and acetate in Leishmania braziliensis panamensis promastigotes

13C-nuclear magnetic resonance (NMR) spectroscopy was used to investigate the products of glycerol and acetate metabolism released by Leishmania braziliensis panamensis promastigotes and also to examine the interaction of each of these substrates with glucose or alanine. The NMR data were supplemented by measurements of the rates of oxygen consumption and substrate utilization, and of 14CO2 production from 14C-labeled substrate. Cells incubated with [2-13C]glycerol released acetate, succinate and D-lactate in addition to CO2. Cells incubated with acetate released only CO2. More succinate C-2/C-3 than C-1/C-4 was released from both [2-13C]glycerol and [2-13C]glucose, indicating that succinate was formed predominantly by CO2 fixation followed by reverse flux through part of the Krebs cycle. Some redistribution of the position of labeling was also seen in alanine and pyruvate, suggesting cycling through pyruvate/oxaloacetate/phosphoenolpyruvate. Cells incubated with combinations of 2 substrates consumed oxygen at the same rate as cells incubated with 1 or no substrate, even though the total substrate utilization had increased. When promastigotes were incubated with both glycerol and glucose, the rate of glucose consumption was unchanged but glycerol consumption decreased about 50%, and the rate of 14CO2 production from [1,(3)-14C]glycerol decreased about 60%. Alanine did not affect the rates of consumption of glucose or glycerol, but decreased 14CO2 production from these substrates by increasing flow of label into alanine. Although glucose decreased alanine consumption by 70%, it increased the rate of 14CO2 production from [U-14C]- and [l-14C]alanine by about 20%.(ABSTRACT TRUNCATED AT 250 WORDS)     

Towards dynamic metabolic network measurements by multi-dimensional NMR-based fluxomics

Novel technologies for measuring biological systems and methods for visualizing data have led to a revolution in the life sciences. Nuclear magnetic resonance (NMR) techniques can provide information on metabolite structure and metabolic dynamics at the atomic level. We have been developing a new method for measuring the dynamic metabolic network of crude extracts that combines [(13)C(6)]glucose stable isotope labeling of Arabidopsis thaliana and multi-dimensional heteronuclear NMR analysis, whereas most conventional metabolic flux analyses examine proteinogenic amino acids that are specifically labeled with partially labeled substrates such as [2-(13)C(1)]glucose or 10% [(13)C(6)]glucose. To show the validity of our method, we investigated how to obtain information about biochemical reactions, C-C bond formation, and the cleavage of the main metabolites, such as free amino acids, in crude extracts based on the analysis of the (13)C-(13)C coupling pattern in 2D-NMR spectra. For example, the combination of different extraction solvents allows one to distinguish complicated (13)C-(13)C fine couplings at the C2 position of amino acids. As another approach, f1-f3 projection of the HCACO spectrum also helps in the analysis of (13)C-(13)C connectivities. Using these new methods, we present an example that involves monitoring the incorporation profile of [(13)C(6)]glucose into A. thaliana and its metabolic dynamics, which change in a time-dependent manner with atmospheric (12)CO(2) assimilation.     

Determination of substrate specificity of carboxylases by nuclear magnetic resonance

Determination of whether CO2 or HCO3- is the substrate for an enzymatic carboxylation has generally been accomplished by taking advantage of the fact that equilibration of these two compounds requires more than a minute at temperatures below 15 degrees C; thus different kinetics of carboxylation are obtained depending on whether CO2 or HCO3- is used to initiate the reaction. We report a new method using 13C18O2 as substrate for determining the CO2/HCO3- specificity of carboxylases. If CO2 is the substrate, then the 18O content of the 13C-containing product is the same as that of the 13CO2 used, whereas if HCO3- is the substrate, the 18O content is 2/3 that of the starting material. The method is independent of the detailed kinetics of the CO2/HCO3- interconversion and independent of the presence of contaminating unlabeled CO2 or HCO3-. Isotopic analysis is accomplished by 13C NMR. The method has been used to confirm that HCO3- is the substrate for phosphoenolpyruvate carboxylase. Studies of oxygen-18 isotope shifts in phosphorus NMR spectra have permitted confirmation of the observation that label is transferred from HC18O3- into Pi during the carboxylation of phosphoenolpyruvate.     

