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Team:ETH Zurich/modeling/whole
From 2014.igem.org
Whole cell model
Model
The whole cell model is the combination of the Quorum sensing, Integrase and XOR modules. The model shows the behaviour of the a single cell in response to incoming signals. The model enables us to understand the effect of leakiness, cross-talk and their combinations on the whole system.
Chemical Species
| Name | Description |
|---|---|
| LuxAHL | 30C6-HSL is an acyl homoserine lactone which mainly binds to LuxR. |
| LuxR | Constitutively expressed regulator protein that can bind LuxAHL and stimulate transcription of Bxb1. |
| RLux | LuxR and LuxAHL complex which can dimerize. |
| DRLux | Dimerized form of RLux. |
| mRNABxb1 | mRNA of the Bxb1 integrase being transcribed by the Lux promoter. |
| Bxb1 | Serine integrase that can fold into two conformations - Bxb1a and Bxb1b. We chose to use a common connotation for both conformations - Bxb1. |
| LasAHL | 30C12-HSL is an acyl homoserine lactone which mainly binds to LasR. |
| LasR | Constitutively expressed regulator protein that can bind LasAHL and stimulate transcription of ΦC31. |
| RLas | LasR and LasAHL complex which can dimerize. |
| DRLas | Dimerized form of RLas. |
| mRNAΦC31 | mRNA of the ΦC31 integrase being transcribed by the Lux promoter. |
| ΦC31 | Serine integrase that can fold into two conformations - ΦC31a and ΦC31b. We chose to use a common connotation for both conformations - ΦC31. |
| SIBxb1 | Inactive DNA binding site for Bxb1. No dimer is bound to this site. |
| SABxb1 | Active DNA binding site for Bxb1. A dimer is bound to this site. |
| SFBxb1 | Flipped DNA binding site for Bxb1. The site generated after recombination by integrase. |
| SIΦC31 | Inactive DNA binding site for ΦC31. No dimer is bound to this site. |
| SAΦC31 | Active DNA binding site for ΦC31. A dimer is bound to this site. |
| SFΦC31 | Flipped DNA binding site for ΦC31. The site generated after recombination by integrase. |
| Ton,i | The number of terminators which are blocking the transcription of GFP and LuxI/LasI initially. |
| ToffBxb1 | The number of terminators turned off by recombination due to Bxb1. Favours the transcription of GFP and LuxI. |
| ToffΦC31 | The number of terminators turned off by recombination due to ΦC31. Favours the transcription of GFP and LuxI. |
| Ton,f | The number of terminators blocking the transcription of GFP and LuxI/LasI after recombination by Bxb1 and ΦC31. No transcription. |
| mRNAGFP | mRNA for Green fluorescent protein which is produced when the cells are ON. |
| GFP | Green fluorescent protein which is produced when the cells are ON. |
| mRNALuxI | mRNA for LuxI which is produced when the cells are ON. |
| LuxI | Enzyme catalysing the production of LuxAHL from SAM and ACP. |
| mRNALasI | mRNA for LasI which is produced when the cell are ON. |
| LasI | Enzyme catalysing the production of LasAHL from SAM and ACP. |
Reactions
$$ \begin{align} &\rightarrow LuxR \\ LuxAHL+LuxR & \leftrightarrow RLux\\ RLux+RLux &\leftrightarrow DRLux\\ DRLux+P_{luxOFF} & \leftrightarrow P_{luxON}\\ P_{luxON}&\rightarrow P_{luxON}+mRNA_{Bxb1}\\ mRNA_{Bxb1}&\rightarrow Bxb1\\ Bxb1 + Bxb1 &\leftrightarrow DBxb1 \\ DBxb1 + SI_{Bxb1} & \leftrightarrow SA_{Bxb1}\\ LuxAHL &\rightarrow \\ LuxR &\rightarrow \\ RLux &\rightarrow\\ DRLux &\rightarrow\\ mRNA_{Bxb1} &\rightarrow\\ Bxb1 &\rightarrow\\ DBxb1 &\rightarrow\\ \\ &\rightarrow LasR \\ LasAHL+LasR & \leftrightarrow RLas \\ RLas+RLas & \leftrightarrow DRLas\\ DRLas+P_{LasOFF} & \leftrightarrow P_{LasON}\\ P_{LasON}&\rightarrow P_{LasON}+mRNA_{\phi C31}\\ mRNA_{\phi C31}&\rightarrow \phi C31\\ \phi C31 + \phi C31 &\leftrightarrow D\phi C 31 \\ D\phi C 31 + SI_{\phi C31} & \leftrightarrow SA_{\phi C31}\\ LasAHL &\rightarrow \\ LasR &\rightarrow \\ RLas &\rightarrow\\ DRLas &\rightarrow\\ mRNA_{\phi C31} &\rightarrow \\ \phi C31 &\rightarrow \\ D\phi C31 &\rightarrow \\ \\ SA_{Bxb1}+SA_{Bxb1}+T_{on,i}& \rightarrow T_{offBxb1}+ SF_{Bxb1}+SF_{Bxb1}\\ T_{offBxb1} &\rightarrow T_{offBxb1} + mRNA_{GFP} + mRNA_{LasI} \\ SA_{\phi C31}+SA_{\phi C31}+T_{on,i}& \rightarrow T_{off\phi C31}+SF_{\phi C31}+SF_{\phi C31}\\ T_{off\phi C31} &\rightarrow T_{off\phi C31} + mRNA_{GFP} + mRNA_{LasI} \\ SA_{Bxb1}+SA_{Bxb1}+T_{off,\phi C31}& \rightarrow T_{on,f}+SF_{Bxb1}+SF_{Bxb1}\\ SA_{\phi C31}+SA_{\phi C31}+T_{offBxb1}& \rightarrow T_{on,f}+SF_{\phi C31}+SF_{\phi C31}\\ mRNA_{GFP} &\rightarrow GFP\\ mRNA_{LasI} &\rightarrow LasI\\ mRNA_{GFP} &\rightarrow \\ mRNA_{LasI}&\rightarrow\\ GFP &\rightarrow \\ LasI&\rightarrow\\ \\ S_{LasI}+LasI & \rightarrow LasAHL\\ \end{align}$$
Equations
The following equations were used for the whole cell model.
