Modeling Biological Bistable Switch And Its Application In Synthetic Biology

Bistable phenomena are widespread in biological system, such as the genetic switch of lambda phage, phase variation of bacterial pili, All-to-None phenomena in lactose metabolic pathway and epigenetics in eukaryote. All the bistable systems have important physiological significance. For example, the phase variation of bacterial pili can help bacterium locating on its host cell and evading from the host immune attack. At the same time, biological bistable switch is a fundamental nonlinear system, the new mathematical model developed from which can be used in other complex biological genetic network.My Theoretical works include two parts. The first part is to build the simplest model to describe the phenotype variation of bacterial drug tolerance. It is reported more than 60% superinfection is caused by the dormant individual. By modeling HipBA toxin-antitoxin module, I found that cooperation for HipB and HipA with their targets are indispensable to explain the phenotype variation. Moreover, the model also explains why dormant individual doesn't generate when the population is growing fast. In the second part, based on the tremendous quantitative data for lambda genetic switch, I try to introduce more quantitative model to resolve the paradox of previous models. My model considers both DNA looping of CI repressor and searching mechanism of transcription factor. In order to describe the two mechanisms, I introduce two new parameters and fit them by two quantitative experiments, then use them in the lambda genetic switch. I found the wild type lambda lysogen is in the monostable region rather than bistable region. The model also explains why Cro is a weak repressor comparing with CI. Furthermore, the model also predicted that Cro is much more important in the induction of lysogeny than in the infection process.Bistable switch is a fundamental functional module in biology, so it can be coupled with other biological modules and form a bigger module to fulfill new function. I try to design a genetic sequential logic circuit by coupling a bistable switch with a NOR gate module. Sequential logic gives an output based on its input and internal states. Thus a same input can generate different output. Furthermore, our designed circuit can function as a genetic a bit genetic counter.In constructing process, we adopted rational design to implement the bistable switch and the NOR gate, and directed evolution to couple them. The expression of connection parts (lacI and CIind-) are fine tuned by mutating their RBS. After two round screening, I got several successful mutants, which could generate different outputs in response to a same input based on their different internal states. Moreover, I also design several control experiments to prove that only our designed circuit could accomplish the sequential logical function.