Dynamical model fitting to a synthetic positive feedback circuit in E. coli

Abstract

Applying the principles of engineering to Synthetic Biology relies on the development of robust and modular genetic components, as well as underlying quantitative dynamical models that closely predict their behaviour. This study looks at a simple positive feedback circuit built by placing filamentous phage secretin pIV under a phage shock promoter. A singleequation ordinary differential equation model is developed to closely replicate the behaviour of the circuit, and its response to inhibition by TetR. A stepwise approach is employed to fit the model's parameters to time-series data for the circuit. This approach allows the dissection of the role of different parameters and leads to the identification of dependencies and redundancies between parameters. The developed genetic circuit and associated model may be used as a building block for larger circuits with more complex dynamics, which require tight quantitative control or tuning.

Engineering Tunable, Low Latency Spatial Computation with Dual Input Quorum Sensing Promoters

“…One major advantage of the simplified one-node system is a reduction in response time. Each step in the transcription factor cascade of larger systems can create delays on a scale of minutes to hours , and impact the robustness of the dynamics. , In our system, computation occurs on the promoter level through the transcription factor and RNA polymerase binding events, which occur at a much faster time scale compared to transcription factor synthesis . In the future, computation could also be engineered through the competition of the diffusers at the receptor level.…”

Reducing metabolic burden in the PACEmid evolver system by remastering high‐copy phagemid vectors

“…Though the high copy number was expected to increase phage titres, its associated burden has resulted in problems in downstream studies, and may have even negatively impacted the system's performance. Interestingly, observations collected with a simple positive feedback circuit [60] show how a lower-copy pBR322 ori can produce even higher phage titres compared to the high-copy pLit ori, due to a reduction in burden (Tica 2018, unpublished data). Although this warrants further investigation, it is likely that the phage-related mechanisms for viral genome replication do not compete with the bacterial mechanisms for plasmid replication and copy number maintenance [16,61].…”

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

“…Turing patterns were then also discovered in the thiourea–iodate–sulfite (TuIS) reaction with a rational design approach (Horváth et al ., 2009). Unlike biological systems, chemical reactions are reliably described by the simpler laws of mass action, and system parameters can often be identified (Turányi, 1994; Kügler et al ., 2009; Pušnik et al ., 2019; Yeoh et al ., 2019; Tica et al ., 2020). Furthermore, the tuning of these systems by changing initial reactant concentration or temperature is easily achieved and has predictable effects on the dynamics of the system (Horváth et al ., 2009; Carballido‐Landeira et al ., 2010; Asakura et al ., 2011).…”