利用气相色谱-质谱联机测定土壤氨基酸手性异构体13C富集比例

氨基酸手性异构体的转化与更新程度在表征土壤有机质的循环转化机制方面具有重要意义.为有效区分土壤中原有的和利用外加碳源新合成的氨基酸,本文建立了稳定同位素培养 气相色谱/质谱联机测定土壤氨基酸手性异构体¹³C富集比例的方法.由于培养过程中加入的¹³C葡萄糖被迅速利用形成氨基酸碳骨架,因而利用质谱技术可检测同位素的富集强度的变化.外加葡萄糖直接合成氨基酸的比例可利用质谱碎片(F+n)的相对强度变化来评价（n为质谱碎片F中含有的碳原子数目）;而源于葡萄糖的¹³C同位素在氨基酸分子中的富集程度是所有同位素峰相对强度变化的总和.¹³C在目标化合物中的富集比例用原子百分超（APE）评价,D 氨基酸的APE还需进一步利用水解诱导的外消旋化系数校正.¹³C在目标化合物中的富集程度可反映各氨基酸手性异构体的碳循环速率大小,是研究土壤氨基酸动态变化的有力工具.     

集约化生产对农田土壤碳氮含量及δ13C和δ15N同位素丰度的影响

集约化生产下农田土壤碳、氮含量变化是衡量土壤肥力持久性的重要指标.对常规水稻-蚕豆轮作地、露地蔬菜地、3年塑料大棚地和10年以上塑料大棚地的土壤pH、电导率(EC)、土壤有机碳(SOC)和总氮(TN)含量及δ13C和δ15N同位素丰度进行测定,研究了集约化生产程度对土壤特性的影响.结果表明： 与水稻-蚕豆轮作地相比,露地蔬菜地、3年塑料大棚地和10年以上塑料大棚地0～20 cm耕层土壤pH分别降低1.1、0.8和0.7,而土壤EC分别是水稻-蚕豆轮作地的4.2、4.9和5.2倍;土壤碳、氮含量随塑料大棚地生产年限的增加总体上呈先增大后减小的趋势.与水稻-蚕豆轮作地相比,10年以上塑料大棚地0～20、20～40、40～60、60～80、80～100 cm土层的土壤SOC含量分别下降了54%、46%、60%、63%和59%,土壤TN含量分别下降了53%、53%、71%、82%和85%.农田集约化生产程度显著影响土壤SOC、TN含量和δ13C、δ15N丰度,土壤δ13C丰度与SOC含量呈显著负相关.土壤δ13C丰度可作为评价农田土壤碳循环受人为干扰强度的指标.     

氮水平对苹果叶片13C光合产物和15N向果实转移分配的影响

以6年生‘烟富3’/M26/平邑甜茶苹果为试材,采用C、N双标记技术,研究在果实膨大后期用不同尿素浓度水溶液(N 0%、0.6%、1.2%、1.8%、2.4%,分别用CK、N₁、N₂、N₃、N₄表示)涂抹果实周围20 cm范围内叶片对叶片¹³C同化能力及¹³C光合产物、¹⁵N向果实转移分配的影响.结果表明: 随着尿素浓度的增加,叶片的叶绿素含量、氮含量、光合速率、山梨醇和蔗糖含量、6-磷酸山梨醇脱氢酶(S6PDH)和蔗糖磷酸合酶(SPS)活性及¹³C同化能力均先升高后降低,均以1.8%尿素涂抹处理最高,清水对照最低.¹³C自留量(自身叶片+自身新梢)以清水对照最高,为81.6%,1.8%尿素涂抹处理最低,为63.5%.向外输出的¹³C光合产物主要分布在标记果实,其次是未标记多年生枝,未标记叶片最低.果实¹³C吸收量随着尿素浓度增加呈先升高后降低趋势,以1.8%尿素涂抹处理最高(1.21 mg·g^-1),清水对照最低(0.51 mg·g^-1);果实¹⁵N吸收量随着尿素浓度增加呈持续升高趋势.表明尿素水溶液叶施可不同程度地提高叶片光合产物和氮素向果实转移分配的能力,以1.8%尿素涂抹处理叶片光合产物向果实转移分配能力最强,同时避免了过多的氮素向果实的输入.     

