Modeling and Analysis of a Cell-Free Gluconate Responsive Biosensor

Abstract

Cell-free synthetic systems are composed of the parts required for transcription and translation processes in a buffered solution. Thus, unlike living cells, cell-free systems are amenable to rapid adjustment of the reaction composition and easy sampling. Further, because cellular growth and maintenance requirements are absent, all resources can go toward synthesizing the product of interest. Recent improvement in key performance metrics, such as yield, reaction duration, and portability, has increased the space of possible applications open to cell-free systems and lowered the time required to design-build-test new circuitry. One promising application area is biosensing. This study describes developing and modeling a D-gluconate biosensor circuit operating in a reconstituted cell-free system. Model parameters were estimated using time-resolved measurements of the mRNA and protein concentration with and without the addition of D-gluconate. Sensor performance was predicted using the model for D-gluconate concentrations not used in model training. The model predicted the transcription and translation kinetics and the dose response of the circuit over several orders of magnitude of D-gluconate concentration. Global sensitivity analysis of the model parameters gave detailed insight into the operation of the sensor circuit. Taken together, this study reported an in-depth, systems-level analysis of a D-gluconate biosensor circuit operating in a reconstituted cell-free system. This circuit could be used directly to estimate D-gluconate or as a subsystem in a more extensive synthetic gene expression program.