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大肠杆菌刺激反应曲线的分析与设计

Analysis and Design of Stimulus Response Curves of E. coli.

作者信息

Kremling Andreas, Goehler Anna, Jahreis Knut, Nees Markus, Auerbach Benedikt, Schmidt-Heck Wolfgang, Kökpinar Oznur, Geffers Robert, Rinas Ursula, Bettenbrock Katja

机构信息

Systems Biotechnology, Technische Universität München, Boltzmannstr. 15, Garching b. München, Germany.

University Osnabrück, Barbarastrasse 11, Osnabrück, Germany.

出版信息

Metabolites. 2012 Nov 12;2(4):844-71. doi: 10.3390/metabo2040844.

DOI:10.3390/metabo2040844
PMID:24957765
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3901224/
Abstract

Metabolism and signalling are tightly coupled in bacteria. Combining several theoretical approaches, a core model is presented that describes transcriptional and allosteric control of glycolysis in Escherichia coli. Experimental data based on microarrays, signalling components and extracellular metabolites are used to estimate kinetic parameters. A newly designed strain was used that adjusts the incoming glucose flux into the system and allows a kinetic analysis. Based on the results, prediction for intracelluar metabolite concentrations over a broad range of the growth rate could be performed and compared with data from literature.

摘要

在细菌中，代谢与信号传导紧密耦合。结合多种理论方法，提出了一个核心模型，该模型描述了大肠杆菌糖酵解的转录调控和变构调控。基于微阵列、信号传导成分和细胞外代谢物的实验数据用于估计动力学参数。使用了一种新设计的菌株，该菌株可调节进入系统的葡萄糖通量并允许进行动力学分析。基于这些结果，可以对广泛生长速率范围内的细胞内代谢物浓度进行预测，并与文献数据进行比较。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/debb/3901224/3022c0bd602a/metabolites-02-00844-g011.jpg
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本文引用的文献

1
Structural analysis of a core model for carbohydrate uptake in Escherichia coli.大肠杆菌中碳水化合物摄取核心模型的结构分析。
J Theor Biol. 2012 Jun 21;303:62-74. doi: 10.1016/j.jtbi.2012.03.004. Epub 2012 Mar 10.
2
Bringing together models from bottom-up and top-down approaches: an application for growth of Escherichia coli on different carbohydrates.将自下而上和自上而下的模型相结合：大肠杆菌在不同碳水化合物上生长的应用。
Adv Exp Med Biol. 2012;736:579-95. doi: 10.1007/978-1-4419-7210-1_34.
3
The phosphoenolpyruvate-dependent glucose-phosphotransferase system from Escherichia coli K-12 as the center of a network regulating carbohydrate flux in the cell.
大肠杆菌 K-12 的磷酸烯醇丙酮酸依赖性葡萄糖磷酸转移酶系统作为调节细胞内碳水化合物通量的网络中心。
Eur J Cell Biol. 2011 Sep;90(9):711-20. doi: 10.1016/j.ejcb.2011.04.002. Epub 2011 May 28.
4
Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase.系统生物学方法表明，大肠杆菌中乙酸盐的溢流代谢是由乙酰辅酶A合成酶的碳分解代谢物阻遏引发的。
BMC Syst Biol. 2010 Dec 1;4:166. doi: 10.1186/1752-0509-4-166.
5
The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.大肠杆菌中的碳同化网络连接紧密，并且其代谢通量的方向在很大程度上决定了网络的信号。
PLoS Comput Biol. 2010 Jun 10;6(6):e1000812. doi: 10.1371/journal.pcbi.1000812.
6
Metabolomic and transcriptomic stress response of Escherichia coli.大肠杆菌的代谢组学和转录组学应激反应。
Mol Syst Biol. 2010 May 11;6:364. doi: 10.1038/msb.2010.18.
7
Bacterial adaptation through distributed sensing of metabolic fluxes.细菌通过代谢通量的分布式感知进行适应性进化。
Mol Syst Biol. 2010;6:355. doi: 10.1038/msb.2010.10. Epub 2010 Mar 9.
8
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.大肠杆菌中的绝对代谢物浓度及隐含的酶活性位点占有率
Nat Chem Biol. 2009 Aug;5(8):593-9. doi: 10.1038/nchembio.186. Epub 2009 Jun 28.
9
Catabolite repression in Escherichia coli- a comparison of modelling approaches.大肠杆菌中的分解代谢物阻遏——建模方法比较
FEBS J. 2009 Jan;276(2):594-602. doi: 10.1111/j.1742-4658.2008.06810.x. Epub 2008 Dec 11.
10
EcoCyc: a comprehensive view of Escherichia coli biology.《大肠杆菌代谢数据库（EcoCyc）：大肠杆菌生物学全景》
Nucleic Acids Res. 2009 Jan;37(Database issue):D464-70. doi: 10.1093/nar/gkn751. Epub 2008 Oct 30.