Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network
Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network
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DOI：
10.1038/s41540-019-0091-6
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发表时间：
2019-04-12
影响因子：
4
通讯作者：
Boogerd, Fred C.
中科院分区：
文献类型：
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作者：
Maeda, Kazuhiro;Westerhoff, Hans V.;Boogerd, Fred C.
研究了E.大肠杆菌中的氨转运蛋白AmtB、调节蛋白GlnK和GlnB以及中心氮同化酶及其高度复杂的相互作用。对这样一个复杂网络的工程和建模似乎是不可能的，因为其功能严重依赖于已知的各种数据，而这些数据的准确性参差不齐。我们开发了一种摆脱这种困境的方法，它采用：（i）基于约束优化的技术，用于将模型同时拟合到通过不同实验装置收集的异质实验数据集，（ii）“橡皮筋方法”，用于处理实验确定或估计的参数值以及测量的瞬态或稳态变量中的不同程度的不确定性（训练数据集），（iii）人类专业知识的整合，以决定参数和变量的准确性，（iv）采用快速算法和超级计算机的大规模计算，（v）量化模型可扩展性的客观方法，这使得有可能决定哪个模型是最好的，以及该模型比其他模型好多少。我们将新技术应用于铵运输和同化网络，整合了来自不同专家实验室的各种精度的最新和较旧数据。动力学模型客观上排在最后，有E。大肠杆菌的AmtB作为氨的主动转运蛋白被GlnK同化，从而最大限度地减少细胞内铵积累的必然结果的无效循环。这是130倍，比一个模型与促进被动运输的氨。
The complex ammonium transport and assimilation network of E. coli involves the ammonium transporter AmtB, the regulatory proteins GlnK and GlnB, and the central N-assimilating enzymes together with their highly complex interactions. The engineering and modelling of such a complex network seem impossible because functioning depends critically on a gamut of data known at patchy accuracy. We developed a way out of this predicament, which employs: (i) a constrained optimization-based technology for the simultaneous fitting of models to heterogeneous experimental data sets gathered through diverse experimental set-ups, (ii) a 'rubber band method' to deal with different degrees of uncertainty, both in experimentally determined or estimated parameter values and in measured transient or steady-state variables (training data sets), (iii) integration of human expertise to decide on accuracies of both parameters and variables, (iv) massive computation employing a fast algorithm and a supercomputer, (v) an objective way of quantifying the plausibility of models, which makes it possible to decide which model is the best and how much better that model is than the others. We applied the new technology to the ammonium transport and assimilation network, integrating recent and older data of various accuracies, from different expert laboratories. The kinetic model objectively ranked best, has E. coli's AmtB as an active transporter of ammonia to be assimilated with GlnK minimizing the futile cycling that is an inevitable consequence of intracellular ammonium accumulation. It is 130 times better than a model with facilitated passive transport of ammonia.