13C代谢流量分析发展30年

~(13)C代谢流量分析(~(13)C metabolic flux analysis,~(13)C-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年的发展历程,尤其在工业生物技术和生物医药领域的应用,并对未来的发展方向进行展望。     

中国暖温带落叶阔叶林中某些树种的13C自然丰度:δ13C值及其生态学意义

利用质谱分析仪对暖温带地区落叶阔叶林优势种稳定碳同位素的分析发现不同树种叶片的稳定碳同位素比率差别较大 ,大多数优势种叶片δ13C值在 -2 4.75 1‰± 0 .85 4‰～ -2 8.1 1 3‰± 1 .5 1 9‰之间。叶片的δ13C值可以分为 3个等级 , 级 ,叶片的 δ13C≥ -2 5 .5‰ , 级 ,叶片的 δ13C值在 -2 5 .5‰～ -2 7.5‰之间 , 级 ,叶片的 δ13C≤ -2 7.5‰ ,由于δ13C值在一定程度上能够反映植物的生理生态特性 ,这表明所研究的植物在生理生态特性方面也可以分为 3个类型。同时 ,由于植物的不同器官具有不同的生理生态特性 ,导致器官对 13C具有不同的分馏特性 ,也导致器官之间的δ13C值产生差异 ,分析结果显示树干、根和小枝的δ13C值一般要较叶片的δ13C值高 ,但不同树种又各具特点。生境的差异是影响稳定碳同位素比率的另一个重要原因 ,良好生境条件下生长的植物的δ13C值一般较生长在干旱瘠薄生境下的低。     

树木年轮δ13C含量幼龄效应的定量化探讨

从实验测得的林内外Ci/Ca差值出发,据已有定量方程,对树木年轮δ^13C含量的幼龄效应进行了定量化探讨,得出林内外植物Ci/Ca的差别将平均造成林内植物δ^13C低于林外植物δ^13C约5.2‰,并由此指出林外比林内植物光合羧化酶RuP2对CO2中^13C和^12C的分部效应b必然要高2‰-4‰,才能补偿由Ci/Ca和δa的差别所造成的林内外树木δ^13C的差值,因此在研究中不应简单地将b作为常数对待。这一结论对于定量地研究和应用树木年轮δ^13C进行环境CO2和δa重建具有重要意义。     

13CO2示踪不同化学形态氮素添加对高寒草甸植物光合碳分配的影响

外源氮素(N)输入陆地生态系统后会引起植物和土壤各碳库的变化,但是对不同化学形态氮素的长期输入如何影响光合碳在植物组织、土壤、土壤呼吸中的分配及转运知之甚少,尤其是对于氮输入引起光合碳分配变化进而作用于植物和土壤碳库的机制的认识还非常匮乏。基于在青藏高原矮嵩草草甸开展的不同化学形态氮素添加的长期实验,利用~(13)C示踪方法揭示了光合碳在植物地上、地下组织的分配,及其随时间在土壤中的滞留和随土壤呼吸的释放。研究结果表明,外源氮素添加10年后,与对照未添加氮素处理相比,氨态氮处理下的地上生物量增加了49.5%,氨态氮处理下的地下生物量增加了111.3%。土壤中滞留的~(13)C整体呈下降趋势,氨态氮处理下的土壤碳库显著高于硝态氮处理下的值。不同处理下的土壤呼吸中~(13)C的滞留量随时间呈指数衰减的变化趋势,其中,硝态氮处理下的~(13)C衰减最快。~(13)C同位素标记后第1天测定植物茎和叶内的~(13)C约占刚刚标定完茎和叶内~(13)C的80%,不同处理之间没有显著性差异。直至标记后的第30天,茎和叶内~(13)C的滞留量约占初始量的30%。硝态氮处理下的值在第21天和第30天显著低于对照和氨态氮处理下的值,表明硝态氮处理下,植物光合固定的碳在短期内迅速输入地下组织和土壤中。这些结果从机理上阐明了植物光合碳分配对不同化学形态氮素长期输入的响应,进而影响到土壤呼吸CO_2的释放,以及对土壤碳库动态的贡献。加深了对高寒草甸土壤有机碳库稳定性维持机制的认识,能够为高寒草地的科学管理以及资源的可持续利用提供理论指导。     

