Silva-Rocha Rafael, de Jong Hidde, Tamames Javier, de Lorenzo Víctor
Systems Biology Program, Centro Nacional de Biotecnología CSIC Cantoblanco-Madrid, 28049, Spain.
BMC Syst Biol. 2011 Nov 11;5:191. doi: 10.1186/1752-0509-5-191.
The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants. Although nearly every metabolic and transcriptional component of this regulatory system is known to an extraordinary molecular detail, the complexity of its architecture is still perplexing. To gain an insight into the inner layout of this network a logic model of the TOL system was implemented, simulated and experimentally validated. This analysis made sense of the specific regulatory topology out on the basis of an unprecedented network motif around which the entire genetic circuit for m-xylene catabolism gravitates.
The most salient feature of the whole TOL regulatory network is the control exerted by two distinct but still intertwined regulators (XylR and XylS) on expression of two separated catabolic operons (upper and lower) for catabolism of m-xylene. Following model reduction, a minimal modular circuit composed by five basic variables appeared to suffice for fully describing the operation of the entire system. In silico simulation of the effect of various perturbations were compared with experimental data in which specific portions of the network were activated with selected inducers: m-xylene, o-xylene, 3-methylbenzylalcohol and 3-methylbenzoate. The results accredited the ability of the model to faithfully describe network dynamics. This analysis revealed that the entire regulatory structure of the TOL system enables the action an unprecedented metabolic amplifier motif (MAM). This motif synchronizes expression of the upper and lower portions of a very long metabolic system when cells face the head pathway substrate, m-xylene.
Logic modeling of the TOL circuit accounted for the intricate regulatory topology of this otherwise simple metabolic device. The found MAM appears to ensure a simultaneous expression of the upper and lower segments of the m-xylene catabolic route that would be difficult to bring about with a standard substrate-responsive single promoter. Furthermore, it is plausible that the MAM helps to avoid biochemical conflicts between competing plasmid-encoded and chromosomally-encoded pathways in this bacterium.
土壤细菌恶臭假单胞菌mt-2的TOL质粒pWW0用于间二甲苯分解代谢的遗传网络是芳香族污染物环境生物降解的典型模型。尽管已知该调控系统几乎每个代谢和转录成分的分子细节都非常详尽，但其结构的复杂性仍然令人困惑。为了深入了解该网络的内部布局，实施、模拟并通过实验验证了TOL系统的逻辑模型。该分析基于一个前所未有的网络基序，解释了特定的调控拓扑结构，围绕该基序，间二甲苯分解代谢的整个遗传回路得以构建。
整个TOL调控网络最显著的特征是由两个不同但仍相互交织的调节因子（XylR和XylS）对两个分开的分解代谢操纵子（上部和下部）的表达进行控制，以实现间二甲苯的分解代谢。经过模型简化后，由五个基本变量组成的最小模块化电路似乎足以完整描述整个系统的运行。对各种扰动效应的计算机模拟与实验数据进行了比较，在实验数据中，网络的特定部分用选定的诱导剂激活：间二甲苯、邻二甲苯、3-甲基苄醇和3-甲基苯甲酸。结果证实了该模型忠实地描述网络动态的能力。该分析表明，TOL系统的整个调控结构能够实现一个前所未有的代谢放大器基序（MAM）的作用。当细胞面对上游途径底物间二甲苯时，该基序可使一个非常长的代谢系统的上部和下部同步表达。
TOL回路的逻辑建模解释了这个原本简单的代谢装置复杂的调控拓扑结构。发现的MAM似乎确保了间二甲苯分解代谢途径上部和下部的同时表达，而这用标准的底物响应单启动子很难实现。此外，MAM有助于避免该细菌中竞争性质粒编码途径和染色体编码途径之间的生化冲突，这似乎是合理的。
