Limits...
A synthetic Escherichia coli predator-prey ecosystem.

Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L - Mol. Syst. Biol. (2008)

Bottom Line: The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator.A simple mathematical model is developed to capture these system dynamics.Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.

ABSTRACT
We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator-prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.

Show MeSH

Related in: MedlinePlus

Dependence of systems dynamics on dilution rate (D). (A) Experimental dynamics of predator and prey populations at different D in the microchemostat: for the pair of predator (MG1655) and prey (Top10F′). (B) For the pair of predator (Top10F′) and prey (Top10F′). (C) Bifurcation diagram of oscillatory period versus D. The inset is the oscillation period versus D. Qualitatively different systems dynamics (sustained and damped oscillations, and steady state) can be obtained by the variation of D. These experiments were carried out at IPTG=50 μM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2387235&req=5

f3: Dependence of systems dynamics on dilution rate (D). (A) Experimental dynamics of predator and prey populations at different D in the microchemostat: for the pair of predator (MG1655) and prey (Top10F′). (B) For the pair of predator (Top10F′) and prey (Top10F′). (C) Bifurcation diagram of oscillatory period versus D. The inset is the oscillation period versus D. Qualitatively different systems dynamics (sustained and damped oscillations, and steady state) can be obtained by the variation of D. These experiments were carried out at IPTG=50 μM.

Mentions: Similarly, we explored the impact of dilution rate (D) on the system dynamics. Figure 3A illustrates coexistence dynamics at D=0.11 h−1, suggestive of an initial phase of long-period oscillations. However, an increase in D (to 0.2 h−1) led to a phase of damped oscillatory dynamics with much shorter periods (∼50 h). We observed similar response with a different circuit configuration: predator (Top10F′) and prey (Top10F′) (Figure 3B; also see Supplementary Figure S4B). These populations initially coexist at a low dilution rate (D=0.15 h−1). They switched to damped oscillations with short periods (∼30 h) upon an increase in D (to 0.23 h−1). Further increase in D (to 0.31 h−1) at ∼250 h led to predator washout. Bifurcation analysis qualitatively accounts for the experimental observations that an increase in the dilution rate can lead to a significant decrease in the period of oscillations (Figure 3C, inset). Simulations further show that an increase in D can shift a slow, sustained oscillation (Figure 3C, bottom left panel) to a fast, damped oscillation (Figure 3C, bottom middle panel). Predator cells will be washed out if D is too large (Figure 3C, bottom right panel).


A synthetic Escherichia coli predator-prey ecosystem.

Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L - Mol. Syst. Biol. (2008)

Dependence of systems dynamics on dilution rate (D). (A) Experimental dynamics of predator and prey populations at different D in the microchemostat: for the pair of predator (MG1655) and prey (Top10F′). (B) For the pair of predator (Top10F′) and prey (Top10F′). (C) Bifurcation diagram of oscillatory period versus D. The inset is the oscillation period versus D. Qualitatively different systems dynamics (sustained and damped oscillations, and steady state) can be obtained by the variation of D. These experiments were carried out at IPTG=50 μM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2387235&req=5

f3: Dependence of systems dynamics on dilution rate (D). (A) Experimental dynamics of predator and prey populations at different D in the microchemostat: for the pair of predator (MG1655) and prey (Top10F′). (B) For the pair of predator (Top10F′) and prey (Top10F′). (C) Bifurcation diagram of oscillatory period versus D. The inset is the oscillation period versus D. Qualitatively different systems dynamics (sustained and damped oscillations, and steady state) can be obtained by the variation of D. These experiments were carried out at IPTG=50 μM.
Mentions: Similarly, we explored the impact of dilution rate (D) on the system dynamics. Figure 3A illustrates coexistence dynamics at D=0.11 h−1, suggestive of an initial phase of long-period oscillations. However, an increase in D (to 0.2 h−1) led to a phase of damped oscillatory dynamics with much shorter periods (∼50 h). We observed similar response with a different circuit configuration: predator (Top10F′) and prey (Top10F′) (Figure 3B; also see Supplementary Figure S4B). These populations initially coexist at a low dilution rate (D=0.15 h−1). They switched to damped oscillations with short periods (∼30 h) upon an increase in D (to 0.23 h−1). Further increase in D (to 0.31 h−1) at ∼250 h led to predator washout. Bifurcation analysis qualitatively accounts for the experimental observations that an increase in the dilution rate can lead to a significant decrease in the period of oscillations (Figure 3C, inset). Simulations further show that an increase in D can shift a slow, sustained oscillation (Figure 3C, bottom left panel) to a fast, damped oscillation (Figure 3C, bottom middle panel). Predator cells will be washed out if D is too large (Figure 3C, bottom right panel).

Bottom Line: The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator.A simple mathematical model is developed to capture these system dynamics.Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.

ABSTRACT
We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator-prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.

Show MeSH
Related in: MedlinePlus