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1.
Yuki Kuriya Mai Inoue Masaki Yamamoto Masahiro Murata Michihiro Araki 《Biotechnology journal》2021,16(12):2000443
2.
Carolina Shene Paris Paredes Liset Flores Allison Leyton Juan A. Asenjo Yusuf Chisti 《Biotechnology and bioengineering》2020,117(10):3006-3017
Production of biomass and lipids in batch cultures of the Antarctic thraustochytrid Oblongichytrium sp. RT2316-13, is reported. The microorganism proved capable of producing nearly 67% docosahexaenoic acid (DHA) and 15% eicosapentaenoic acid (EPA) in its total lipid fraction. Biomass with a maximum total lipid content of 33.5% (wt/wt) could be produced at 15°C in batch culture using a medium containing glucose (20 g/L), yeast extract (10.5 g/L), and other minor components. A lower culture temperature (5°C) reduced biomass and lipid productivities compared to culture at 15°C, but enhanced the DHA and EPA content of the lipids by 6.4- and 3.3-fold, respectively. Both a simple minimally structured mathematical model and a more complex genome-scale metabolic model (GEM) allowed the fermentation profiles in batch cultures to be satisfactorily simulated, but the GEM provided much greater insight in the biochemical and physiological phenomena underlying the observed behavior. Unlike the simpler model, the GEM could be interrogated for the possible effects of various external factors such as oxygen supply, on the expected outcomes. In silico predictions of oxygen effects were consistent with literature observations for DHA producing thraustochytrids. 相似文献
3.
细胞中自发或由酶催化的代谢反应组成了高度复杂的代谢网络,其与细胞生理代谢活动运作密切相关。细胞生理代谢网络模型的重构有助于从系统层面上解析基因型与生长表型之间的关联,为细胞生理代谢活动精准刻画与生物绿色制造等研究提供重要的计算生物学工具。本文系统介绍了全基因组尺度代谢网络模型(genome-scale metabolic models, GEMs)、动力学模型、酶约束代谢模型(enzyme-constrained genome-scale metabolic models, ecGEMs)等不同类型细胞生理代谢网络模型发展与应用的最新研究进展;同时还介绍了GEMs自动化构建研究进展以及条件特异性GEMs建模策略。人工智能技术为高精度细胞生理代谢网络模型构建提供了全新机遇,本文进一步总结了人工智能技术在动力学模型和酶约束模型构建等领域的应用。各类细胞生理代谢网络模型的高质量重构将为今后的定量合成生物学与系统生物学等研究提供强大计算支撑。 相似文献
4.
Diana Széliová Dmytro Iurashev David E Ruckerbauer Gunda Koellensperger Nicole Borth Michael Melcher Jürgen Zanghellini 《Biotechnology journal》2021,16(4):2000320
Chinese hamster ovary (CHO) cells are the most popular mammalian cell factories for the production of glycosylated biopharmaceuticals. To further increase titer and productivity and ensure product quality, rational system-level engineering strategies based on constraint-based metabolic modeling, such as flux balance analysis (FBA), have gained strong interest. However, the quality of FBA predictions depends on the accuracy of the experimental input data, especially on the exchange rates of extracellular metabolites. Yet, it is not standard practice to devote sufficient attention to the accurate determination of these rates. In this work, we investigated to what degree the sampling frequency during a batch culture and the measurement errors of metabolite concentrations influence the accuracy of the calculated exchange rates and further, how this error then propagates into FBA predictions of growth rates. We determined that accurate measurements of essential amino acids with low uptake rates are crucial for the accuracy of FBA predictions, followed by a sufficient number of analyzed time points. We observed that the measured difference in growth rates of two cell lines can only be reliably predicted when both high measurement accuracy and sampling frequency are ensured. 相似文献
5.
In this work, a novel optimization-based metabolic control analysis (OMCA) method is introduced for reducing data requirement for metabolic control analysis (MCA). It is postulated that using the optimal control approach, the fluxes in a metabolic network are correlated to metabolite concentrations and enzyme activities as a state-feedback control system that is optimal with respect to a homeostasis objective. It is then shown that the optimal feedback gains are directly related to the elasticity coefficients (ECs) of MCA. This approach requires determination of the relative "importance" of metabolites and fluxes for the system, which is possible with significantly reduced experimental data, as compared with typical MCA requirements. The OMCA approach is applied to a top-down control model of glycolysis in hepatocytes. It is statistically demonstrated that the OMCA model is capable of predicting the ECs observed experimentally with few exceptions. Further, an OMCA-based model reconciliation study shows that the modification of four assumed stoichiometric coefficients in the model can explain most of the discrepancies, with the exception of elasticities with respect to the NADH/NAD ratio. 相似文献
6.
