地衣芽孢杆菌发酵生产b-甘露聚糖酶的代谢通量分析

基于代谢通量分析理论研究了地衣芽孢杆菌生物合成b-甘露聚糖酶的胞内代谢活动. 首先构建了地衣芽孢杆菌产b-甘露聚糖酶的代谢网络,并依据代谢物质量平衡原则建立了反应网络的代谢流模型;进一步采用线性规划的优化方法分别以b-甘露聚糖酶合成反应通量最大和菌体生长速率最大为目标函数对模型进行求解,由此计算得到b-甘露聚糖的最大理论转化率为57.87%. 最后对代谢网络中的5个关键节点进行了比较分析,得到了2个类似非刚性的代谢节点(5-磷酸核酮糖节点和草酰乙酸节点),为利用基因工程方法提高b-甘露聚糖酶的生产能力提供了理论依据.     

新型生物絮凝剂REA-11的代谢模型建立与代谢网络分析

利用代谢通量分析方法,对谷氨酸棒杆菌Corynebacterium glutamicum CCTCC M201005分批发酵不同阶段和不同溶氧浓度下的代谢网络模型进行了计算,考察了代谢节点对絮凝剂REA-11合成的影响,并对C. glutamicum生长代谢过程中能量和还原力的产生及消耗问题进行分析.结果发现,磷酸戊糖途径(PP)通量在整个发酵过程中始终维持在较高的水平;REA-11合成通量随溶氧浓度的增加而降低,菌体合成通量则随溶氧水平的增加而增加;ATP通量的增加可以促进菌体生长,而与REA-11的合成呈负相关.     

大尺度代谢网络通量平衡分析的进展与应用

利用大尺度代谢网络分析生物体内部复杂的生化机制已经研究了很多年,大尺度代谢网络的算法也有很多,在这其中通量平衡分析是一个有效的定量研究基因组尺度代谢网络的方法,并在很多分析中都有应用。总结了通量平衡分析算法的最新进展,包括基本的通量平衡分析以及扩展的通量平衡分析算法,然后介绍了一些应用通量平衡分析算法模拟大型生物网络的单机的和在线的工具,最后还比较了这些工具的优缺点,并讨论了目前代谢网络分析算法与软件存在的难题和未来的研究方向。     

人工代谢路径适配性的研究进展

微生物细胞工厂以可再生资源为原料,实现了大宗化学品和天然产物的可持续生产,并有望替代石油化工炼制和动植物提取。剪接天然或人工代谢路径是构建微生物细胞工厂的基础。然而,剪接代谢路径造成的代谢流扰动,导致微生物细胞工厂的适配性差,降低了微生物细胞工厂的生产性能。提高人工代谢路径之间的适配性,以及人工代谢路径与底盘微生物细胞之间的适配性,将是改善微生物细胞工厂生产性能的关键。本文从强化与平衡人工代谢路径的代谢通量,解除人工代谢路径与底盘细胞内源代谢路径的交互作用,以及强化人工代谢路径与底盘细胞整体代谢网络的适配性层面,对提高微生物细胞工厂适配性的研究现状进行介绍。开发高效的多重适配性调控策略,在细胞水平重置代谢路径的适配性与提高微生物细胞对代谢产物的适配性,将是未来的研究重点。     

克雷伯氏杆菌代谢灵活性分析

微生物对外界环境的变化具有灵活的适应性,通过代谢网络的通量可变性分析可以对代谢灵活性进行量化,得到影响菌体代谢灵活性的因素。使用代谢流分析软件COBRA Toolbox,对克雷伯氏杆菌基因组尺度代谢网络进行通量平衡分析与通量可变性分析,分别得到内部反应的可变性、交换反应的可变性和生长速率的可变性等3个因素对菌体代谢灵活性的影响程度,其中生长速率的可变性是影响代谢灵活性的主要因素,调控菌体至次优模式下生长可使其具有更大的代谢灵活性。通过进一步研究生长速率对通量可变性的影响,找到提高代谢灵活性的两个必要条件,从而增强菌体应对外界环境改变的能力。     

克雷伯氏杆菌发酵生产1,3-丙二醇的代谢通量优化分析

以克雷伯氏杆菌为研究对象,系统研究了1,3-丙二醇厌氧和微氧代谢途径.采用代谢通量分析法建立了代谢通量平衡模型,通过线性规划对1,3-丙二醇厌氧和微氧发酵进行了优化分析,得到其最优代谢通量分布和最大理论得率,并分析了比生长速率、底物浓度以及乙醇生成速率、氧气消耗速率、呼吸商对1,3-丙二醇得率的影响.     

