Thomas Spencer Angus, Jin Yaochu
Department of Computing, University of Surrey, Guildford, Surrey GU2 7XH, UK.
J Bioinform Comput Biol. 2013 Jun;11(3):1341001. doi: 10.1142/S0219720013410011.
Although hypothesised there has been little investigation into how complex gene regulatory networks can evolve from simple regulatory motifs through modularisation, duplication and specialisation processes. In order to simulate natural evolution in a computational environment we evolve the connection between a genetic oscillator and a toggle switch motif using an evolutionary algorithm. We observe a connectivity preference between the motifs that is dependent on the coupling arrangement rather than on objective set-up. In addition, our results indicate the existence of a threshold in the connection parameters for the resulting dynamics for a specific coupling arrangement and objective set-up. We demonstrate that simple motifs can successfully be coupled through artificial evolution to form more complex, modular regulatory networks. These findings support, in principle, the above-mentioned hypothesis on evolutionary mechanisms in biological systems.
尽管有人提出了假设，但对于复杂的基因调控网络如何通过模块化、复制和特化过程从简单的调控基序进化而来，却鲜有研究。为了在计算环境中模拟自然进化，我们使用进化算法来进化遗传振荡器和拨动开关基序之间的连接。我们观察到基序之间的连接偏好取决于耦合方式，而非目标设置。此外，我们的结果表明，对于特定的耦合方式和目标设置，连接参数存在一个阈值，该阈值会影响最终的动力学。我们证明，简单的基序可以通过人工进化成功耦合，形成更复杂的模块化调控网络。这些发现原则上支持了上述关于生物系统进化机制的假设。