Sofia Ferreira Rui Pereira S. A. Wahl Isabel Rocha 《Biotechnology and bioengineering》2020,117(8):2571-2587
The global market of butanol is increasing due to its growing applications as solvent, flavoring agent, and chemical precursor of several other compounds. Recently, the superior properties of n-butanol as a biofuel over ethanol have stimulated even more interest. (Bio)butanol is natively produced together with ethanol and acetone by Clostridium species through acetone-butanol-ethanol fermentation, at noncompetitive, low titers compared to petrochemical production. Different butanol production pathways have been expressed in Escherichia coli, a more accessible host compared to Clostridium species, to improve butanol titers and rates. The bioproduction of butanol is here reviewed from a historical and theoretical perspective. All tested rational metabolic engineering strategies in E. coli to increase butanol titers are reviewed: manipulation of central carbon metabolism, elimination of competing pathways, cofactor balancing, development of new pathways, expression of homologous enzymes, consumption of different substrates, and molecular biology strategies. The progress in the field of metabolic modeling and pathway generation algorithms and their potential application to butanol production are also summarized here. The main goals are to gather all the strategies, evaluate the respective progress obtained, identify, and exploit the outstanding challenges. 相似文献
7.
【背景】电化学厌氧消化(electrochemical anaerobic digestion,EAD)系统的代谢途径由具备不同功能的微生物所主导,其代谢通量与功能微生物丰度、活性及群落结构相关。【目的】探究EAD产甲烷代谢通量与微生物的关系。【方法】采用代谢通量分析(metabolic flux analysis,MFA)方法,以pH为扰动因子得到微生物群落与产甲烷通量的响应关系。【结果】pH 7.5扰动时产甲烷通量最大为0.398 4±0.029 3,较对照组(pH 6.9)的0.297 4±0.012 7和扰动组(pH 6.3)的0.136 5±0.012 0分别提高了25%和65%。另外,平均有33.8%±3.1%的氢气(通量)用于还原二氧化碳产甲烷和乙酸,平均有21.0%±2.6%的乙酸(通量)转化为甲烷。此外,产甲烷通量与Mariniphaga、Methanosaeta和Desulfomicrobium的丰度呈正相关,与Sedimentibacter的丰度呈负相关且影响显著。【结论】在EAD产甲烷体系中产甲烷菌和产酸菌共存时,pH值略大于7.0的环境有利于甲烷的生成,改变E... 相似文献
8.
Using optimization based methods to predict fluxes in metabolic flux balance models has been a successful approach for some microorganisms, enabling construction of in silico models and even inference of some regulatory motifs. However, this success has not been translated to mammalian cells. The lack of knowledge about metabolic objectives in mammalian cells is a major obstacle that prevents utilization of various metabolic engineering tools and methods for tissue engineering and biomedical purposes. In this work, we investigate and identify possible metabolic objectives for hepatocytes cultured in vitro. To achieve this goal, we present a special data-mining procedure for identifying metabolic objective functions in mammalian cells. This multi-level optimization based algorithm enables identifying the major fluxes in the metabolic objective from MFA data in the absence of information about critical active constraints of the system. Further, once the objective is determined, active flux constraints can also be identified and analyzed. This information can be potentially used in a predictive manner to improve cell culture results or clinical metabolic outcomes. As a result of the application of this method, it was found that in vitro cultured hepatocytes maximize oxygen uptake, coupling of urea and TCA cycles, and synthesis of serine and urea. Selection of these fluxes as the metabolic objective enables accurate prediction of the flux distribution in the system given a limited amount of flux data; thus presenting a workable in silico model for cultured hepatocytes. It is observed that an overall homeostasis picture is also emergent in the findings. 相似文献
9.
Di Liu Ni Wan Fuzhong Zhang Yinjie J. Tang Stephen G. Wu 《Biotechnology and bioengineering》2017,114(2):463-467
10.
