A central goal of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to construct basic biological functional modules, and through rational design, to b...A central goal of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to construct basic biological functional modules, and through rational design, to build synthetic biological systems with predetermined functions. Here, we apply the reverse engineering design principle of biological networks to synthesize a gene circuit that executes semi-log dose-response, a logarithmically linear sensing function, in Escherichia coil cells. We first mathematically define the object function semi-log dose-response, and then search for tri-node network topologies that can most robustly execute the object function. The simplest topology, transcriptional coherent feed-forward loop （TCFL）, among the searching results is mathematically analyzed; we find that, in TCFL topology, the semi-log dose-response function arises from the additive effect of logarithmical linearity intervals of Hill functions. TCFL is then genetically implemented in E. coil as a logarithmically linear sensing biosensor for heavy metal ions [mercury （II）]. Functional characterization shows that this rationally designed biosensor circuit works as expected. Through this study we demonstrated the potential application of biological network reverse engineering to broaden the computational power of synthetic biology.展开更多
基金This work is part of the project for the 2010 team of Peking University in the international genetically engineered machine （iGEM） competition. H. Zhang. designed the project, performed the experiments and modeling simulation, and wrote the manuscript. Y. Sheng., A. Liu, and Q. Wu performed the experiments. Y. Lu and Z. Yin performed the modeling simulation. Y. Cao and W. Zeng performed the modeling simulation and wrote the manu- script. Q. Ouyang designed the project and wrote the manuscript. We would like to thank F. Hao, X. He, W. Wei, C. Xu, and L. Ji for their technical assistance the BioBrick Foundation for providing DNA materials and Anne O. Summers for supplying the plasmid carrying MerR gene. We thank Peking University for its financial support. This work is also partially supported by the National Nature Science Foundation of China （Nos. 10721463, 110740 09）, the National Basic Research Program of China （Nos. 2009CB918500, 2012AA02A702）, and the National Science Fund for Talent Training in Basic Science of China （Nos. J1030310, J1103205）.
文摘A central goal of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to construct basic biological functional modules, and through rational design, to build synthetic biological systems with predetermined functions. Here, we apply the reverse engineering design principle of biological networks to synthesize a gene circuit that executes semi-log dose-response, a logarithmically linear sensing function, in Escherichia coil cells. We first mathematically define the object function semi-log dose-response, and then search for tri-node network topologies that can most robustly execute the object function. The simplest topology, transcriptional coherent feed-forward loop （TCFL）, among the searching results is mathematically analyzed; we find that, in TCFL topology, the semi-log dose-response function arises from the additive effect of logarithmical linearity intervals of Hill functions. TCFL is then genetically implemented in E. coil as a logarithmically linear sensing biosensor for heavy metal ions [mercury （II）]. Functional characterization shows that this rationally designed biosensor circuit works as expected. Through this study we demonstrated the potential application of biological network reverse engineering to broaden the computational power of synthetic biology.
