Schwall, C. P. | bioRxiv Science

bioRxiv2025

Mixed positive and negative feedback loops drive diverse single-cell gene expression dynamics

Genetic circuits with only a few components can generate complex gene regulatory dynamics. Here, we combine stochastic modelling and single-cell time-lapse microscopy to reveal the possible dynamics generated by a key gene circuit motif: the mixed positive/negative feedback loop. Our minimal stochastic model of this motif reveals ten distinct classes of dynamic output, including stochastic pulsing, oscillations, and bistability. We systematically map how the circuits core parameters can be tuned to generate each of the behaviours. Experimental validation in two different mixed feedback circuits in the bacterium Bacillus subtilis, {sigma}B and {sigma}V, confirms our models predictive power. Guided by our simulations, we are able to transition between dynamic behaviours by modulating in vivo parameters. Together, these results demonstrate how mixed feedback loops generate diverse single-cell dynamics, improving our understanding of this common biological network motif and informing our efforts to engineer them for synthetic biology applications.

systems biology↗

bioRxiv2020

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit

Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in B. subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history, and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