$$\begin{align*} \frac{d[LuxAHL]}{dt} &= k_{-RLux}[R_{Lux}]-k_{RLux}[LuxAHL][LuxR]-d_{LuxAHL}[LuxAHL]\\ \frac{d[LuxR]}{dt} &= \alpha_{LuxR} -k_{RLux}[LuxAHL][LuxR] + k_{-RLux}[RLux] - d_{LuxR}[LuxR] \\ \frac{d[RLux]}{dt} &= k_{RLux}[LuxAHL][LuxR] - k_{-RLux}[RLux] - d_{RLux} [RLux] \\ \frac{d[mRNA_{Bxb1}]}{dt} &= L_{P_{Lux}} + \frac{K_{mRNA_{Bxb1}}[RLux]^2}{K_{mLux} + [RLux]^2 }- d_{mRNA_{Bxb1}} [mRNA_{Bxb1}]\\ \frac{d[Bxb1]}{dt} &= k_{Bxb1} [mRNA_{Bxb1}] -2 k_{DBxb1}[Bxb1]^2+ 2 k_{-DBxb1}[DBxb1] - d_{Bxb1}[Bxb1]\\ \frac{d[DBxb1]}{dt}&= k_{DBxb1}[Bxb1]^2-k_{-DBxb1}[DBxb1]-k_{SABxb1}[DBxb1][SI_{Bxb1}]+k_{-SABxb1}[SA_{Bxb1}]-d_{DBxb1}[DBxb1]\\ \frac{d[SI_{Bxb1}]}{dt}&=-k_{SABxb1}[DBxb1][SI_{Bxb1}]+k_{-SABxb1}[SA_{Bxb1}]\\ \frac{d[SA_{Bxb1}]}{dt}&=k_{SABxb1}[DBxb1][SI_{Bxb1}]-k_{-SABxb1}[SA_{Bxb1}] - 2 k_{ToffBxb1} [SA_{Bxb1}]^2 [T_{on,i}] - 2 k_{-ToffBxb1} [SA_{Bxb1}]^2 [T_{off\phi C31}]\\ \frac{d[SF_{Bxb1}]}{dt}&= 2 k_{ToffBxb1} [SA_{Bxb1}]^2 [T_{on,i}] + 2 k_{-ToffBxb1} [SA_{Bxb1}]^2 [T_{off\phi C31}]\\ \\ \frac{d[LasAHL]}{dt} &= k_{-RLas}[R_{Las}]-k_{RLas}[LasAHL][LasR]-d_{LasAHL}[LasAHL]\\ \frac{d[LasR]}{dt} &= \alpha_{LasR} -k_{RLas}[LasAHL][LasR] + k_{-RLas}[RLas] - d_{LasR}[LasR] \\ \frac{d[RLas]}{dt} &= k_{RLas}[LasAHL][LasR] - k_{-RLas}[RLas] - d_{RLas} [RLas] \\ \frac{d[mRNA_{\phi c31}]}{dt} &= L_{P_{Las}} + \frac{K_{mRNA_{\phi C31}}[RLas]^2}{K_{mLas} + [RLas]^2 } - d_{mRNA_{\phi c31}} [mRNA_{\phi c31}]\\ \frac{d[\phi c31]}{dt} &= k_{\phi c31} [mRNA_{\phi c31}] -2 k_{D\phi c31}[\phi c31]^2+ 2 k_{-D\phi c31}[D\phi c31] - d_{\phi c31}[\phi c31]\\ \frac{d[D\phi c31]}{dt}&= k_{D\phi c31}[\phi c31]^2-k_{-D\phi c31}[D\phi c31]-k_{SA\phi c31}[D\phi c31][SI_{\phi c31}]+k_{-SA\phi c31}[SA_{\phi c31}]-d_{D\phi c31}[D\phi c31]\\ \frac{d[SI_{\phi c31}]}{dt}&=-k_{SA\phi c31}[D\phi c31][SI_{\phi c31}]+k_{-SA\phi c31}[SA_{\phi c31}]\\ \frac{d[SA_{\phi C31}]}{dt}&=k_{SA\phi C31}[D\phi C31][SI_{\phi C31}]-k_{-SA\phi C31}[SA_{\phi C31}] - 2 k_{Toff\phi C31} [SA_{\phi C31}]^2 [T_{on,i}] - 2 k_{-Toff\phi C31} [SA_{\phi C31}]^2 [T_{off\phi C31}]\\ \frac{d[SF_{\phi C31}]}{dt}&= 2 k_{Toff\phi C31} [SA_{\phi C31}]^2 [T_{on,i}] + 2 k_{-Toff\phi C31} [SA_{\phi C31}]^2 [T_{off\phi C31}]\\ \\ \frac{d[T_{on,i}]}{dt}&= -k{ToffBxb1}[T_{on,i}][SA_{Bxb1}]^2 -k{Toff\phi C31} [T_{on,i}][SA_{\phi C31}]^2 \\ \end{align*}$$
Dynamics
Ideal case
With Leakiness
With Leakiness and Crosstalk
