Single cell characterization of a synthetic bacterial clock with a hybrid feedback loop containing dCas9-sgRNA

Genetic networks that generate oscillations in gene expression activity are found in a wide range of organisms throughout all kingdoms of life. Oscillatory dynamics facilitates the temporal orchestration of metabolic and growth processes inside cells and organisms, as well as the synchronization of such processes with periodically occurring changes in the environment. Synthetic oscillator gene circuits such as the ‘repressilator’ can perform similar functions in bacteria. Until recently, such circuits were mainly based on a relatively small set of well-characterized transcriptional repressors and activators. A promising, sequence-programmable alternative for gene regulation is given by CRISPR interference (CRISPRi), which enables transcriptional repression of nearly arbitrary gene targets directed by short guide RNA molecules. In order to demonstrate the use of CRISPRi in the context of dynamic gene circuits, we here replaced one of the nodes of a repressilator circuit by the RNA-guided dCas9 protein. Using single cell experiments in microfluidic reactors we show that this system displays robust relaxation oscillations over multiple periods and over the time course of several days. Through statistical analysis of the single cell data, the potential for the circuit to act as a synthetic pacemaker for cellular processes is evaluated. The use of CRISPRi in the context of an oscillator circuit is found to have profound effects on its dynamics. Specifically, irreversible binding of dCas9-sgRNA appears to prolong the period of the oscillator. Further, we demonstrate that the oscillator affects cellular growth, leading to variations in growth rate with the oscillator’s frequency.