The identification of enzyme targets for the optimization of a valine producing Corynebacterium glutamicum strain using a kinetic model

The enzyme targets for the rational optimization of a Corynebacterium glutamicum strain constructed for valine production are identified by analyzing the control of flux in the valine/leucine pathway. The control analysis is based on measurements of the intracellular metabolite concentrations and on a kinetic model of the reactions in the investigated pathway. Data‐driven and model‐based methods are used and evaluated against each other. The approach taken gives a quantitative evaluation of the flux control and it is demonstrated how the understanding of flux control is used to reach specific recommendations for strain optimization. The flux control coefficients (FCCs) with respect to the valine excretion rate were calculated, and it was found that the control is distributed mainly between the acetohydroxyacid synthase enzyme (FCC = 0.32), the branched chain amino acid transaminase (FCC = 0.27), and the exporting translocase (FCC = 0.43). The availability of the precursor pyruvate has substantial influence on the valine flux, whereas the cometabolites are less important as demonstrated by the calculation of the respective response coefficients. The model is further used to make in‐silico predictions of the change in valine flux following a change in enzyme level. A doubling of the enzyme level of valine translocase will result in an increase in valine flux of 31%. By optimizing the enzyme levels with respect to valine flux it was found that the valine flux can be increased by a factor 2.5 when the optimal enzyme levels are implemented. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Granier树干液流测定系统在马占相思的水分利用研究中的应用

介绍了Granier热消散探针在树干液流测定中的工作原理,并利用该系统长期监测广东鹤山马占相思林14株样树的液流密度,分析了树木个体内和个体之间液流密度的差异、整树和林段水分利用的量化特征.由于树木边材结构以及周围微环境的差别,树木内和个体间的液流密度差异非常明显,变异系数的平均值分别为15.51%-37.26%、37.46%-50.73%.尽管液流密度的差异较大,但同一株树木不同方位的液流密度之间却呈现明显的线性相关（p＜0.0001）,这是重要的特征值,使得只需测定某一方位的液流密度经尺度外推计算整树和林段蒸腾成为可能.树木液流对环境因子响应的变化规律取决于所参照的时间尺度,日变化主要受光辐射、水汽压差等气候因子的控制,而土壤水份对液流的季节变化影响较大.形态特征明显影响树木的液流,高大树木由于边材较厚、树干粗壮和冠幅较宽而承载较多的辐射能量,因而水分蒸腾较高.对树木液流密度在径向和方位上进行适当的整合,可较准确地计算整树和林段蒸腾.由液流估测的马占相思整树和林段蒸腾的结果显示,该群落的水分利用在时间和空间上均有明显的分化.     

葡萄糖和麦芽糖碳源底物对粪产碱杆菌合成凝胶多糖的胞内代谢流影响*

麦芽糖和葡萄糖对粪产碱杆菌发酵合成凝胶多糖有着显著的影响,为了详细分析两种底物对凝胶多糖合成的影响机制,利用恒化培养实验及稳态碳平衡代谢分析,研究发现在稀释速率为0.1h^-1时,利用麦芽糖和葡萄糖为碳源底物的条件下粪产碱杆菌的微观代谢途径通量有较大的差异。以麦芽糖为底物时凝胶多糖的摩尔得率为53.8%,比葡萄糖为碳源时的摩尔得率(36.9%)高出了45.8%以上。同时以麦芽糖为碳源时HMP途径的绝对代谢通量比葡萄糖时的通量提升了40%以上。这条途径通量的增加,提升了NADPH还原力供给速率,促进了依赖于还原力NADPH的凝胶多糖合成途径通量,提升了碳源底物向产物的摩尔转化速率。而且代谢流分析结果显示ED途径通量和能量提供也是影响粪产碱杆菌凝胶多糖合成效率的关键因素。麦芽糖作为碳源底物过程中维持的较低的残留葡萄糖浓度解除了高葡萄糖浓度条件下对凝胶多糖合成的抑制,能够实现更高通量的ATP能量提供效率,更加促进了凝胶多糖合成通量。     

Isolated cardiomyocytes in conjunction with NMR spectroscopy techniques to study metabolism and ion flux.