等量分次施氮对冬枣15N和13C利用与分配特性的影响

以4年生盆栽冬枣为试材,采用¹³C、¹⁵N双标记示踪技术,在果实发育期研究了等氮量分次追施氮肥对冬枣植株¹⁵N和¹³C吸收、利用、积累和分配的影响.结果表明: 至果实采收期,冬枣各器官Ndff值(植株器官从肥料中吸收分配到的¹⁵N量对该器官全氮量的贡献率)随追氮次数的增多而显著增大.生殖器官(果实)和营养器官(叶片、枣吊、新生枣头枝和细根)的¹⁵N分配率以4次追氮处理最高,1次追氮处理最低,贮藏器官(主干、多年生枝和粗根)¹⁵N分配率的趋势相反;4次追氮处理¹⁵N利用率分别比1次和2次追氮处理高27.4%和15.5%.追氮次数越多,植株总氮量和¹⁵N吸收量越大;随时间的推移,1次追氮处理土壤¹⁵N丰度和总氮含量持续降低,2次追氮处理呈先升高后降低的趋势,4次追氮处理变化相对最为平稳,至处理后期显著高于其他处理;果实白熟至采收期,叶片叶绿素、氮含量和净光合速率均表现为4次追氮>2次追氮>1次追氮.不同处理¹³C同化物积累与分配不同.4次追氮处理¹³C固定总量分别是1次和2次追氮处理的1.1和1.2倍.增加追氮次数,促进了¹³C同化物向果实和贮藏器官的转移,而减少了向当年生营养器官的分配.综上,果实发育期4次追氮通过保证根层稳定、充足的氮素供应,提高了对氮素的吸收和利用,进而维持了较高的净光合速率,促进并优化了光合同化物的积累和分配,最有利于冬枣树体的生长及产量和品质的提高.     

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。     

甲烷氧化菌20Z利用Embden-Meyerhof-Parnas途径高效同化甲烷

为了探究γ-变形菌纲 (Gammaproteobacteria) 甲烷氧化菌Methylomicrobium alcaliphilum 20Z的甲烷同化代谢过程。文中整合RNA-seq、LC-MS技术并结合13C标记策略对核酮糖单磷酸途径 (Ribulose monophosphate pathway) 及下游途径展开系统组学分析。M. alcaliphilum 20Z代谢物组定量分析表明Entner-Doudoroff (EDD) 途径的中间代谢物6-磷酸葡萄糖的浓度是(150.95±28.75) μmol/L,2-酮-3-脱氧-6-磷酸葡糖酸浓度低于质谱定量分析检测限,而Embden-Meyerhof-Parnas (EMP) 途径中果糖1,6-二磷酸、甘油醛-3-磷酸/二羟丙酮磷酸和磷酸烯醇式丙酮酸的浓度分别是 (1 142.02±302.88) μmol/L、(1 866.76±388.55) μmol/L和 (3 067.57±898.13) μmol/L。通过EDD和EMP途径的代谢物13C同位素动态富集研究,进一步揭示3位标记丙酮酸丰度是1位标记丙酮酸丰度的4~6倍。最后,基因表达比较分析发现EMP途径的关键基因 (如：fbaA、tpiA、gap和pykA) 的表达水平 (RPKM) 分别是2 479.2、2 493.9、2 274.6和1 846.0,而EDD途径中基因 (如：pgi、eda和edd) 的RPKM仅是263.8、341.2和225.4。综合上述结果阐明EMP途径才是M. alcaliphilum 20Z进行甲烷同化的关键通路。EMP途径代谢功能的全新阐述不但改变对Gammaproteobacteria甲烷氧化菌甲烷同化模式的传统认知,而且为甲烷高效生物催化转化提供重要的理论基础。     