Inhibitory effect of carbon dioxide on the fed-batch culture of Ralstonia eutropha: evaluation by CO2 pulse injection and autogenous CO2 methods

In order to see the effect of CO(2) inhibition resulting from the use of pure oxygen, we carried out a comparative fed-batch culture study of polyhydroxybutyric acid (PHB) production by Ralstonia eutropha using air and pure oxygen in 5-L, 30-L, and 300-L fermentors. The final PHB concentrations obtained with pure O(2) were 138.7 g/L in the 5-L fermentor and 131.3 g/L in the 30-L fermentor, which increased 2.9 and 6.2 times, respectively, as compared to those obtained with air. In the 300-L fermentor, the fed-batch culture with air yielded only 8.4 g/L PHB. However, the maximal CO(2) concentrations in the 5-L fermentor increased significantly from 4.1% (air) to 15.0% (pure O(2)), while it was only 1.6% in the 30-L fermentor with air, but reached 14.2% in the case of pure O(2). We used two different experimental methods for evaluating CO(2) inhibition: CO(2) pulse injection and autogenous CO(2) methods. A 10 or 22% (v/v) CO(2) pulse with a duration of 3 or 6 h was introduced in a pure-oxygen culture of R. eutropha to investigate how CO(2) affects the synthesis of biomass and PHB. CO(2) inhibited the cell growth and PHB synthesis significantly. The inhibitory effect became stronger with the increase of the CO(2) concentration and pulse duration. The new proposed autogenous CO(2) method makes it possible to place microbial cells under different CO(2) level environments by varying the gas flow rate. Introduction of O(2) gas at a low flow rate of 0.42 vvm resulted in an increase of CO(2) concentration to 30.2% in the exit gas. The final PHB of 97.2 g/L was obtained, which corresponded to 70% of the PHB production at 1.0 vvm O(2) flow rate. This new method measures the inhibitory effect of CO(2) produced autogenously by cells through the entire fermentation process and can avoid the overestimation of CO(2) inhibition without introducing artificial CO(2) into the fermentor.     

A review of the calibration methods for measuring the carbon and oxygen isotopes in CO2 based on isotope ratio infrared spectroscopy北大核心CSCD

With the development of isotope ratio infrared spectroscopy (IRIS) technology, it is now possible for the in situ high temporal resolution and high precision measurement of carbon isotopic composition (d13C) and oxygen isotopic composition (d18O) of atmospheric CO2, which overcomes the low temporal resolution and labor intensive shortcoming of traditional isotope ratio mass spectrometry (IRMS). The dependence of d13C and d18O on CO2 concentration (termed as concentration dependence) and the drift due to sensitivity to changing environmental conditions (termed as instrumental drift) are the two main sources of error affecting the IRIS measurements. Therefore, it is important to obtain precise measurements by constructing a proper calibration strategy to solve the concentration dependence and instrumental drift. In this study, we briefly discussed the definition and related theoretical principle of concentration dependence, and elaborated the theoretical and empirical calibration methods of concentration dependence. Moreover, we introduced the calibration methods of instrumental drift, and reviewed the state of the art of calibration methods and its application of IRIS technology. Additionally, we briefly discussed the definition and method of data traceability to the international standard, and reviewed its application of IRIS technology. Finally, we recommend that concentration dependence is corrected by using three standards or above with known CO2 concentration and its d13C and d18O, bracketing the CO2 concentration of samples. The instrumental drift is corrected by setting appropriate calibration frequency and all dataset are traceable to the international standard. In the future, the comparative study of different IRIS instruments and calibration methods should be enhanced, and the similar methods should be used for measuring CH4, N2O and H2O isotopes by IRIS technique. The IRIS technology combined with other technology will provide a new opportunity for ecological research. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All rights reserved.