13C标记代谢流分析中天然稳定性同位素修正矩阵构建方法及应用

稳定性同位素¹³C标记实验是分析细胞代谢流的一种重要手段,主要通过质谱检测胞内代谢物中¹³C标记的同位素分布,并作为胞内代谢流计算时的约束条件,进而通过代谢流分析算法得到相应代谢网络中的通量分布。然而在自然界中,并非只有C元素存在天然稳定性同位素¹³C,其他元素如O元素也有其天然稳定性同位素¹⁷O、¹⁸O等,这使得质谱方法所测得的同位素分布中会夹杂除¹³C标记之外的其他元素的同位素信息,特别是分子中含有较多其他元素的分子,这将导致很大的实验误差,因此需要在进行代谢流计算前进行质谱数据的矫正。本研究提出了一种基于Python语言的天然同位素修正矩阵的构建方法,用于修正同位素分布测量值中由于天然同位素分布引起的测定误差。文中提出的基本修正矩阵幂方法用于构建各元素修正矩阵,结构简单、易于编码实现,可直接应用于¹³C代谢流分析软件数据前处理。将该修正方法应用于¹³C标记的黑曲霉（Aspergillus niger）胞内代谢流分析,结果表明本研究提出的方法准确有效,为准确获取微生物胞内代谢流分析提供了可靠的数据修正方法。     

13C代谢流量分析发展30年

13C代谢流量分析(13C metabolic flux analysis,13C-MFA),是通过标记实验分析蛋白氨基酸或胞内代谢物同位素标记异构体的分布情况,从而准确定量胞内反应速率.该技术在系统理解细胞代谢特性、指导代谢工程改造和揭示病理生理学等方面起着重要作用,引起研究者的广泛重视.文中重点综述了代谢流分析30...     

生理代谢参数RQ在指导发酵过程优化中的应用

过程在线参数检测是进行发酵过程工程优化控制的基础。呼吸熵RQ是微生物胞内微观代谢流在宏观代谢参数上的响应,反映了微生物培养过程中底物的利用情况、产物和副产物的合成情况、及微观代谢途径通量的变化。结合发酵葡萄糖酸、2,3-丁二醇谷氨酸、柠檬酸、头孢菌素C、毕赤酵母α-干扰素产品的工业生产过程,分析了以微生物胞内微观代谢与宏观的生理参数RQ为指导的发酵工艺优化策略。RQ值在发酵过程中可以根据尾气数据进行在线采集,对指导通过宏观代谢参数的调控来最优化微生物胞内的代谢途经通量,提高目的产物的产率具有非常重要的意义。     

氧化磷酸化抑制剂对光滑球拟酵母糖酵解速度的影响

研究了不同浓度电子传递链抑制剂 ( 鱼藤酮和抗霉素 A) 和 F_OF₁-ATPase 抑制剂 ( 寡霉素 ) 对光滑球拟酵母胞内 ATP 水平、葡萄糖消耗速度、糖酵解途径关键酶的影响 . 在培养液中添加 10 mg/L 鱼藤酮和抗霉素 A ,相对于对照组,胞内 ATP 分别下降了 43% 和 27.7% ,使糖酵解关键酶磷酸果糖激酶 (PFK) 的活性分别提高 340% 和 230% ,从而导致葡萄糖消耗速度增加 360% 和 240% ,丙酮酸生成速度提高了 17% 和 8.5%. 改变胞内 ATP 水平并不影响糖酵解途径其他关键酶 HK 、 PK 活性 . 微量的寡霉素 (0.05 mg/L) 可使胞内 ATP 含量下降 64.3% ,当培养液中寡霉素浓度达到 0.4 mg/L 时,细胞不能继续生长,葡萄糖消耗速度和丙酮酸的生成速度却随着寡霉素浓度 ( 小于 0.6 mg/L) 的增加而增加 . 表明氧化磷酸化途径中, ATPase 决定着 ATP 的生成 . 降低胞内 ATP 含量能显著提高 PFK 活性 (r²=0.9971) ,葡萄糖消耗速度 (r²= 0.9967) 以及丙酮酸生产速度 (r²= 0.965) ,葡萄糖消耗速度的增加是糖酵解途径中关键酶 PFK 活性 (r² = 0.9958) 和 PK 活性 (r²= 0.8706) 增加所导致的 . 这一结果有利于揭示真核微生物细胞中氧化磷酸化与中心代谢途径 ( 酵解 ) 的关系 .     