To distinguish cellular from vascular responses to physiological and pathophysiological stimuli, we developed methods to perform NMR spectroscopy on isolated ventricular cardiomyocytes. Isolated adult rat cardiomyocytes, placed in agarose beads and superfused with phosphate-free buffer (Media 199 (GIBCO 400-1100) gassed with 95% O2, 5% CO2), were used to evaluate a variety of cellular processes during different pharmacological and physiological interventions. Bioenergetic function was monitored with 31P NMR. Intermediary metabolism, gluconeogenesis, and glycolysis were monitored with 13C NMR. Sodium flux was monitored with 23Na NMR. Calcium flux was monitored with 19F NMR in conjunction with an intracellular calcium-chelating agent, 5F-1,2-bis(2-amino-phenoxy)ethane-N,N,N',N'-tetraacetic acid. Creatine kinase kinetics (forward rate constant (Kf) and flux of phosphocreatine to ATP) were estimated with 31P NMR saturation transfer data. Various combinations of NMR parameters were monitored simultaneously so that the interaction of metabolism and ion flux could be evaluated. We have demonstrated that it is possible to simultaneously monitor a variety of cellular processes in intact heart cells in real time, without the confounding influences of perfusion, contractile function, and extrinsic blood-borne neurohumoral agents. This model will be useful for longitudinal studies of myocyte metabolism and ion flux.     

Comparative 13C metabolic flux analysis of pyruvate dehydrogenase complex-deficient, L-valine-producing Corynebacterium glutamicum

L-Valine can be formed successfully using C. glutamicum strains missing an active pyruvate dehydrogenase enzyme complex (PDHC). Wild-type C. glutamicum and four PDHC-deficient strains were compared by (13)C metabolic flux analysis, especially focusing on the split ratio between glycolysis and the pentose phosphate pathway (PPP). Compared to the wild type, showing a carbon flux of 69% ± 14% through the PPP, a strong increase in the PPP flux was observed in PDHC-deficient strains with a maximum of 113% ± 22%. The shift in the split ratio can be explained by an increased demand of NADPH for l-valine formation. In accordance, the introduction of the Escherichia coli transhydrogenase PntAB, catalyzing the reversible conversion of NADH to NADPH, into an L-valine-producing C. glutamicum strain caused the PPP flux to decrease to 57% ± 6%, which is below the wild-type split ratio. Hence, transhydrogenase activity offers an alternative perspective for sufficient NADPH supply, which is relevant for most amino acid production systems. Moreover, as demonstrated for L-valine, this bypass leads to a significant increase of product yield due to a concurrent reduction in carbon dioxide formation via the PPP.     

Cell harvesting by cross-flow microfiltration using a shear-enhanced module

Protein, produced by a bacterial culture of recombinant Vibrio cholerae, was separated from cells in a fermentation broth by cross-flow microfiltration. A new, mechanically agitated (rotational) shear filter, the DMF(TM) filter from Pall, was used to perform the separation. Higher protein recovery and permeate flux than commonly obtained during cell harvesting were demonstrated using sixfold concentration followed by twofold diafiltration. The transmembrane pressure only increased by 10 kPa when the flux was kept constant at 150 L/m(2) h during both concentration and diafiltration. The protein transmission was about 100% initially, and over 90% at the end of the concentration process. The protein transmission during the diafiltration was over 80%. The total recovery of protein was 97%. When using an enzymatic cleaning agent, no significant pure water flux decrease was detected during the course of the experiments. (c) 1996 John Wiley & Sons, Inc.     

Quantification of metabolism in Saccharomyces cerevisiae under hyperosmotic conditions using elementary mode analysis

