Novel tunable spatio-temporal patterns from a simple genetic oscillator circuit

Abstract

<jats:title>Abstract</jats:title><jats:p>Multicellularity, the coordinated collective behaviour of cell populations, gives rise to the emergence of self-organized phenomena at many different spatio-temporal scales. At the genetic scale, oscillators are ubiquitous in regulation of multicellular systems, including during their development and regeneration. Synthetic biologists have successfully created simple synthetic genetic circuits that produce oscillations in single cells. Studying and engineering synthetic oscillators in a multicellular chassis can therefore give us valuable insights into how simple genetic circuits can encode complex multicellular behaviours at different scales. Here we develop a study of the coupling between the repressilator synthetic genetic ring oscillator and constraints on cell growth in colonies. We show <jats:italic>in silico</jats:italic> how mechanical constraints generate characteristic patterns of growth rate inhomogeneity in growing cell colonies. Next, we develop a simple one-dimensional model which predicts that coupling the repressilator to this pattern of growth rate via protein dilution generates travelling waves of gene expression. We show that the dynamics of these spatio-temporal patterns are determined by two parameters; the protein degradation and maximum expression rates of the repressors. We derive simple relations between these parameters and the key characteristics of the travelling wave patterns: firstly, wave speed is determined by protein degradation and secondly, wavelength is determined by maximum gene expression rate. Our analytical predictions and numerical results were in close quantitative agreement with detailed individual based simulations of growing cell colonies. Confirming published experimental results we also found that static ring patterns occur when protein stability is high. Our results show that this pattern can be induced simply by growth rate dilution and does not require transition to stationary phase as previously suggested. Our method generalizes easily to other genetic circuit architectures thus providing a framework for multi-scale rational design of spatio-temporal patterns from genetic circuits. We use this method to generate testable predictions for the synthetic biology design-build-test-learn cycle.</jats:p>

Bacterial degrons in synthetic circuits

“…Another clever use of degradation tags is employing them to create localized protein expression patterns. There is an increasing interest in developing spatial patterning strategies in bacteria [139–141], as this could give us a better understanding of fundamental biological processes from developmental biology to tissue engineering [142,143]. For example, FtsH [144] and Prc (Tsp) [145] are proteases responsible for the degradation of membrane proteins and periplasmic proteins, respectively, and hold potential for the design of membrane-localized or periplasmic circuits.…”

Novel Tunable Spatio-Temporal Patterns From a Simple Genetic Oscillator Circuit

“…We also thank the members of the Synthetic Biology Lab for their support and encouragement—Anibal Arce, Kevin Simpson, Tamara Matute, Isaac Nuñez, Fernán Federici, among others. A preprint of this work is available on bioRxiv (Yáñez Feliu et al, 2020 ).…”