Accidental and Regulated Cell Death in Yeast Colony Biofilms

Abstract

The yeast species Saccharomyces cerevisiae is one of the most intensively studied organisms on the planet due to it being an excellent eukaryotic model organism in molecular and cell biology. In this work, we investigate the growth and morphology of yeast colony biofilms, where proliferating yeast cells reside within a self-produced extracellular matrix. This research area has garnered significant scientific interest due to its applicability in the biological and biomedical sectors. A central feature of yeast colony biofilm expansion is cellular demise, which is onset by one of two independent mechanisms: either accidental cell death (ACD) or regulated cell death (RCD). In this article, we generalise a continuum model for the nutrient-limited growth of a yeast colony biofilm to include the effects of ACD and RCD. This new model involves a system of four coupled nonlinear reaction-diffusion equations for the yeast-cell density, the nutrient concentration, and two species of dead cells. Numerical solutions of the spatially one and two-dimensional governing equations reveal the impact that ACD and RCD have on expansion speed, morphology and cell distribution within the colony biofilm. Our results are in good qualitative agreement with our own experiments.

Keywords: Saccharomyces cerevisiae; Apoptosis; Instability; Necrosis; Phloxine B; Reaction–diffusion.

Fig. 1

Three experimental photographs of yeast colony biofilm formation. Dark pink/red regions in each photograph show regions where yeast cells have taken up Phloxine B dye, indicating regions of cell death. The experimental method is described in Section 2.2. (A) Magnusiomyces magnusii colony biofilm grown from a small spot inoculation at the centre of a circular Petri dish (10 days), with cell death occurring in the centre of the colony. (B) S. cerevisiae colony biofilm grown on agar (5 days). (C) S. cerevisiae colony biofilm grown from an inoculum streaked from top to bottom of a rectangular Petri dish filled with 0.9% YPD agar (19 days), with a stripe of death trailing the expanding edge, and an unstable front pattern

Fig. 2

Numerical solutions for the living-cell density n, ACD-cell density, $m_1$, and nutrient concentration g, plotted against x for increasing ${\mathrm{\Lambda }}_1$. The top-left panel indicates the initial condition. The bottom-right panel shows the expansion speed plotted against ${\mathrm{\Lambda }}_1$. The remaining panels indicate solutions at $t=300$. The parameter values used used to obtain these numerical results are given by: $D_n=0.47$, $D_{m1}=0.001$, $C=1$, ${\mathrm{\Gamma }}_1=0$, $g_{†}=0.25$

Fig. 3

Numerical solutions for the living-cell density n, ACD-cell density, $m_1$, and nutrient concentration g, plotted as a function of x for increasing $K_1$. The top-left panel indicates the initial condition. The bottom-right panel shows the expansion speed plotted against $K_1$. The remaining panels indicate solutions at $t=300$. The parameter values used for this simulation are: ${\mathrm{\Lambda }}_1=0.5,D_n=0.47$, $D_{m1}=0.001$, $C=1$, ${\mathrm{\Gamma }}_1=0.5$, $g_{†}=0.25$

Fig. 4

Numerical solutions for the living-cell density n, ACD-cell density, $m_1$, RCD-cell density, $m_2$, and nutrient concentration, g, plotted at $t=300$ against x with $K_1=0$, $K_2=0.5$ and increasing ${\mathrm{\Gamma }}_2$. The top-left panel indicates the initial condition. The bottom-right panel shows the expansion speed plotted against ${\mathrm{\Gamma }}_2$. The remaining parameter values used for this simulation are: $D_n=0.47$, $D_{m1}=0.001$, ${\mathrm{\Lambda }}_1=0.001$, ${\mathrm{\Lambda }}_2=0.5$, $C=1$, ${\mathrm{\Gamma }}_1=0$, $g_{†}=0.25,g_1=0,g_2=1$

Fig. 5

Spatially two-dimensional numerical solution of (2.5) and (2.7a) subject to the transversely perturbed initial condition (3.1) on the domain $x\in (0,150),y\in (-50,50)$ in the absence of cell death. The first panel shows the initial condition, the centre panel shows the corresponding solution at $t=100$, and the final panel is a schematic illustrating the instability mechanism. The specific parameter values that have been used are: $D_n=0.47,C=1,{\mathrm{\Lambda }}_1=0,{\mathrm{\Lambda }}_2=0$, $\delta =0.1,$ $q=6\pi /50$

Fig. 6

Spatially two-dimensional numerical solution of (2.5) and (2.7a) subject to the transversely perturbed initial condition (3.1) on the domain $x\in (0,150),y\in (-50,50)$. There is ACD, but no nutrient release or RCD. The left-hand panel shows the initial condition. The right-hand panel shows the solution at $t=100$. The parameter values that have been used are: $D_n=0.47,C=1,{\mathrm{\Lambda }}_1=0.5,{\mathrm{\Lambda }}_2=0,{\mathrm{\Gamma }}_1=0,K_1=0$

Fig. 7

Spatially two-dimensional numerical solution of (2.5) and (2.7a) subject to the transversely perturbed initial condition (3.1) on the domain $x\in (0,150),y\in (-50,50)$. There is ACD and nutrient release, but no RCD. The left-hand panel shows the initial condition. The right-hand panel shows the solution at time $t=100$. The parameter values that have been used are: $D_n=0.47,C=1,{\mathrm{\Lambda }}_1=0.5,{\mathrm{\Lambda }}_2=0,{\mathrm{\Gamma }}_1=0.5,K_1=1$

Fig. 8

Spatially two-dimensional numerical solution of (2.5) and (2.7a) subject to the transversely perturbed initial condition (3.1) on the domain $x\in (0,150),y\in (-50,50)$. There is ACD, RCD and nutrient release. The top row shows the living-cell density in its initial (left) and evolved (state). The middle panel shows the ACD-cell density (left) and RCD-cell density (right) in their evolved states. The bottom panel shows the sum $m_1+m_2$ of the dead cell densities. The parameter values that were used are: $D_n=0.47,C=1,{\mathrm{\Lambda }}_1=0.001,{\mathrm{\Lambda }}_2=0.5,{\mathrm{\Gamma }}_1=0,{\mathrm{\Gamma }}_2=0.05,K_2=0.5$

Fig. 9

Spatially two-dimensional numerical solution of (2.5) and (2.7a) subject to the transversely perturbed initial condition (3.1) on the domain $x\in (0,700),y\in (-50,50)$ for the case of linear diffusion. The parameters were chosen to match Figure 8