Light-driven synchronization of optogenetic clocks

Abstract

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system's response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.

From resonance to chaos: modulating spatiotemporal patterns through a synthetic optogenetic oscillator

“…Cells also showed higher synchronisation rate at half of the resonance frequency (undertone), at T light of 44 h. In fact, these parameter regions where synchronisation is enhanced are called Arnold’s tongues. Apart from resonance, this region allows entrainment of the oscillator to the driving force, a phenomenon observed both in our experiments (Figure 3c) and in prior studies involving synthetic oscillators [37, 38]. It is therefore not surprising to find that many biological oscillators are influenced by periodic environmental cues to keep their physiology and behaviour synchronised [50, 51].…”

“…The irregularity arose from small differences in the period of the individual cells caused by stochastic effects [23]. Over generations these differences increased, meaning that synchronization between the cells decreased with time [38]. As a consequence of this increasing phase difference, the variation in time and position of the next peak increased as the colony grew, resulting in deviations from the initially circular ring pattern.…”

“…In both studies, the use of a microfluidic system was essential to enable the periodic supplementation and removal of the chemical inducer in the medium. Recently, Cannarsa and colleagues [38] used optogenetics to construct a repressilator that was periodically inhibited by light, which allowed for a long lasting synchronisation of individual E. coli cells and detuning from their natural frequency. Contrary to chemical inducers, using light with varying intensity and period to control oscillatory behaviour confers the advantage of adjusting the level of induction in space and time with precision, without the need of refreshing the medium [39, 40].…”