有机锗对巨噬细胞激活与磷脂代谢转换的影响

有机锗(CGS、DGS、Ge-132)于活体内能激活小鼠腹腔巨噬细胞(Mφ),后者于体外对肿瘤细胞Hca-16H₃和J6-2表达Mφ介导的肿瘤细胞毒(MTC),CGS与DGS的激活效应高于Ge-132,CGS为最强.它们激活的Mφ磷脂PC代谢转换较常驻Mφ(R-Mφ)明显增高,表现在［³H］胆碱掺入PC增加,CGS的增加效应最强.Ge-132激活的Mφ(Ge-12-Mφ)与R-Mφ比较,增加［³²P］Pi掺入PC,降低［³²P］Pi或［³H］肌醇掺入PI,但［³²P］Pi或［³H］肌醇掺入PIP、PIP₂未有显著差异.PC代谢转换的增加很可能是有机锗激活Mφ表达MTC的信息传递所需要的.     

叶施NO对NaCl胁迫下红砂幼苗叶片和根系中氮代谢酶及营养物质的影响

以当年生红砂(Reaumuria soongorica)幼苗为材料,采用盆栽实验,考察叶面喷施不同浓度(0、0.01、0.10、0.25、0.50、1.00 mmol·L^-1)NO供体硝普钠 (SNP) 对NaCl(300 mmol·L^-1)胁迫下红砂根、叶中可溶性蛋白、游离氨基酸和硝态氮含量,以及谷氨酰胺合成酶(GS)、谷氨酸合酶(GOGAT)、硝酸还原酶(NR)活性的影响,并采用主成分分析和隶属函数法筛选NO对NaCl胁迫缓解效应的氮代谢指标和最佳NO浓度,以探讨外源NO对NaCl 胁迫下红砂缓解效应的氮代谢响应机制。结果表明：(1)在300 mmol·L^-1 NaCl胁迫处理下,红砂幼苗根、叶中可溶性蛋白、硝态氮含量以及GS、GOGAT、NR活性均比对照显著下降。(2)外源NO能显著提高盐胁迫下红砂叶、根中GS、GOGAT、NR活性和硝态氮含量,增加根中可溶性蛋白和游离氨基酸含量。(3)NR和GOGAT活性可用于评价NO对NaCl胁迫下红砂幼苗的缓解作用,外源NO(SNP)对红砂幼苗在NaCl胁迫下的缓解效果强弱表现为0.25 mmol·L^-1> 0.50 mmol·L^-1> 0.10 mmol·L^-1> 1.00 mmol·L^-1> 0.01 mmol·L^-1。研究发现,300 mmol·L^-1 NaCl胁迫显著抑制了红砂幼苗氮代谢,外源NO(SNP)有助于提高盐胁迫下红砂NR活性,加快硝态氮转化为铵态氮,促进红砂叶片和根中GS/GOGAT对转化物的同化,从而增强红砂幼苗的耐盐性,并以0.25 mmol·L^-1SNP处理时缓解作用最佳;NR和GOGAT活性可作为NO缓解盐胁迫的评价指标。     

外源CaCl2对NaCl胁迫下酸枣幼苗氮代谢的影响

为了研究CaCl₂对NaCl胁迫下酸枣幼苗根、茎、叶的氮代谢影响,探索钙缓解幼苗NaCl胁迫的作用途径。该研究以酸枣幼苗为试验材料,检测不同浓度CaCl₂(0、5、10、20 mmol/L)对NaCl(150 mmol/L)胁迫下幼苗叶片H₂O₂、O^-·₂含量,根、茎、叶中硝酸还原酶(NR)、谷氨酰胺合成酶(GS)、谷氨酸合酶(GOGAT)活性及游离氨基酸、可溶性蛋白、硝态氮含量的影响,并采用主成分分析法筛选出评价CaCl₂缓解NaCl胁迫效应的生理指标。结果表明：与NaCl胁迫相比,盐胁迫幼苗叶片的H2O₂、O^-·₂积累量在5、10 mmol/L CaCl₂处理下显著减少;GOGAT活性在5、10 mmol/L CaCl₂处理下的植株根和茎内以及各浓度 CaCl₂处理的叶内均显著升高, GS、NR活性在10、20 mmol/L CaCl₂处理的根内和10 mmol/L CaCl₂处理的茎内以及5、10、20 mmol/L CaCl₂处理的叶内均显著升高;可溶性蛋白含量在5、10、20 mmol/L CaCl₂处理的根、茎、叶内均显著升高,游离氨基酸含量在10、20 mmol/L CaCl₂处理的根和茎内以及10 mmol/L CaCl₂处理的叶内均显著升高,硝态氮含量在10 mmol/L CaCl₂处理的根和茎内以及5、10、20 mmol/L CaCl₂处理的叶内均显著升高。研究发现,150 mmol/L NaCl胁迫对酸枣幼苗造成明显过氧化伤害,抑制了体内氮代谢;外源CaCl₂可通过促进幼苗根和茎内GS/GOGAT循环对NH₄⁺的同化作用,提高叶片NR活性,加快硝态氮的转化速率,从而增强幼苗对NaCl胁迫的适应性,并以10 mmol/L CaCl₂处理缓解效果最佳;游离氨基酸、GOGAT、NR可以作为CaCl₂缓解幼苗NaCl胁迫伤害的评价指标。     