Verónica S. Martínez Stefanie Dietmair Lake‐Ee Quek Mark P. Hodson Peter Gray Lars K. Nielsen 《Biotechnology and bioengineering》2013,110(2):660-666
Mammalian cell cultures typically exhibit an energy inefficient phenotype characterized by the consumption of large quantities of glucose and the concomitant production of large quantities of lactate. Under certain conditions, mammalian cells can switch to a more energy efficient state during which lactate is consumed. Using a metabolic model derived from a mouse genome scale model we performed flux balance analysis of Chinese hamster ovary cells before and after a metabolic switch from lactate production (in the presence of glucose) to lactate consumption (after glucose depletion). Despite a residual degree of freedom after accounting for measurements, the calculated flux ranges and associated errors were narrow enough to enable investigation of metabolic changes across the metabolic switch. Surprisingly, the fluxes through the lower part of the TCA cycle from oxoglutarate to malate were very similar (around 60 µmol/gDW/h) for both phases. A detailed analysis of the energy metabolism showed that cells consuming lactate have an energy efficiency (total ATP produced per total C‐mol substrate consumed) six times greater than lactate producing cells. Biotechnol. Bioeng. 2013; 110: 660–666. © 2012 Wiley Periodicals, Inc. 相似文献
11.
Dynamic flux balance analysis (dFBA) has been widely employed in metabolic engineering to predict the effect of genetic modifications and environmental conditions in the cell׳s metabolism during dynamic cultures. However, the importance of the model parameters used in these methodologies has not been properly addressed. Here, we present a novel and simple procedure to identify dFBA parameters that are relevant for model calibration. The procedure uses metaheuristic optimization and pre/post-regression diagnostics, fixing iteratively the model parameters that do not have a significant role. We evaluated this protocol in a Saccharomyces cerevisiae dFBA framework calibrated for aerobic fed-batch and anaerobic batch cultivations. The model structures achieved have only significant, sensitive and uncorrelated parameters and are able to calibrate different experimental data. We show that consumption, suboptimal growth and production rates are more useful for calibrating dynamic S. cerevisiae metabolic models than Boolean gene expression rules, biomass requirements and ATP maintenance. 相似文献
12.
Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform. 相似文献
13.
高通量数据的产出为基因组尺度代谢网络的构建提供了基础,但同时也对网络构建和分析方法的改进提出了挑战。随着数据量的不断增大,耗时耗力的人工构建及分析已经无法满足模型发展的需要,因而各种自动化的方法应运而生。模型构建和分析的自动化不仅能够大幅度提高模型构建和解析的速度,同时对于模型构建和分析方法的标准化和程序化也有着不可替代的作用。文中结合作者的实际研究经验,对基因组尺度代谢网络构建的自动化进程和主要的代谢网络分析工具进行了较为详细的介绍,总结了代谢网络自动重构的流程,并提出了目前面对的主要问题和未来的研究方向。 相似文献
14.
Zhuangrong Huang Dong‐Yup Lee Seongkyu Yoon 《Biotechnology and bioengineering》2017,114(12):2717-2728
15.
Maxime Durot Pierre-Yves Bourguignon & Vincent Schachter 《FEMS microbiology reviews》2009,33(1):164-190
Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities. 相似文献
16.
An optimization-based framework is introduced for testing whether experimental flux data are consistent with different hypothesized objective functions. Specifically, we examine whether the maximization of a weighted combination of fluxes can explain a set of observed experimental data. Coefficients of importance (CoIs) are identified that quantify the fraction of the additive contribution of a given flux to a fitness (objective) function with an optimization that can explain the experimental flux data. A high CoI value implies that the experimental flux data are consistent with the hypothesis that the corresponding flux is maximized by the network, whereas a low value implies the converse. This framework (i.e., ObjFind) is applied to both an aerobic and anaerobic set of Escherichia coli flux data derived from isotopomer analysis. Results reveal that the CoIs for both growth conditions are strikingly similar, even though the flux distributions for the two cases are quite different, which is consistent with the presence of a single metabolic objective driving the flux distributions in both cases. Interestingly, the CoI associated with a biomass production flux, complete with energy and reducing power requirements, assumes a value 9 and 15 times higher than the next largest coefficient for the aerobic and anaerobic cases, respectively. 相似文献
17.
