Managing bacterial growth and phenotypic diversification through the external control of synthetic gene circuits

Understanding how cells are able to tune their phenotype when faced with environmental perturbations is a central question in microbiology. To characterize this particular feature, two different approaches have been considered i.e., on one hand, the design of synthetic gene circuits exhibiting bistability and/or ultrasensitivity to extracellular conditions and, on the other hand, the design of cell-machine machine allowing to get access to the phenotypic trajectories followed by cells under fluctuating environmental conditions.
In this work, we implemented a combination of these two approaches in order to address the phenotypic diversification of E. coli populations growing in continuous culture. The cell-machine interface that will be used is a bioreactor equipped with on-line flow cytometry. Based on the flow cytometry measurements, it is possible to send pulses of inducers in the medium and manage cell phenotypes.
This interface will be used to control a synthetic gene circuit, the toggle-switch. The toggle-switch is a bistable circuit that can be switched from one stable state to the other using specific inducers. This toggle-switch is, by itself, independent from the cell machinery. Therefore, in order to modulate bacterial growth, E. coli was made auxotrophic through the deletion of serA, and serA was added to one side of the toggle-switch. This effectively creates a system in which controlling the state of the genetic circuit, with the abovementioned cell-machine interface, controls the growth of the population.
This experimental framework makes it possible to manage growth, but could be extended to control metabolic fluxes or other phenotypes. Further, it opens new possibilities in bioprocesses relying on co-cultures as well. Indeed, not only does it provide a way to dynamically control the growth of a single species, but the toggle-switch itself is independent from the cells. It could therefore be used to control the phenotype of multiple species at once, and dynamically regulate consortia based on desired bioprocess outputs.