Yeast metabolism under hyperosmotic stress conditions was quantified using elementary mode analysis to obtain insights into the metabolic status of the cell. The fluxes of elementary modes were determined as solutions to a linear program that used the stoichiometry of the elementary modes as constraints. The analysis demonstrated that distinctly different sets of elementary modes operate under normal and hyperosmotic conditions. During the adaptation phase, elementary modes that only produce glycerol are active, while elementary modes that yield biomass, ethanol, and glycerol become active after the adaptive phase. The flux distribution in the metabolic network, calculated using the fluxes in the elementary modes, was employed to obtain the flux ratio at key nodes. At the glucose 6-phosphate (G6P) node, 25% of the carbon influx was diverted towards the pentose phosphate pathway under normal growth conditions, while only 0.3% of the carbon flux was diverted towards the pentose phosphate pathway during growth at 1?M NaCl, indicating that cell growth is arrested under hyperosmotic conditions. Further, objective functions were used in the linear program to obtain optimal solution spaces corresponding to the different accumulation rates. The analysis demonstrated that while biomass formation was optimal under normal growth conditions, glycerol synthesis was closer to optimal during adaptation to osmotic shock.     

Actinobacillus succinogenes抗氟乙酸突变株的选育及其代谢流量分析

琥珀酸是一种用于合成树脂、可降解塑料及许多化学中间体的重要绿色化工原料。为了提高琥珀酸的发酵产率, 基于Actinobacillus succinogenes的代谢流量分布情况对其育种机制进行了研究。以Actinobacillus succinogenes CGMCC1593为原始菌株进行NTG诱变, 挑选在含有50~100 mmol/L氟乙酸平板生长较快的菌落, 经过初筛和复筛, 发现SF-9菌株产生更多琥珀酸且积累乙酸较少。以50 g/L的葡萄糖为碳源, 在5 L发酵罐上进行分批发酵, 该菌株发酵32 h时琥珀酸产量(34.8 g/L)提高了23.4%, 琥珀酸/乙酸比率为9:1, 副产物乙酸量比原始菌株降低了约50%。代谢流量分析(MFA)结果表明, PEP是影响琥珀酸合成的关键节点, PYR是影响乙酸等杂酸生成比例的关键节点, 并且这两个节点均非刚性节点。通过氟乙酸抗性诱变, 成功地筛选出了流向乙酸、甲酸和乳酸等杂酸的流量相对减少, 而流向琥珀酸的流量明显增强的突变菌株SF-9。     

Actinobacillus succinogenes抗氟乙酸突变株的选育及其代谢流量分析

琥珀酸是一种用于合成树脂、可降解塑料及许多化学中间体的重要绿色化工原料。为了提高琥珀酸的发酵产率, 基于Actinobacillus succinogenes的代谢流量分布情况对其育种机制进行了研究。以Actinobacillus succinogenes CGMCC1593为原始菌株进行NTG诱变, 挑选在含有50~100 mmol/L氟乙酸平板生长较快的菌落, 经过初筛和复筛, 发现SF-9菌株产生更多琥珀酸且积累乙酸较少。以50 g/L的葡萄糖为碳源, 在5 L发酵罐上进行分批发酵, 该菌株发酵32 h时琥珀酸产量(34.8 g/L)提高了23.4%, 琥珀酸/乙酸比率为9:1, 副产物乙酸量比原始菌株降低了约50%。代谢流量分析(MFA)结果表明, PEP是影响琥珀酸合成的关键节点, PYR是影响乙酸等杂酸生成比例的关键节点, 并且这两个节点均非刚性节点。通过氟乙酸抗性诱变, 成功地筛选出了流向乙酸、甲酸和乳酸等杂酸的流量相对减少, 而流向琥珀酸的流量明显增强的突变菌株SF-9。     

Effects of insulin on perfused liver from streptozotocin-diabetic and untreated rats: 13C NMR assay of pyruvate kinase flux

The effects of insulin in vitro on perfused liver from streptozotocin-diabetic rats and their untreated littermates during gluconeogenesis from either [3-13C]alanine + ethanol or [2-13C]pyruvate + NH4Cl + ethanol were studied by 13C NMR. A 13C NMR determination of the rate of pyruvate kinase flux under steady-state conditions of active gluconeogenesis was developed; this assay includes a check on the reuse of recycled pyruvate. The preparations studied provided gradations of pyruvate kinase flux within the confines of the assay's requirement of active gluconeogenesis. By this determination, the rate of pyruvate kinase flux was 0.74 +/- 0.04 of the gluconeogenic rate in liver from 24-h-fasted controls; in liver from 12-h-fasted controls, relative pyruvate kinase flux increased to 1.0 +/- 0.2. In diabetic liver, this flux was undetectable by our NMR method. Insulin's hepatic influence in vitro was greatest in the streptozotocin model of type 1 diabetes: upon treatment of diabetic liver with 7 nM insulin in vitro, a partial reversal of many of the differences noted between diabetic and control liver was demonstrated by 13C NMR. A major effect of insulin in vitro upon diabetic liver was the induction of a large increase in the rate of pyruvate kinase flux, bringing relative and absolute fluxes up to the levels measured in 24-h-fasted controls. By way of comparison, the effects of ischemia on diabetic liver were studied by 13C NMR to test whether changes in allosteric effectors under these conditions could also increase pyruvate kinase flux. A large increase in this activity was demonstrated in ischemic diabetic liver.     