Analysis of 13C labeling enrichment in microbial culture applying metabolic tracer experiments using gas chromatography-combustion-isotope ratio mass spectrometry

The applicability of gas chromatography–combustion–isotope ratio mass spectrometry (GC–C–IRMS) for the quantification of ¹³C enrichment of proteinogenic amino acids in metabolic tracer experiments was evaluated. Measurement of the ¹³C enrichment of proteinogenic amino acids from cell hydrolyzates of Corynebacterium glutamicum growing on different mixtures containing between 0.5 and 10% [1-¹³C]glucose shows the significance of kinetic isotope effects in metabolic flux studies at low degree of labeling. We developed a method to calculate the ¹³C enrichment. The approach to correct for these effects in metabolic flux studies using δ¹³C measurement by GC–C–IRMS uses two parallel experiments applying substrate with natural abundance and ¹³C-enriched tracer substrate, respectively. The fractional enrichment obtained in natural substrate is subtracted from that of the enriched one. Tracer studies with C. glutamicum resulted in a statistically identical relative fractional enrichment of ¹³C in proteinogenic amino acids over the whole range of applied concentrations of [1-¹³C]glucose. The current findings indicate a great potential of GC–C–IRMS for labeling quantification in ¹³C metabolic flux analysis with low labeling degree of tracer substrate directly in larger scale bioreactors.     

Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein

Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully ¹³C‐labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Evaluating (13)C enrichment data of free amino acids for precise metabolic flux analysis

Metabolic flux analysis using (13)C enrichment data of intracellular free amino acids (FAAs) can improve the time resolution of flux estimation compared to analysis of proteinogenic amino acid data owing to the faster turnover times of FAAs. The nature of the (13)C enrichment dynamics of FAAs remains obscure, however, especially with regard to its dependence on culture conditions, even though an understanding of dynamic behavior is important for precise metabolic flux estimation. In this study, we analyzed the (13)C enrichment dynamics of free and proteinogenic amino acids in a series of continuous culture experiments with Escherichia coli. The results indicated that the effect of protein degradation on the (13)C enrichment of FAAs was negligible under cellular growth conditions. Furthermore, they showed that the time scale necessary for (13)C enrichment dynamics of FAAs to reach a steady state depends on culture conditions such as oxygen uptake rate, which was likely due to different pool sizes of intracellular metabolites. The results demonstrate the importance of analyzing (13)C enrichment dynamics for the precise estimation of metabolic fluxes using FAA data.     

Comparative study on central metabolic fluxes of <Emphasis Type="Italic">Bacillus megaterium</Emphasis> strains in continuous culture using <Superscript>13</Superscript>C labelled substrates

Fluxes of central carbon metabolism [glycolysis, pentose phosphate pathway (PPP), tricarboxylic acid cycle (TCA cycle), biomass formation] were determined for several Bacillus megaterium strains (DSM319, WH320, WH323, MS941) in C- and N-limited chemostat cultures by ¹³C labelling experiments. The labelling patterns of proteinogenic amino acids were analysed by GC/MS and therefrom flux ratios at important nodes within the metabolic network could be calculated. On the basis of a stoichiometric metabolic model flux distributions were estimated for the different B. megaterium strains used at various cultivation conditions. Generally all strains exhibited similar metabolic flux distributions, however, several significant changes were found in (1) the glucose flux entering the PPP via the oxidative branch, (2) the reversibilities within the PPP, (3) the relative fluxes of pyruvate and acetyl-CoA fed to the TCA cycle, (4) the fluxes around the pyruvate node involving a futile cycle.     