GM3抑制人白血病J6－2细胞肌醇磷脂代谢循环

采用无载体 ³²P和[ ³H]肌醇标记磷脂,观察了促分化剂神经节苷脂GM₃对人单核样白血病J6-2细胞肌醇磷脂代谢的影响.GM₃抑制[ ³²P]Pi和[ ³H]肌醇掺入J6-2细胞磷脂酰肌醇(PI),促进[ ³²P]Pi和[ ³H]肌醇掺入磷脂酰肌醇-4,5-二磷酸(PIP₂),抑制[ ³²P]Pi掺入磷脂酸(PA),抑制[ ³H]肌醇掺入三磷酸肌醇(IP₃).GM₃的上述作用均为浓度依赖性的,随GM₃浓度的提高而增强.上述结果表明,GM₃抑制J6-2细胞的肌醇磷脂代谢循环.     

HCO-3对植物生长发育及代谢的促进作用

重碳酸盐(bicarbonate, HCO^-₃)是碳酸盐岩经岩溶作用风化的产物,它深刻地影响着植物的生长发育和岩溶地区的生态环境。以往研究大都关注HCO^-₃对植物生长代谢的负面影响,如抑制植物的光合作用、降低碳氮代谢关键酶活性、破坏离子平衡等,少有人关注其对植物生长代谢的积极作用。该文依据前人的研究结果,综述了HCO^-₃对植物生长代谢的促进作用。已有的研究工作显示,HCO^-₃不仅在干旱等逆境胁迫下为植物提供短期的碳源和水源,促进气孔打开,恢复光合作用,而且通过调节碳氮代谢关键酶活性促进植物的碳氮代谢,参与调控植物的碳同化和氮还原等复杂的生理过程; 此外,HCO^-₃还通过影响葡萄糖代谢歧化,改变植物糖酵解途径和磷酸戊糖途径的分配,以增强植物的抗逆能力,从而获取生存机会。HCO^-₃的这些积极作用不仅使之成为促进植物生理代谢的关键因子,而且成为连接光合作用和岩溶作用的纽带。阐明HCO^-₃对植物生长发育的积极作用,可为维护喀斯特生态系统的生物多样性和稳定性、优化喀斯特生态系统功能提供理论依据。     

基于PKS和NRPS基因的海洋来源抗病原菌活性菌株筛选及其代谢产物活性分析

基于聚酮合成酶基因(polyketide synthases gene,PKS)和非核糖体多肽合成酶基因(non ribosomal polypeptide synthase gene,NRPS),本研究从77株分离于北冰洋海泥的菌株中筛选出1株具有较高抗病原菌活性的菌株并对其进行了菌种鉴定。通过优化培养基组成和发酵条件提高了该菌株活性代谢产物的产量,并利用高分辨率质谱(high resolution mass spectrometry,HRMS)、核磁氢谱(¹H nuclear magnetic hydrogen,¹H NMR)和碳谱(¹³C NMR)对其主要代谢产物进行了结构鉴定。测定了该菌株主要代谢产物的抗菌谱及代谢产物对黄瓜枯萎病的影响。研究结果表明,该菌株为贝莱斯芽孢杆菌(Bacillus velezensis),其对植物具有一定的促生作用。当发酵条件为麦芽糖5g/L、胰蛋白胨10g/L、氯化钠10g/L、温度30℃、转速150r/min、发酵时间60h时,该菌株代谢产物的抑菌圈直径由(16.23±0.42)mm提高至(24.42±0.57)mm。菌株代谢产物含有大环内酯类化合物macrolactin A,其对多种病原细菌和真菌具有明显拮抗作用。黄瓜幼苗实验表明,该菌株代谢产物对黄瓜枯萎病具有防护作用,其作为生防菌剂具有一定的开发应用潜力。     

