Team:METU Turkey modeling

Our Project's Model

This graph shows us that E.coli during adding catechol to media, diffuses quickly because of the high diffusion rate. Therefore you can see catechol concentration inintiates with a high value. Then our bacteria degrade catechol to 2-hydoxymuconate semialdehyde then it degrades to 2-oxopent 4-enoate then continues to 4-hydroxy 2-oxopentoonate, finally we get our last degraded product of pyruvate. Our paramaeters of this cycle shows us that. While our bacteria diffuses catechol in its cytosol, its enzymes starts to degrade catechol fast to obtain pyruvate.

SimBiology Results of our Kill-Switch Model:

Interpretation of Kill-Switch:

Arabinose Promoter: (K808000) is activated when arabinose is present.

Antiholin: (K515004) is specific negative regulator of holin function.

TetR+LVA: (C0040) tetracycline repressor modified with LVA tail for rapid degradation of the protein and faster fall time for the emission.

TetR Promoter: (R0040) TetR repressible promoter.

T4 Endolysin: (K112806) degrades peptiodoglycan layer.

Holin: (K124014) protein causes pores in the inner membrane, which allows lysozyme to access and brakedown the peptidoglycan of the cell wall, causing lysis and death.

First Graph:

When arabinose is present TetR+LVA and Anti-Holin are produced, TetR+LVA suppress the production of Holin and Endolysin by binding with TetR Promoter.

Second Graph:

When arabinose is absent, TetR+LVA is not produced so TetR Promoter does not suppress producing of Holin and T4 Endolysin. Therefore, Holin protein causes pores and T4 endolysin degrades peptidoglycan layer and cell dies. If the promoter and RBS are strengthened the kill-switch circuit will be more effective.