为探究微生物电解池耦合厌氧消化(MEC-AD)产甲烷代谢通量与微生物的关系。实验以电压为扰动因子,采用代谢通量分析(MFA)的方法,得到微生物群落与产甲烷通量的响应关系。结果表明:电压扰动后产甲烷通量和产氢通量均发生显著变化,而电压扰动对产乙酸通量的影响较小,其中0.6 V扰动时产甲烷通量最大为0.522±0.051,较对照组1.0 V的0.295±0.013和1.4 V的0.395±0.029分别提高了77%和32%。另外,平均有15.7%±2.9%的H_(2)(通量)用于还原CO_(2)产甲烷和乙酸,平均有27.7%±6.9%的乙酸(通量)转化为CH_(4)。毛螺旋菌(Lachnospiraceae)的丰度对乙酸通量有显著影响,产CH_(4)通量与理研菌属(Petrimonas)、互营单胞菌属(Syntrophomonas)、拟杆菌属(Blvii28)、假单胞菌属(Acinetobacter)的丰度呈正相关,与梭菌属(Tuzzerella)、球形螺旋菌属(Sphaerochaeta)的丰度呈负相关。而影响产H2通量和产CH_(4)通量的物种具有相似性,多为拟杆菌、梭菌、假单胞菌和厚壁菌。此外,物种种间互作关系也是影响MEC-AD产甲烷通量的重要因素。 相似文献
18.
Azuyuki Shimizu 《Biotechnology and Bioprocess Engineering》2002,7(5):237-251
The recent progress on metabolic systems engineering was reviewed based on our recent research results in terms of (1) metabolic
signal flow diagram approach, (2) metabolic flux analysis (MFA) in particular with intracellular isotopomer distribution using
NMR and/or GC-MS, (3) synthesis and optimization of metabolic flux distribution (MFD), (4) modification of MFD by gene manipulation
and by controlling culture environment, (5) metabolic control analysis (MCA), (6) design of metabolic regulation structure,
and (7) identification of unknown pathways with isotope tracing by NMR. The main characteristics of metabolic engineering
is to treat metabolism as a network or entirety instead of individual reactions. The applications were made for poly-3-hydroxybutyrate
(PHB) production usingRalstonia eutropha and recombinantEscherichia coli, lactate production by recombinantSaccharomyces cerevisiae, pyruvate production by vitamin auxotrophic yeastToluropsis glabrata, lysine production usingCorynebacterium glutamicum, and energetic analysis of photosynthesic microorganisms such as Cyanobateria. The characteristics of each approach were
reviewed with their applications. The approach based on isotope labeling experiments gives reliable and quantitative results
for metabolic flux analysis. It should be recognized that the next stage should be toward the investigation of metabolic flux
analysis with gene and protein expressions to uncover the metabolic regulation in relation to genetic modification and/or
the change in the culture condition. 相似文献
19.
Andrew L. Damiani Q. Peter He Thomas W. Jeffries Jin Wang 《Biotechnology and bioengineering》2015,112(6):1250-1262
20.
Yan Zhu Jiangning Song Zixiang Xu Jibin Sun Yanping Zhang Yin Li Yanhe Ma 《Biotechnology and bioengineering》2013,110(3):914-923
Flux balance analysis (FBA) has been widely used in calculating steady‐state flux distributions that provide important information for metabolic engineering. Several thermodynamics‐based methods, for example, quantitative assignment of reaction directionality and energy balance analysis have been developed to improve the prediction accuracy of FBA. However, these methods can only generate a thermodynamically feasible range, rather than the most thermodynamically favorable solution. We therefore developed a novel optimization method termed as thermodynamic optimum searching (TOS) to calculate the thermodynamically optimal solution, based on the second law of thermodynamics, the minimum magnitude of the Gibbs free energy change and the maximum entropy production principle (MEPP). Then, TOS was applied to five physiological conditions of Escherichia coli to evaluate its effectiveness. The resulting prediction accuracy was found significantly improved (10.7–48.5%) by comparing with the 13C‐fluxome data, indicating that TOS can be considered an advanced calculation and prediction tool in metabolic engineering. Biotechnol. Bioeng. 2013; 110: 914–923. © 2012 Wiley Periodicals, Inc. 相似文献