Space-induced bifurcation in repression-based transcriptional circuits

Authored by Van Amanda Lo, Hedi A Soula, Hugues Berry

Date Published: 2014

DOI: 10.1186/s12918-014-0125-z

Sponsors: No sponsors listed

Platforms: C

Model Documentation: Other Narrative Mathematical description

Model Code URLs: Model code not found

Abstract

Background: Albeit the molecular mechanisms of gene expression are well documented, our understanding of their dynamics is much less advanced. Recent experimental evidence has revealed that gene expression might be accurately organized in space, with several molecular actors localized to specific positions in the cell. However, the influence of this spatial localization on the dynamics of gene expression is unclear. This issue is also central in synthetic biology, where one usually considers the spatial localization in the cell of the genes of the inserted synthetic construct as irrelevant for its temporal dynamics. Results: Here, we assessed the influence of the spatial distribution of the genes on the dynamics of 3-gene transcriptional ring networks regulated by repression, i.e. repressilator circuits, using individual-based modelling to simulate their dynamics in two and three space dimensions. Our simulations suggest that variations of spatial parameters - namely the degree of demixing of the positions of the gene or the spatial range of the mRNA and proteins (i.e. the typical distance they travel before degradation) - have dramatic effects by switching the dynamical regime from spontaneous oscillations to a stationary state where each species fluctuates around a constant value. By analogy with the bifurcations arising from the variation of kinetic parameters, we referred to those transitions as space-induced bifurcations. Conclusions: Taken together, our results strongly support the idea that the spatial organization of the molecular actors of transcriptional networks is crucial for the dynamics of gene expression and suggest that the spatial localization of the synthetic genes in the cell could be used as an additional toggle to control the dynamics of the inserted construct in synthetic biology experiments.

Tags

networks diffusion kinetics Gene-expression Escherichia-coli Cell Protein Spatial-organization Ligand-binding Cytoplasm