Application of 13C-[2] - and 13C-[1,2] acetate in metabolic labelling studies of yeast and insect cells

The advantage of using ¹³C-labelled glucose in metabolic studies is that it is an important carbon and energy source for almost all biotechnologically and medically important organisms. On the other hand, the disadvantage is its relatively high cost in the labelling experiments. Looking for cheaper alternatives we found that ¹³C-[2] acetate or ¹³C-[1,2] acetate is a prospective compound for such experiments. Acetate is well incorporated by many organisms, including mammalian and insect cell cultures as preferred source of acetyl-CoA. Our experimental results using ¹³C NMR demonstrated that acetate was efficiently incorporated into glutamate and alanine secreted by the insect cell culture. Using D-stat culture of Saccharomyces uvarum on glucose/¹³C-acetate mineral media we demonstrated that the labelling patterns of proteinogenic amino acids can be well predicted on the basis of specific substrate consumption rates using the modified scheme of yeast metabolism and stoichiometric modelling. According to this scheme aspartate and alanine in S. uvarum under the experimental conditions used is synthesised in the mitochondria. Synthesis of alanine in the mitochondria was also demonstrated for Spodoptera frugiperda. For both organisms malic enzyme was also operative. For S. uvarum it was shown that the activity of malic enzyme is sufficient for supporting the mitochondrial biosynthetic reactions with NADPH.     

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.     

Evaluation of isotope discrimination in C-based metabolic flux analysis

In a ¹³C experiment for metabolic flux analysis (¹³C MFA), we examined isotope discrimination by measuring the labeling of glucose, amino acids, and hexose monophosphates via mass spectrometry. When Escherichia coli grew in a mix of 20% fully labeled and 80% naturally labeled glucose medium, the cell metabolism favored light isotopes and the measured isotopic ratios (δ¹³C) were in the range of −35 to −92. Glucose transporters might play an important role in such isotopic fractionation. Flux analysis showed that both isotopic discrimination and isotopic impurities in labeled substrates could affect the solution of ¹³C MFA.     

Current status of 13C-metabolic flux analysis and future perspectives

Current ¹³C-metabolic flux analysis methods were reviewed as well as the weakness of the conventional metabolic flux analysis without ¹³C-labeled experiments. Although it has been recognized that ¹³C-labeling technique is powerful in estimating the metabolic fluxes, and the program-based flux analysis is necessary, one may not be confident with the result obtained without experiences and exhaustive trial and errors in practice due to its black box nature. In the present article, we call attention to the importance of investigating the relationships between fluxes and isotopomer or mass isotopomer distributions to understand the mechanism of generating specific isotopomers. Then, the experimental design for the preferred mixture of the specific ¹³C-labeled substrate was discussed. The effect of the reversibility in the bidirectional flux on the isotopomer distribution was also mentioned, and it was shown why the reliability of the bidirectional fluxes becomes lower. Moreover, by noting that recent development of measurement techniques enables us to measure the isotopomer patterns of intracellular metabolites instead of proteinogenic amino acids, it is mentioned that this enables us to estimate the flux changes during time-variant batch culture. Some future perspectives are discussed in relation to the integration of different levels of information in the cell.     

Metabolic response of <Emphasis Type="Italic">Geobacter sulfurreducens</Emphasis> towards electron donor/acceptor variation

Background  

Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen) and acceptors (Fe(III), fumarate) was investigated via ¹³C-based metabolic flux analysis. We examined the ¹³C-labeling patterns of proteinogenic amino acids obtained from G. sulfurreducens cultured with ¹³C-acetate.