In Vivo Real-Time Control of Gene Expression: A Comparative Analysis of Feedback Control Strategies in Yeast
In Vivo Real-Time Control of Gene Expression: A Comparative Analysis of Feedback Control Strategies in Yeast
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DOI：
10.1021/acssynbio.5b00135
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发表时间：
2016-02-01
影响因子：
4.7
通讯作者：
di Bernardo, Diego
中科院分区：
文献类型：
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作者：
Fiore, Gianfranco;Perrino, Giansimone;di Bernardo, Diego
基因表达的实时自动调控是合成生物学的一项关键技术，例如使合成电路的元件在最佳范围内工作。计算机引导控制各种诱导启动子的基因表达直到最近才被成功证明。在这里，我们在硅和体内比较了三种不同的控制算法：比例积分（PI）和模型预测控制（MPC）控制器，它们已经被用于控制基因表达，以及零平均动力学（ZAD），一种用于调节电力系统的控制技术。我们选择酵母中最常用的诱导启动子：半乳糖反应型GAL1启动子作为实验平台。我们设置了两个控制任务：强迫细胞表达GAL1启动子下游报告蛋白的所需恒定荧光水平（设定点）或时变荧光（跟踪）。利用微流体为基础的实验平台，其中葡萄糖或半乳糖都可以提供给细胞，我们证明了MPC和ZAD控制策略都可以成功地调节活细胞中GAL1启动子的基因表达数千分钟。MPC控制器可以比ZAD更好地跟踪快速参考信号，但由于它需要大量的输入开关，因此需要更高的驱动努力。相反，PI控制器的性能与MPC和ZAD控制器仅在设定点调节方面的性能相当。
Real-time automatic regulation of gene expression is a key technology for synthetic biology enabling, for example, synthetic circuit's components to operate in an optimal range. Computer-guided control of gene expression from a variety of inducible promoters has been only recently successfully demonstrated. Here we compared, in silico and in vivo, three different control algorithms: the Proportional Integral (PI) and Model Predictive Control (MPC) controllers, which have already been used to control gene expression, and the Zero Average Dynamics (ZAD), a control technique used to regulate electrical power systems. We chose as an experimental testbed the most commonly used inducible promoter in yeast: the galactose-responsive GAL1 promoter. We set two control tasks: either force cells to express a desired constant fluorescence level of a reporter protein downstream of the GAL1 promoter (set-point) or a time-varying fluorescence (tracking). Using a microfluidics-based experimental platform, in which either glucose or galactose can be provided to the cells, we demonstrated that both the MPC and ZAD control strategies can successfully regulate gene expression from the GAL1 promoter in living cells for thousands of minutes. The MPC controller can track fast reference signals better than ZAD but with a higher actuation effort due to the large number of input switches it requires. Conversely, the PI controller's performance is comparable to that achieved by the MPC and the ZAD controllers only for the set-point regulation.