Team:SJTU-BioX-Shanghai/Gene Circuit

Gene Circuit

Summary

Since the wet-lab has designed the circuits, it is natural for us to think of this question: how does the circuits work, or can we actually achieve the desired function in reality? And there are also many questions which we may find it not easy to answer: how does the amount of drug molecules produced and metabolized change? What will happen when we adjust the concentration of NO?

Furthermore, we also want to get to know about the logical relationship between the promoter, terminator, protein, inducer, and so on of the genetic circuits. And it is one of the most important things we concern about that whether the results obtained in the experiment consistent with those obtained in the simulation or not.

With these questions, we conducted simulation modeling for the genetic circuits. We hope to provide references for the selection of the wet-lab scheme by changes of the relative concentration of each factor in the simulated circuits, and further verify the correctness and feasibility of our circuits.

Procedure

We used the Simbiology toolbox in MATLAB for simulation.

Five genetic circuits were established, which were responsible for localization, imaging, drug synthesis and cell lysis. We also creatively combined localization and imaging circuits to save plasmids.

The modeling process is showed below. Since ARG2 works the same way as ARG1, we just show one model of them.

Establishing the ODE equations for each circuit and representing them as diagrams.

  • No.1 Circuit(Locating and Imaging)

    ODEs:
    d(mRNA_OmpA)/dt = ReactionFlux1 - ReactionFlux2
    d(protein_azurin)/dt = ReactionFlux4 - ReactionFlux6
    d(mRNA_azurin)/dt = -ReactionFlux3 + ReactionFlux5
    Fluxes:
    ReactionFlux1 = k1*DNA_OmpA
    ReactionFlux2 = k3*mRNA_OmpA
    ReactionFlux3 = k7*mRNA_azurin
    ReactionFlux4 = k6*mRNA_azurin
    ReactionFlux5 = k5*DNA_azurin
    ReactionFlux6 = k8*protein_azurin
    Parameter Values:
    k1 = 0.2 mol/second
    k2 = 10 mol/second
    k3 = 1.5 mol/second
    k4 = 1 mol/second
    k7 = 1 mol/second
    k6 = 15 mol/second
    k5 = 0.2 mol/second
    k8 = 1 mol/second
    unnamed = 1 liter
    Initial Conditions:
    mRNA_OmpA = 0 molecule
    protein_azurin = 0 molecule
    mRNA_azurin = 0 molecule
    protein_OmpA = 0 molecule
    DNA_OmpA = 50 molecule
    DNA_azurin = 50 molecule

    Diagram

  • No.2 Circuit(Drug Synthesis)

    ODEs:
    d(mRNA_ARG1)/dt = ReactionFlux1 - ReactionFlux3
    d(protein_ARG1)/dt = ReactionFlux2 - ReactionFlux4
    Fluxes:
    ReactionFlux1 = k1*DNA_ARG1
    ReactionFlux2 = k2*mRNA_ARG1
    ReactionFlux3 = k3*mRNA_ARG1
    ReactionFlux4 = k4*protein_ARG1
    Parameter Values:
    k1 = 0.2 mol/second
    k2 = 20 mol/second
    k3 = 1.5 mol/second
    k4 = 1 mol/second
    unnamed = 1 liter
    Initial Conditions:
    mRNA_ARG1 = 0 molecule
    protein_ARG1 = 0 molecule
    DNA_ARG1 = 50 molecule

    Diagram

  • No.3 Circuit(Cell Lysis)

    ODEs:
    d(mRNA_X17E)/dt = ReactionFlux1 - ReactionFlux3
    d(protein_X17E)/dt = ReactionFlux2 - ReactionFlux4
    Fluxes:
    ReactionFlux1 = k1*DNA_X17E
    ReactionFlux2 = k2*mRNA_X17E
    ReactionFlux3 = k3*mRNA_X17E
    ReactionFlux4 = k4*protein_X17E
    Parameter Values:
    k1 = 0.2 mol/second
    k2 = 20 mol/second
    k3 = 1.5 mol/second
    k4 = 1 mol/second
    unnamed = 1 liter
    Initial Conditions:
    mRNA_X17E = 0 molecule
    protein_X17E = 0 molecule
    DNA_X17E = 30 molecule

    Diagram

Results

By solving the ODE equations for simulation, we obtained the figures of the change of factor concentration over time in several circuits as shown below.

Analysis

It can be seen from the above simulation curves that all the target proteins we need can be successfully expressed, especially azurin protein is very sensitive to the promoter. So as long as the NO concentration is sufficient, azurin protein can be induced.