Reciprocal 13C-labeling: a method for investigating the catabolism of cosubstrates

The principle of reciprocal labeling is to use a uniformly 13C-labeled substrate as the primary carbon source and a naturally labeled cosubstrate. Metabolites derived from a naturally labeled cosubstrate, in this case amino acids, can then be identified by their relatively lower content of 13C, and information on the degradation pathway can be deduced. The technique is based on GC-MS measurements of amino acid labeling patterns, making the technique well suited for investigating the relative importance of amino acid biosynthesis and amino acid uptake from the medium, as the 13C content of the amino acids incorporated into biomass is a direct measure of the amino acid biosyntheses. The technique is illustrated by the investigation of the degradation of phenoxyacetic acid, a medium component that is essential for production of penicillin V by Penicillium chrysogenum. Glucose was used as the uniformly labeled primary carbon source.     

13C Nuclear Magnetic Resonance Evidence for γ-Aminobutyric Acid Formation via Pyruvate Carboxylase in Rat Brain: A Metabolic Basis for Compartmentation0

The compartmentation of amino acid metabolism is an active and important area of brain research. 13C labeling and 13C nuclear magnetic resonance (NMR) are powerful tools for studying metabolic pathways, because information about the metabolic histories of metabolites can be determined from the appearance and position of the label in products. We have used 13C labeling and 13C NMR in order to investigate the metabolic history of gamma-aminobutyric acid (GABA) and glutamate in rat brain. [1-13C]Glucose was infused into anesthetized rats and the 13C labeling patterns in GABA and glutamate examined in brain tissue extracts obtained at various times after infusion of the label. Five minutes after infusion, most of the 13C label in glutamate appeared at the C4 position; at later times, label was also present at C2 and C3. This 13C labeling pattern occurs when [1-13C]glucose is metabolized to pyruvate by glycolysis and enters the pool of tricarboxylic acid (TCA) intermediates via pyruvate dehydrogenase. The label exchanges into glutamate from the TCA cycle pool through glutamate transaminases or dehydrogenase. After 30 min of infusion, approximately 10% of the total 13C in brain extracts appeared in GABA, primarily (greater than 80%) at the amino carbon (C4), indicating that the GABA detected is labeled through pyruvate carboxylase. The different labeling patterns observed for glutamate and GABA show that the large detectable glutamate pool does not serve as the precursor to GABA. Our NMR data support previous experiments suggesting compartmentation of metabolism in brain, and further demonstrate that GABA is formed from a pool of TCA cycle intermediates derived from an anaplerotic pathway involving pyruvate carboxylase.     

Determination of metabolic flux changes during fed-batch cultivation from measurements of intracellular amino acids by LC-MS/MS

Metabolic flux analysis using (13)C-labeled substrates is a well-developed method for investigating cellular behavior in steady-state culture condition. To extend its application, in particular to typical industrial conditions, such as batch and fed-batch cultivations, a novel method of (13)C metabolic flux analysis is proposed. An isotopomer balancing model was developed to elucidate flux distributions in the central metabolism and all amino acids synthetic pathways. A lysine-producing strain of Escherichia coli was cultivated by fed-batch mode in a growth medium containing yeast extract. Mass distribution data was derived from both intracellular free amino acids and proteinogenic amino acids measured by LC-MS/MS, and a correction parameter for the protein turnover effect on the mass distributions of intracellular amino acids was introduced. Metabolic flux distributions were determined in both exponential and stationary phases. Using this new approach, a culture phase-dependent metabolic shift was detected in the fed-batch culture. The approach presented here has great potential for investigating cellular behavior in industrial processes, independent of cultivation modes, metabolic phase and growth medium.     

Biosynthetic pathways in Methanospirillum hungatei as determined by 13C nuclear magnetic resonance

The main metabolic pathways in Methanospirillum hungatei GP1 were followed by using 13C nuclear magnetic resonance, with 13C-labeled acetate and CO2 as carbon sources. The labeling patterns found in carbohydrates, amino acids, lipids, and nucleosides were consistent with the formation of pyruvate from acetate and CO2 as the first step in biosynthesis. Carbohydrates are formed by the glucogenic pathway, and no scrambling of label was observed, indicating that the oxidative or reductive pentose phosphate pathways are not functioning at significant rates. The pathways for amino acid biosynthesis are the usual ones, with the exception of that for isoleucine. The tricarboxylic acid pathway is incomplete and operates in a reductive direction to form alpha-ketoglutarate. The phytanyl chains of lipids are synthesized from acetate via mevalonic acid.     

