Lim Lab | Papers

Design of Tunable Oscillatory Dynamics in a Synthetic NF-kB Signaling Circuit.

Zhi-Bo Zhang, Qiu-Yue Wang, Yu-Xi Ke, Shi-Yu Liu, Jian-Qi Ju, Wendell A Lim, Chao Tang, Ping Wei.
Cell Syst. 2017

Although oscillatory circuits are prevalent in tran- scriptional regulation, it is unclear how a circuit’s structure and the specific parameters that describe its components determine the shape of its oscilla- tions. Here, we engineer a minimal, inducible human nuclear factor kB (NF-kB)-based system that is composed of NF-kB (RelA) and degradable inhibitor of NF-kB (IkBa), into the yeast, Saccharomyces cerevisiae. We define an oscillation’s waveform quantitatively as a function of signal amplitude, rest time, rise time, and decay time; by systematically tuning RelA concentration, the strength of negative feedback, and the degradation rate of IkBa, we demonstrate that peak shape and frequency of oscil- lations can be controlled in vivo and predicted math- ematically. In addition, we show that nested negative feedback loops can be employed to specifically tune the frequency of oscillations while leaving their peak shape unchanged. In total, this work establishes design principles that enable function-guided design of oscillatory signaling controllers in diverse syn- thetic biology applications.