Robustness of synthetic oscillators in growing and dividing cells

TL;DR

This paper investigates how synthetic gene oscillators behave within dividing cells, revealing that gene positioning and replication timing noise influence their stability and coupling to the cell cycle, with implications for designing robust biological systems.

Contribution

It extends previous work by analyzing the effects of gene location and replication timing noise on the stability and cell cycle coupling of synthetic oscillators.

Findings

Gene position affects oscillator-cell cycle coupling strength.

Replication timing noise weakens but does not eliminate coupling.

Synthetic oscillators remain coupled to the cell cycle even with high noise levels.

Abstract

Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator (Elowitz and Leibler, Nature, 2000). More recently, Stricker et al. presented another synthetic oscillator, called the dual-feedback oscillator (Stricker et al., 2008), which is more stable. How the stability of these oscillators is affected by the intrinsic noise of the interactions between the components and the stochastic expression of their genes, has been studied in considerable detail. However, as all biological oscillators reside in growing and dividing cells, an important question is how these oscillators are perturbed by the cell cycle. In previous work we showed that the periodic doubling of the gene copy numbers due to DNA replication can couple not only natural, circadian oscillators to the cell cycle (Paijmans et al., PNAS, \textbf{113}, 4063, (2016)), but also these synthetic oscillators. Here we expand this study. We find that the strength of the locking between oscillators depends not only on the positions of the genes on the chromosome, but also on the noise in the timing of gene replication: noise tends to weaken the coupling. Yet, even in the limit of high levels of noise in the replication times of the genes, both synthetic oscillators show clear signatures of locking to the cell cycle. This work enhances our understanding of the design of robust biological oscillators inside growing and diving cells.