Metabolic flux analysis in Escherichia coli by integrating isotopic dynamic and isotopic stationary 13C labeling data

The novel concept of isotopic dynamic 13C metabolic flux analysis (ID-13C MFA) enables integrated analysis of isotopomer data from isotopic transient and/or isotopic stationary phase of a 13C labeling experiment, short-time experiments, and an extended range of applications of 13C MFA. In the presented work, an experimental and computational framework consisting of short-time 13C labeling, an integrated rapid sampling procedure, a LC-MS analytical method, numerical integration of the system of isotopomer differential equations, and estimation of metabolic fluxes was developed and applied to determine intracellular fluxes in glycolysis, pentose phosphate pathway (PPP), and citric acid cycle (TCA) in Escherichia coli grown in aerobic, glucose-limited chemostat culture at a dilution rate of D = 0.10 h(-1). Intracellular steady state concentrations were quantified for 12 metabolic intermediates. A total of 90 LC-MS mass isotopomers were quantified at sampling times t = 0, 91, 226, 346, 589 s and at isotopic stationary conditions. Isotopic stationarity was reached within 10 min in glycolytic and PPP metabolites. Consistent flux solutions were obtained by ID-13C MFA using isotopic dynamic and isotopic stationary 13C labeling data and by isotopic stationary 13C MFA (IS-13C MFA) using solely isotopic stationary data. It is demonstrated that integration of dynamic 13C labeling data increases the sensitivity of flux estimation, particularly at the glucose-6-phosphate branch point. The identified split ratio between glycolysis and PPP was 55%:44%. These results were confirmed by IS-13C MFA additionally using labeling data in proteinogenic amino acids (GC-MS) obtained after 5 h from sampled biomass.     

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, ¹³C Metabolic Flux Analysis (¹³C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during ¹³C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of ¹³C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based ¹³C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species.     

Metabolic Flux Responses to Pyruvate Kinase Knockout in Escherichia coli

The intracellular carbon flux distribution in wild-type and pyruvate kinase-deficient Escherichia coli was estimated using biosynthetically directed fractional 13C labeling experiments with [U-13C6]glucose in glucose- or ammonia-limited chemostats, two-dimensional nuclear magnetic resonance (NMR) spectroscopy of cellular amino acids, and a comprehensive isotopomer model. The general response to disruption of both pyruvate kinase isoenzymes in E. coli was a local flux rerouting via the combined reactions of phosphoenolpyruvate (PEP) carboxylase and malic enzyme. Responses in the pentose phosphate pathway and the tricarboxylic acid cycle were strongly dependent on the environmental conditions. In addition, high futile cycling activity via the gluconeogenic PEP carboxykinase was identified at a low dilution rate in glucose-limited chemostat culture of pyruvate kinase-deficient E. coli, with a turnover that is comparable to the specific glucose uptake rate. Furthermore, flux analysis in mutant cultures indicates that glucose uptake in E. coli is not catalyzed exclusively by the phosphotransferase system in glucose-limited cultures at a low dilution rate. Reliability of the flux estimates thus obtained was verified by statistical error analysis and by comparison to intracellular carbon flux ratios that were independently calculated from the same NMR data by metabolic flux ratio analysis.     

Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models.

Complete isotopomer models that simulate distribution of label in 13C tracer experiments are applied to the quantification of metabolic fluxes in the primary carbon metabolism of E. coli under aerobic and anaerobic conditions. The concept of isotopomer mapping matrices (IMMs) is used to simplify the formulation of isotopomer mass balances by expressing all isotopomer mass balances of a metabolite pool in a single matrix equation. A numerically stable method to calculate the steady-state isotopomer distribution in metabolic networks in introduced. Net values of intracellular fluxes and the degree of reversibility of enzymatic steps are estimated by minimization of the deviations between experimental and simulated measurements. The metabolic model applied includes the Embden-Meyerhof-Parnas and the pentose phosphate pathway, the tricarboxylic acid cycle, anaplerotic reaction sequences and pathways involved in amino acid synthesis. The study clearly demonstrates the value of complete isotopomer models for maximizing the information obtainable from 13C tracer experiments. The approach applied here offers a completely general and comprehensive analysis of carbon tracer experiments where any set of experimental data on the labeling state and extracellular fluxes can be used for the quantification of metabolic fluxes in complex metabolic networks.