代谢通量分析在酶合成过程中的应用研究进展

代谢通量分析可以有效预测微生物的代谢状况,指导生物合成过程,已在多个领域得到成功应用。本文概括分析了三大代谢通量分析技术（基于物料平衡、基于同位素示踪技术以及基于基因组尺度规模网络）在工业生物技术领域的应用,阐述了相关技术的优势及局限性。在此基础上重点论述了基于物料平衡及同位素示踪这两类通量分析技术在酶合成领域的研究进展,分析了代谢通量分析应用于复杂代谢产物可能存在的问题,指出如何将信号转导、转录调控等信息纳入代谢网络将成为未来酶合成过程代谢分析的研究重点。     

葡萄糖浓度对杂交瘤细胞代谢通量分布的影响

将代谢工程理论应用于动物细胞的流加培养过程。通过构建代谢网络模型，研究了杂交瘤细胞从动态到拟稳态过程中物质和能量代谢通量的时间分布图。结果表明：当葡萄糖浓度较高时，葡萄糖在乳酸生成途径和TCA循环的代谢通量分配比例分别为90%和10%，ATP生成的比例分别为20%和60%，说明葡萄糖大部分经糖酵解途径生成乳酸，而进入TCA循环的少量部分则提供大部分的能量生成。当葡萄糖浓度降至其限制细胞生长的浓度时，进入TCA循环的葡萄糖比例逐步提高到100%，葡萄糖的氧化程度从0. 6 mmol·mmol^-1增至4. 52 mmol·mmol^-1，说明葡萄糖代谢逐渐从乳酸生成途径迁移到TCA循环，从无氧代谢逐渐转移到有氧代谢。     

丙酸杆菌的两种固定化细胞反应器发酵生产丙酸及其代谢通量分析

根据构建的费氏丙酸杆菌合成丙酸的生化反应网络,利用代谢通量分析法分析了课题组构建的两种固定化细胞反应器对丙酸发酵的影响.结果表明,固定化细胞发酵可以调节葡萄糖-6-磷酸、磷酸烯醇式丙酮酸和丙酮酸节点处的代谢通量分布,从而最终影响生物量和各种有机酸的合成.与游离发酵相比,两种固定化发酵方式戊糖磷酸途径通最都有显著提高,乙...     

微生物代谢工程：绘制细胞工厂的蓝图

代谢工程是一种理解并利用代谢过程的方法,其目的是优化或改变生物细胞中的代谢网络和表达调控网络,提高其代谢产物的产量或合成新的化合物.后基因组时代系统生物学和功能基因组学技术的发展,为构建能够实现特定目标的微生物细胞工厂提供了空前机遇.本文回顾代谢工程在技术和应用上的最新进展,讨论代谢工程中的关键问题和发展趋势,并提出中国在该领域的发展策略.     

Analysis of Data on Xanthan Fermentation in Stationary Phase Using Black Box and Metabolic Network Models

The xanthan fermentation data in the stationary phase was analyzed using the black box and the metabolic network models. The data consistency ls checked through the elemental balance in the black box model. In the metabolic network model, the metabolic flux distribution in the cell is calculated using the metabolic flux analysis method, then the maintenance coefficients is calculated.     

