Team:Grenoble/Modeling/Signaling
From 2012.igem.org
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- | Once the dipeptide molecule is fixed to the TAP receptor, it activates the phosphorylation of ompR. | + | Once the dipeptide molecule is fixed to the TAP receptor, it activates the phosphorylation of ompR. ompR* (the phosphorylated form of ompR) is the transcription factor that activates the gene expression of <i>cyaA</i>. |
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- | + | Further details about the receptor design, are available <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#10">here</a>. | |
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- | + | A computer model was developped to answer 2 questions: | |
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- | 1- How sensitive is the signaling module? | + | 1- How sensitive is the signaling module? Wich dipeptide concentration should be present in order to trigger a response? |
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- | Answering these two questions will help us assess the sensitivity and the | + | Answering these two questions will help us assess the sensitivity and the response time of the whole system (ie the signaling module, the amplification module and the quorum sensing). |
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- | + | First, we define the ordinary differential equations that govern adenylate cyclase (Ca) evolution. Thus we plot the evolution of Ca concentration versus initial dipeptide concentration (sensitivity) as well as the temporal evolution of Ca concentration (time response). | |
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Revision as of 15:09, 26 September 2012
Overview
The design of signaling module is given by the figure below:ODEs
Let’s begin by considering the cya gene activation by the transcription factor ompR*. As it is a gene activation, the transcription rate is usually modelized by a hill function:Parameters
Here is the link to the parameters of the amplification module we sometimes refer to.Constants | Value | Derivation |
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Total quantity [ompR]tot | 6.8 10-8 mol.L-1 | The average number of ompR molecules per cell is 80.769 ± 0.719 [2]. Knowing the cell volume (vc = 1.1 10-15 L[3]) and the Avogadro number NA = 6.02 10-23 mol.L-1, we deduce [ompR]tot = 80/(NA*vc) = 6.8 10-8 mol.L-1 |
Goldbeter-Koshland model constants | v = 80 L-1.min-1 V' = 7 10-8 mol.L-1.min-1 K = 7 10-7 mol.L-1 K' = 9 10-8 mol.L-1 |
We could not find these parameters in literature and we hope we will be able to conduct the necessary experiments to set them. Nevertheless, we could use a simple approach to estimate them : The receptor should at least be sensitive to [dipeptide]=10-5 mol.L-1 (it represents the maximum concentration expected [4]). We consider V = v[dipeptide], the equation is given by : and we have a high phosphorylation rate even if almost all ompR has been phosphorylated. We chose KcyaA = 7 10-7 mol.L-1 and K'cyaA = 9 10-8 mol.L-1 Given that , if we consider [ompR]~[omprR]tot≅6.8 10-8 and [ompR*]≅10-11»[omprR]tot we find that V≥104 V'. |
Maximal transcription rate of cyaA | VmcyaA = 2 10-9 mol.L-1.min-1 | The value of this constant should be understood in the continuity of the network. For full details, consider the amplification section, parameters, explanation2 | Basal production of Ca | pCa = 2*10-12 mol.L-1.min-1 | The value of this constant should be understood in the continuity of the network. For full details, consider the amplification section, parameters, explanation1 |
Degradation rate of Ca | αCa = 6 10-3 min-1 | The value of this constant should be understood in the continuity of the network. For full details, consider the amplification section, parameters, explanation4 |
Activation coefficient of cyaA | KcyaA = 10-7 mol.L-1 | The value KCa was set considering the maximum value of [Ca]. Indeed if we consider the steady state and assume that pCa is negligible compared to the other terms we have : where h stands for the Hill function, 0<h<1. We have then : KCa should be in the same range as [Ca]max not too high otherwise the gene would never be expressed and not too low otherwise the protein is always produced. We chose KcyaA = 10-7 mol.L-1 |
Hill Coefficient | n = 2 | We took a number greater than one to indicate positive cooperativity. |
References
- [1] Alejandra C.Ventura, Jacques-A. Sepulchre, Sofia D.Merajver. A Hidden Feedback in Signaling Cascades Is Revealed. PLOS Computational Biology, 2008, 4, 3, e1000041.
- [4] Michael D.Manson, Volker BlanK and Gabriele Brade. Peptide chemotaxis in E.Coli involves the Tap signal transducer and the dipeptide permease.Nature,15 May 1986,321,253-256.
- [5] Edith Gstrein-Reider and Manfred Schweiger, Institut fur Biochemie (nat. Fak.),UniversitAt Innsbruck, A-6020 Innsbruck, Austria. Regulation of adenylate cyclase in E. coli.