Marching along to an Offbeat Drum: Entrainment of Synthetic Gene Oscillators by a Noisy Stimulus

Abstract

Modulation of biological oscillations by stimuli lies at the root of many phenomena, including maintenance of circadian rhythms, propagation of neural signals, and somitogenesis. While it is well established that regular periodic modulation can entrain an oscillator, an aperiodic (noisy) modulation can also robustly entrain oscillations. This latter scenario may describe, for instance, the effect of irregular weather patterns on circadian rhythms, or why irregular neural stimuli can still reliably transmit information. A synthetic gene oscillator approach has already proven to be useful in understanding the entrainment of biological oscillators by periodic signaling, mimicking the entrainment of a number of noisy oscillating systems. We similarly seek to use synthetic biology as a platform to understand how aperiodic signals can strongly correlate the behavior of cells. This study should lead to a deeper understanding of how fluctuations in our environment and even within our body may promote substantial synchrony among our cells. Specifically, we investigate experimentally and theoretically the entrainment of a synthetic gene oscillator in E. coli by a noisy stimulus. This phenomenon was experimentally studied and verified by a combination of microfluidics and microscopy using the real synthetic circuit. Stochastic simulation of an associated model further supports that the synthetic gene oscillator can be strongly entrained by aperiodic signals, especially telegraph noise. Finally, widespread applicability of aperiodic entrainment beyond the synthetic gene oscillator is supported by results derived from both a model for a natural oscillator in D. discoideum and a model for predator-prey oscillations.

Proteolytic queues at ClpXP increase antibiotic tolerance

“…No apparent change in growth was observed by induction ( Fig. S1) as reported previously 29,30 . The effects of queue formation on antibiotic survival are shown as the percentage of the population that survived ampicillin treatment (Fig 2).…”

“…For example, synthetic oscillators require rapid degradation of proteins, which is accomplished using the ssrA degradation tag [26][27][28] ; the ssrA degradation tag is the amino acid sequence, AANDENYALAA 18 , which we abbreviate to LAA throughout. Previous work establishes that multiple circuits can be coordinated by overproduction of a common degradation tag to target proteins to a protease 29,30 . When a protease is overloaded, protein species compete for degradation; the enzyme is unable to keep up with the influx of new proteins 31 .…”

“…The queueing effect at the protease ClpXP is essential in allowing for oscillation of the highly used synthetic oscillator (often called Stricker oscillator or dual-feedback oscillator) 27,33 . Variations of this oscillator have been used in different strains of E. coli 27,29,30,34 , and in Salmonella typhimurium 35 , demonstrating that the queueing at ClpXP is not specific to one strain or species. The coupling of otherwise independent synthetic systems via proteolytic queueing demonstrates that queueing affects protein degradation and thus provides a tunable method of studying proteolytic degradation with little effect on cell growth [28][29][30]32 compared to gene knockouts and overexpression of proteases 15,36,37 .…”

“…The variability between results of knockout mutations could be due to differences in growth rates, which would modulate antibiotic efficacy. Proteolytic queueing is preferred over protease knockouts when probing antibiotic efficacy because protease knockouts often result in growth defects 15,36 , but proteolytic queueing does not noticeably affect cell growth or death [28][29][30]32 , even in stationary phase ( Fig. S1).…”

Incoherent Inputs Enhance the Robustness of Biological Oscillators

“…(B) Example of synthetic oscillators with incoherent inputs (Atkinson et al, 2003; Butzin et al, 2016; Chen et al, 2015; Fung et al, 2005; Hussain et al, 2014; Stricker et al, 2008; Tigges et al, 2009, 2010; Toettcher et al, 2010). …”