Multiscale Modeling of Bistability in the Yeast Polarity Circuit

• Published in: Cells (Basel, Switzerland) Switzerland), 2024-08, Vol.13 (16), p.1358
• Main Authors: Hladyshau, Siarhei, Guan, Kaiyun, Nivedita, Nivedita, Errede, Beverly, Tsygankov, Denis, Elston, Timothy C
• Format: Article
• Language: English
• Subjects: biochemical networks; Boundary conditions; Cdc42 Rho GTPase; Cell culture; Cell migration; Cell Polarity; Datasets; Differential equations; Down-regulation; Experiments; Feedback; hysteresis; Mathematical models; Models, Biological; Molecular modelling; Ordinary differential equations; Partial differential equations; Pheromones; Polarity; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Signal Transduction; Simulation; Stochasticity; Turing instability; Yeast
• ISSN: 2073-4409; 2073-4409
• DOI: 10.3390/cells13161358

Cell polarity refers to the asymmetric distribution of proteins and other molecules along a specified axis within a cell. Polarity establishment is the first step in many cellular processes. For example, directed growth or migration requires the formation of a cell front and back. In many cases, polarity occurs in the absence of spatial cues. That is, the cell undergoes symmetry breaking. Understanding the molecular mechanisms that allow cells to break symmetry and polarize requires computational models that span multiple spatial and temporal scales. Here, we apply a multiscale modeling approach to examine the polarity circuit of yeast. In addition to symmetry breaking, experiments revealed two key features of the yeast polarity circuit: bistability and rapid dismantling of the polarity site following a loss of signal. We used modeling based on ordinary differential equations (ODEs) to investigate mechanisms that generate these behaviors. Our analysis revealed that a model involving positive and negative feedback acting on different time scales captured both features. We then extend our ODE model into a coarse-grained reaction-diffusion equation (RDE) model to capture the spatial profiles of polarity factors. After establishing that the coarse-grained RDE model qualitatively captures key features of the polarity circuit, we expand it to more accurately capture the biochemical reactions involved in the system. We convert the expanded model to a particle-based model that resolves individual molecules and captures fluctuations that arise from the stochastic nature of biochemical reactions. Our models assume that negative regulation results from negative feedback. However, experimental observations do not rule out the possibility that negative regulation occurs through an incoherent feedforward loop. Therefore, we conclude by using our RDE model to suggest how negative feedback might be distinguished from incoherent feedforward regulation.