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balaggade1

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balaggade1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000296) Biomodels notes: Reproduction of parts of figure 2 of the original publication using Copasi 4.6. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Manuscript information

A synthetic Escherichia coli predator-prey ecosystem.

  • Frederick K Balagaddé
  • Hao Song
  • Jun Ozaki
  • Cynthia H Collins
  • Matthew Barnet
  • Frances H Arnold
  • Stephen R Quake
  • Lingchong You
Mol. Syst. Biol. 2008; 4 : 187
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.

Unit definitions 2

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
— 1e-09 mole
— 3600.0 second

Compartments 1

Id Name Spatial dimensions Size
environment — 3.0 1.0

Species 7

Id Name Initial quantity Compartment Fixed
A1 — 0.1 environment ✘
A2 — 0.1 environment ✘
C1 — 20.0 environment ✘
C2 — 20.0 environment ✘
IPTG — 5.0 environment ✘
sink — 0.0 environment ✔
source — 0.0 environment ✔

Initial assignments 0

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Reactions 8
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
J0 predator growth source > C1

environment * kc1 * C1 * (1 - (C1 + C2) / Cm)
J1 predator death C1 > sink

environment * (D + d1 * K1 / (K1 + pow(A2, 2))) * C1
J2 prey growth source > C2

environment * kc2 * C2 * (1 - (C1 + C2) / Cm)
J3 prey death C2 > sink

environment * (D + d2 * pow(A1, 2) / (K2 + pow(A1, 2))) * C2
J4 3OC12HSL synthesis source > A1

environment * kA1 * C1
J5 3OC12HSL removal A1 > sink

environment * (dAA1 + D) * A1
J6 3OC6HSL synthesis source > A2

environment * kA2 * C2
J7 3OC6HSL removal A2 > sink

environment * (dAA2 + D) * A2

Parameters 0   12

Global parameters

Id Value
Cm 100.0
D 0.1125
K1 10.0
K2 10.0
d1 0.0
d2 0.3
dAA1 0.017
dAA2 0.11
kA1 0.1
kA2 0.0
kc1 0.8
kc2 0.4

Local parameters

Id Value Reaction

Rules 0   0   2

Assignment rules

Definition
kA2 = 0.02 + 0.03 * (pow(IPTG, 2.0) / (pow(5.0, 2.0) + pow(IPTG, 2.0)))
d1 = 0.5 + pow(IPTG, 2.0) / (pow(5.0, 2.0) + pow(IPTG, 2.0))

Rate rules

Definition

Algebraic rules

Definition

Events 0

Trigger Assignments