Cardiac creatine kinase metabolite compartments revealed by NMR magnetization transfer spectroscopy and subcellular fractionation

In the perfused rat heart NMR inversion transfer revealed the existence of a compartment of ATP not exchanging through creatine kinase (CK), as demonstrated by an apparent discrepancy between the forward (F(f)) and reverse (F(r)) CK flux if this compartment was neglected in the analysis [Joubert et al. (2000) Biophys. J. 79, 1-13]. To localize this compartment, CK fluxes were measured by inversion of PCr (inv-PCr) or gamma ATP (inv-ATP), and the distribution of metabolites between mitochondria and cytosol was studied by subcellular fractionation. Physiological conditions were designed to modify the concentration and distribution of CK metabolites (control, adenylate depletion, inhibition of respiration, KCl arrest). Depending on cardiac activity, mitochondrial ATP (mito-ATP) assessed by fractionation varied from 11% to 30% of total ATP. In addition, the apparent flux discrepancy increased together with mito-ATP (F(f)/F(r) ranged from 0.85 to 0.50 in inv-PCr and from 1.13 to 1.88 in inv-ATP). Under conditions masking the influence of the ATP-P(i) exchange on CK flux, the ATP compartment could be directly quantified by the apparent flux discrepancy; its size was similar to that of mito-ATP measured by fractionation. Thus NMR inversion technique is a potential tool to assess metabolite compartmentation in the whole organ.     

华南丘陵区冬闲稻田二氧化碳、甲烷和氧化亚氮的排放特征

采用静态箱 气相色谱法对收获后冬闲稻田CO₂、CH₄和N₂O排放进行了田间原位测定,探讨了越冬稻田3种温室气体的排放规律.结果表明,残茬稻田和裸田的CO₂的排放峰值分别出现在18:00和16:00左右.日间CH₄排放为净值,夜间表现为弱吸收.残茬稻田和裸田N₂O夜间排放分别为日间平均的1.79和1.58倍.残茬稻田的昼夜CO₂平均排放通量显著高于裸田(P＜0.05).在测定期间,残茬稻田CO₂排放随温度升高而增高.相关分析表明,CO₂排放与土温、地表温度和气温均呈显著相关,表明温度是影响收获后稻田CO₂排放的主要因素.在11月10日至翌年1月18日测定期间,残茬稻田的CO₂和CH₄平均排放通量分别为(180.69±21.21) mg·m^-2·h^-1和(-0.04±0.01) mg·m^-2·h^-1,CO₂排放通量较裸田高13.06％,CH₄吸收增高50%.残茬稻田的N₂O排放通量为(21.26±19.31) μg·m^-2·h^-1,较裸田低60.75％.由此说明华南丘陵区冬闲稻田是大气CO₂和N₂O的源,CH₄的汇.     

High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints

13C-constrained flux balancing analysis based on gas chromatography-mass spectrometry data is presented here as a simple and robust method for the estimation of intracellular carbon fluxes. In this approach, the underdetermined system of metabolite balances deduced from stoichiometric relations and measured extracellular rates is complemented with 13C constraints from metabolic flux ratio analysis. Fluxes in central carbon metabolism of exponentially growing Escherichia coli were estimated by 13C-constrained flux balancing from three different 13C-labeled glucose experiments. The best resolution of the network was achieved using 13C constraints derived from [U-13C]glucose and [1-13C]glucose experiments. The corresponding flux estimate was in excellent agreement with a solution that was independently obtained with a comprehensive isotopomer model. This new methodology was also demonstrated to faithfully capture the intracellular flux distribution in E. coli shake flasks and 1-ml deep-well microtiter plates. Due to its simplicity, speed, and robustness, 13C-constrained metabolic flux balancing is promising for routine and high-throughput analysis on a miniaturized scale.     

