A dynamic model of the phosphate response system with synthetic promoters in Escherichia coli

Abstract

The bacteria E. coli have developed one of the most efficient regulatory response to phosphate starvation that is known in detail. Achieving a mechanistic understanding of this system, realized by Pho regulon at the genetic level, has implications for applications in artificial life and for others in biotechnology that exploit such mechanisms. To this end, we present a dynamical model of Pho regulon, coupled with a layered description of its regulation in the experimental conditions of phosphate starvation. The model describes the dynamics of two-component regulatory system together with the key regulatory promoter PhoB and experimental data on promoter PhoA. The model is parameterized according to the feasible range given in the literature, and fitted to the dynamic response of our experimental data on alkaline phosphatase production, coded as Gfp. Sensitivity analysis demonstrates that the rate of Pho transcription has a significant influence over the expression of Pho-controlled genes. Variations in the transcription rates alter the sensitivity of the phosphate starvation response to external phosphate concentration, whereas variations in the translation rates affect the gain of the system. Our model provides a dynamic description of the core determinants of Pho regulon and promoter activities and their response to the change of external phosphate level. As the model architecture is intrinsically open to integrate supplementary layers, together with experimental findings, it should provide insights in investigations on engineering new dynamic sensors and regulators for living technologies.

Mechanisms of Switching Response to External Phosphate Levels in Escheria coli

“…The parameters for the rates are listed in Table 1. The rate of reaction 1 is obtained in accordance with our previous works (Uluşeker et al, 2018(Uluşeker et al, , 2017). The unknown rates of reaction 2 and 3 have been estimated to reproduce decreasing dynamics of the PhoR according to the external P i concentration change with respect to the switching of dynamics.…”

“…However, when the external P i is in excess, the E. coli begins to enhance P i accumulation and switches the TCS off. To explain this system, we have previously designed and analysed a two component system model that quantifies the dynamic mechanisms of auto-regulation in E. coli, and explored and verified emerging phenotypes with synthetic promoters (Uluşeker et al, 2018(Uluşeker et al, , 2017. Moreover, we have analysed the response of the model to variations in the external P i levels.…”

“…The signal is thus propagated to PhoR, resulting in its inhibition state P hoR r . has been quantified in our previous work (Uluşeker et al, 2018(Uluşeker et al, , 2017. In the current work, this framework is used as a basis to describe mechanistically the effect of external P i concentration change and TCS inhibition.…”

“…The models have been tested with 0, 50, and 100 µM external P i . The concentrations of proteins PhoR and ABC are set to 0.22 µM based on literature and verified by our previous work (Van Dien and Keasling, 1997;Uluşeker et al, 2018Uluşeker et al, , 2017. The parameters for the rates are listed in Table 1.…”

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

“…Synthetic biology strategies are feasible for removing a particular toxic compound because the genetic circuits can be developed against the exogenous environmental toxin (Checa et al, 2012;Tay et al, 2017). The synthetic genetic circuits are assembled via a two-component regulatory system (TCRS) in bacteria (Futagami et al, 2014;Uluşeker et al, 2017). This system acts upon environmental change, and thereby, cells respond to these changes.…”