Metabolic network modelling: Including stochastic effects

We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, translocation matrix, degradation matrix, and stochastic force. These four elements are balanced to determine the network dynamics, which gives arise to a special stochastic differential equation supplemented by a relationship between the stochastic force and the degradation matrix. Important network behaviors can be obtained from the potential function without explicitly solving for the time-dependent solution. The existence of such a potential function suggests a global optimization principle. The existence stochastic force corresponds naturally to the hierarchical structure in metabolic networks. We provide theoretical evidences to justify our proposal by discussing its connections to others large-scale biochemical systems approaches, such as the network thermodynamics theory, biochemical systems theory, metabolic control analysis, and flux balance analysis. Experimental data displaying stochasticity which carries important biological information are also pointed out.     

利用基元模式分析酿酒酵母的葡萄糖厌氧发酵过程以提高乙醇产量

Elementary flux mode （EFM） analysis was used in the metabolic analysis of central carbon metabolism in Saccharomyces cerevisiae based on constructed cellular network. Calculated from the metabolic model, the ethanol-producing pathway No. 37 furthest converts the substrate into ethanol among the 78 elementary flux modes. The in silico metabolic phenotypes predicted based on this analysis fit well with the fermentation performance of the engineered strains, KAM3 and KAMll, which confirmed that EFM analysis is valid to direct the construction of Saccharomyces cerevisiae engineered strains, to increase the ethanol yield.     

Dynamic Modeling and Metabolic Flux Analysis for Optimized Production of Rhamnolipids

A comprehensive metabolic network based on the fundamental pathways representing the central metabolism of rhamnolipid by Pseudomonas aeruginosa is proposed and a dynamic model compatible with the underlying metabolic network is developed involving the macro-reactions derived from the elementary flux modes of the reaction network. The experimentally validated mathematical model is then coupled with a global optimization technique called differential evolution (DE) to optimize the medium composition as well as the extracellular and intracellular fluxes of the metabolic network. The analysis of the results shows the usefulness of the integrated approach involving the development of a dynamic model based on the metabolic network structure and model-based optimization of the medium composition and metabolic fluxes by an efficient evolutionary optimization technique to enhance the productivity of rhamnolipid.     

产朊假丝酵母分批发酵生产谷胱甘肽的代谢通量分析

根据产朊假丝酵母利用葡萄糖作为惟一碳源生物合成谷胱甘肽的代谢网络,利用代谢通量分析方法分析了谷胱甘肽分批发酵不同阶段各代谢途径碳通量的分布和变化规律.在此基础上,通过分阶段温度控制和L-半胱氨酸添加等策略,调节谷胱甘肽分批发酵过程中的代谢通量分布,谷胱甘肽生物合成的产量明显提高,最大增加幅度分别达到23%和91%.同时对这些策略下谷胱甘肽的过量合成机理进行了解释.     

Dynamical reduction of linearized metabolic networks through quasi steady state approximation

Metabolic modeling has gained accuracy in the last decades, but the resulting models are of high dimension and difficult to use for control purpose. Here we propose a mathematical approach to reduce high dimensional linearized metabolic models, which relies on time scale separation and the quasi steady state assumption. Contrary to the flux balance analysis assumption that the whole system reaches an equilibrium, our reduced model depends on a small system of differential equations which represents the slow variables dynamics. Moreover, we prove that the concentration of metabolites in quasi steady state is one order of magnitude lower than the concentration of metabolites with slow dynamics (under some flux conditions). Also, we propose a minimization strategy to estimate the reduced system parameters. The reduction of a toy network with the method presented here is compared with other approaches. Finally, our reduction technique is applied to an autotrophic microalgae metabolic network. © 2018 American Institute of Chemical Engineers AIChE J, 65: 18–31, 2019     

通过通量平衡分析计算经验和真实维持系数

The stoichiometric matrix of a simplified metabolic network in Bacillus Subtillis was contructed from the flux balance equations, which were used for reconciliation of the measured rates and determination of the inner metabolic rates. Thus more reliable results of the true and empirical maintenance coefficients were obtained. The true maintenance coefficient is linearly related to the specific growth rate and changes with the P/O ratiol. The neasured biomass yield of adenosine triphosphate (ATP) is also linearly related to the P/O ratio.