Effects of photoperiod on sodium flux in Corbicula fluminea (Mollusca:Bivalvia)

• 1.1. A significant diurnal rhythm of net sodium flux was demonstrated in the freshwater clam Corbicula fluminea entrained to either a 12L:12D or 24L photoperiod.
• 2.2. Highest net flux occurred during the dark hours on 12L: 12D. The overall mean net flux over 24 hr was not significantly different from a steady state condition.
• 3.3. Net flux values of clams on a 24L photoperiod were negative and significantly lower than the net flux on a 12L:12D photoperiod.
• 4.4. The 12L: 12D net sodium flux rhythm pattern is similar to rhythmic patterns of other physiological processes in another freshwater clam.

     

不同溶氧条件下L-苏氨酸生物合成菌株的代谢流量分析

[目的]探索L-苏氨酸生物合成机理及影响因素.[方法]建立了大肠杆菌L-苏氨酸的代谢流平衡模型,应用MATLAB软件计算出不同溶氧条件下发酵中后期代谢网络的代谢流分布及理想代谢流分布.[结果]5%溶氧条件下,25.5%碳架进入HMP途径,74.5%碳架进入糖酵解途径,获得33.9%质量转化率;20%溶氧条件下,58.08%碳架进入HMP途径,41.92%碳架进入糖酵解途径,获得46.5%质量转化率;[结论]与理想代谢流(88.23%质量转化率)相比,应从菌种改造和发酵控制方面通过改变6-磷酸葡萄糖异构酶借以增加HMP途径代谢流量,通过增加磷酸烯醇式丙酮酸羧化反应代谢流提高天冬氨酸族合成代谢流,减少TCA循环代谢流量,从而达到减少副产物生成,增加L-苏氨酸生物合成的目的.     

Seasonal and interindividual variation in field water metabolism of female meadow voles Microtus pennsylvanicus.

We analyzed variations in water flux rates on a large sample of meadow voles (Microtus pennsylvanicus) to quantify the effect of season on water metabolism of individuals and to examine patterns of intra- and interindividual variability. Voles were nonreproductive females maintained in outdoor enclosures where they fed on natural vegetation. They were injected one to three times with doubly labeled water, which resulted in one to six measures of daily water flux rate per individual. Summer water flux rates of voles were 258% of the predicted values for herbivorous eutherian mammals of similar size. To date, very few studies have focused on mammals with such high water flux rates. Body water volume of individuals was higher in summer than in winter (75.6% vs. 72.5%), and water flux rate of animals was 12.5% higher in the winter season (0.99 vs. 0.88 mL H2O g-1 d-1). Between-season differences in water fluxes were proportional to differences in energy expenditures, hence the water economy index remained constant across seasons (0.30 mL H2O kJ-1). Intraindividual variability of water flux rate was high compared to interindividual variability (repeatability, r<0.30), which will make it difficult to study natural selection of water metabolism in a microevolutionary framework, at least in meadow voles.     

Studies on enhanced post-illumination respiration in microalgae

The extent of enhanced post-illumination respiration (EPIR)has been investigated in a number of microalgae. Respirationrates, as determined by O₂ consumption, were enhanced (in allbut one case) by 50–140% following pre-exposure to highphoton flux compared to rates obtained for steady-state darkrespiration. The extent of EPIR was dependent more on photonflux than on duration of exposure, although the latter did havesome effect. In Isochrysis galbana and Chaetoceros calcitrens,EPIR effects were also demonstrated using [¹⁴C]CO₂ evolution.In I.galbana, release of CO₂ from cells pre-exposed to a periodof high photon flux was most rapid from carbohydrate and low-molecular-weightmetabolites. Data obtained from Thalassiosira weisflogii indicatethat cells grown at low photon flux are more susceptible toEPIR than those grown under high photon flux. These resultsare discussed in the context of various hypotheses that havebeen proposed regarding the mechanism of EPIR effects. ⁸Present address: RIVM-LWD, PO Box 1, 3720 BA Bilthoven, TheNetherlands     

Antagonistic regulation of the glucose/glucose 6-phosphate cycle by insulin and glucagon in cultured hepatocytes.

Flux through the glucose/glucose 6-phosphate cycle in cultured hepatocytes was measured with radiochemical techniques. Utilization of [2-3H]glucose was taken as a measure of glucokinase flux. Liberation of [14C]glucose from [U-14C]glycogen and from [U-14C]lactate, as well as the difference between the utilization of [2-3H]glucose and of [U-14C]glucose, were taken as measures of glucose-6-phosphatase flux. At constant 5 mM-glucose and 2 mM-lactate concentrations insulin increased glucokinase flux by 35%; it decreased glucose-6-phosphatase flux from glycogen by 50%, from lactate by 15% and reverse flux from external glucose by 65%, i.e. overall by 40%. Glucagon had essentially no effect on glucokinase flux; it enhanced glucose-6-phosphatase flux from glycogen by 700%, from lactate by 45% and reverse flux from external glucose by 20%, i.e. overall by 110%. At constant glucose concentrations cellular glucose 6-phosphate concentrations were essentially not altered by insulin, but were increased by glucagon by 230%. In conclusion, under basic conditions without added hormones the glucose/glucose 6-phosphate cycle showed only a minor net glucose uptake, of 0.03 mumol/min per g of hepatocytes; this flux was increased by insulin to a net glucose uptake of 0.21 mumol/min per g and reversed by glucagon to a net glucose release of 0.22 mumol/min per g. Since the glucose 6-phosphate concentrations after hormone treatment did not correlate with the glucose-6-phosphatase flux, it is suggested that the hormones influenced the enzyme activity directly.     

Effects of benthic macroinvertebrates on the exchange of solutes between sediments and freshwater

Infaunal macrobenthos (tubificid oligochaetes, chironomid larvae, and unionid bivalves) were studied in laboratory microcosms to determine their effects on freshwater sediment diagnesis and the exchange of solutes between sediments and water. Tubificids enhanced the flux of ammonium, bicarbonate, and silica from sediments. After the onset of anoxia, they decreased the flux of iron and phosphate. Chironomids increased the flux of nitrate, bicarbonate, and silica, but did not affect the flux of phosphate. Pore water concentrations were low within the irrigated burrowed zone for chemical species normally high in reduced sediments. Concentration gradients were less steep in the actively irrigated burrow zone, but radial diffusion to and from burrows, increased rates of organic decomposition, and enhanced diatom frustule dissolution rates result in enhanced mass transport from sediments. Data from an experiment with unionid clams demonstrated the presence of radial diffusion gradients. These clams enhanced the chloride and nitrate flux from sediments, decreased the bicarbonate flux, but did not affect the flux of either phosphate or silicate. Although the clams did not actively irrigate their burrows, their effect on sediments was similar to that of chironomids. Comparison of direct and indirect flux estimates showed that both types of estimates could be highly variable. In general, indirect flux estimates were higher than direct flux estimates.     

Comparing membrane and spacer biofouling by Gram-negative Pseudomonas aeruginosa and Gram-positive Anoxybacillus sp. in forward osmosis

Bacteria of different Gram-types have inherently different outer cell structures, influencing cell surface properties and bacterial attachment. Dynamic biofouling experiments were conducted over four days in a bench-scale forward osmosis (FO) system with Gram-negative Pseudomonas aeruginosa or Gram-positive Anoxybacillus sp. Biofouling resulted in ～10% decline in FO permeate water flux and was found to be significant for Anoxybacillus sp. but not for P. aeruginosa. Additionally, a stronger permeate water flux decline for P. aeruginosa in experiments with a superhydrophilic feed spacer demonstrated that mitigation methods require testing with different bacterial Gram-types. It was found that although permeate water flux decline can be affected by bacterial Gram-type the stable performance under enhanced biofouling conditions highlights the potential of FO for wastewater reclamation.