"
Team:Grenoble/Biology/Network
From 2012.igem.org
(Difference between revisions)
| Line 25: | Line 25: | ||
<h2 id="10">The signaling module</h2> | <h2 id="10">The signaling module</h2> | ||
| - | The signaling module allows our bacteria strain to integrate the input signal = the | + | The signaling module allows our bacteria strain to integrate the input signal = the presence of a pathogene.<br/> |
<br/> | <br/> | ||
| - | You can find | + | You can find <a href="https://2012.igem.org/Team:Grenoble/Modeling/Signaling">here</a> the mathematical model and numerical simulation this module.<br/> |
<br/> | <br/> | ||
<center><img src="https://static.igem.org/mediawiki/2012/e/e1/Signaling_gre.png"/></center> | <center><img src="https://static.igem.org/mediawiki/2012/e/e1/Signaling_gre.png"/></center> | ||
| Line 37: | Line 37: | ||
Once <i>S. aureus</i> is present, the linker is cut by the toxin and the dipeptide is released.<br/> | Once <i>S. aureus</i> is present, the linker is cut by the toxin and the dipeptide is released.<br/> | ||
<br/> | <br/> | ||
| - | The dipeptide binds | + | The dipeptide binds an engineered receptor <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[3]</a> <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[4]</a> that consists of: |
| - | <ul><li>the extracellular part of Tap <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[5]</a> | + | <ul><li>the extracellular part of Tap <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[5]</a>, a dipeptide receptor involved in the chemotaxism</li> |
| - | <li>the intracellular part of EnvZ <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[6]</a> | + | <li>the intracellular part of EnvZ <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[6]</a>, a histidine kinase involved in the osmoregulation</li> |
</ul> | </ul> | ||
<br/> | <br/> | ||
Once the dipeptide binds the Tap part <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[7]</a>, the intracellular EnvZ part allows the phosphorylation of OmpR <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[8]</a> <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[9]</a>, which is a constitutively produced transcriptional activator.<br/> | Once the dipeptide binds the Tap part <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[7]</a>, the intracellular EnvZ part allows the phosphorylation of OmpR <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[8]</a> <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[9]</a>, which is a constitutively produced transcriptional activator.<br/> | ||
<br/> | <br/> | ||
| - | OmpR phosphorylation | + | OmpR phosphorylation allows the activation of the ompC promoter <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[10]</a>. We introduced <i>cyaA</i> (that code for adenyl cyclase) downstream of this promoter. |
</section> | </section> | ||
| Line 52: | Line 52: | ||
The amplification module allows our bacteria to amplify the input signal and to produce an output signal = fluorescence.<br/> | The amplification module allows our bacteria to amplify the input signal and to produce an output signal = fluorescence.<br/> | ||
<br/> | <br/> | ||
| - | As for the previous module you can read | + | As for the previous module you can read <a href="https://2012.igem.org/Team:Grenoble/Modeling/Amplification">here</a> our mathematical model and numerical simulation.<br/> |
| - | <br/> | + | |
<center><img src="https://static.igem.org/mediawiki/2012/f/fc/Amplifcation1.png"/></center> | <center><img src="https://static.igem.org/mediawiki/2012/f/fc/Amplifcation1.png"/></center> | ||
<br/> | <br/> | ||
| Line 60: | Line 59: | ||
<center><img src="https://static.igem.org/mediawiki/2012/c/c7/AND.png"/></center> | <center><img src="https://static.igem.org/mediawiki/2012/c/c7/AND.png"/></center> | ||
<br/> | <br/> | ||
| - | The binding of cAMP to CRP ( | + | The binding of cAMP to CRP (cAMP Receptor Protein) leads to the production of AraC by activating the pmalT promoter <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[12]</a>.<br/> |
In the presence of arabinose, AraC and cAMP-CRP, cooperatively activate the paraBAD promoter <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[13]</a>, thus forming an "AND" gate. This allows the production of: | In the presence of arabinose, AraC and cAMP-CRP, cooperatively activate the paraBAD promoter <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[13]</a>, thus forming an "AND" gate. This allows the production of: | ||
| - | <ul><li>Adenyl cyclase which reproduces cAMP, forming thus | + | <ul><li>Adenyl cyclase which reproduces cAMP, forming thus a positive amplification loop |
| - | <li>GFP (Green Fluorescent Protein) = | + | <li>GFP (Green Fluorescent Protein) = the output signal |
</ul> | </ul> | ||
</section> | </section> | ||
Revision as of 15:27, 26 September 2012
Network details
Our system is divided in two modules:
The signaling module
The signaling module allows our bacteria strain to integrate the input signal = the presence of a pathogene.You can find here the mathematical model and numerical simulation this module.
The idea behind this module comes from the iGEM London Imperial College 2010 Team's work on Parasight [1].
Staphylococcus aureus secretes the exfoliative toxin B [2] which cleaves a specific amino-acids sequence (Desmoglein 1). This specific sequence can be used as a linker between a membrane protein and a dipeptide.
Once S. aureus is present, the linker is cut by the toxin and the dipeptide is released.
The dipeptide binds an engineered receptor [3] [4] that consists of:
- the extracellular part of Tap [5], a dipeptide receptor involved in the chemotaxism
- the intracellular part of EnvZ [6], a histidine kinase involved in the osmoregulation
Once the dipeptide binds the Tap part [7], the intracellular EnvZ part allows the phosphorylation of OmpR [8] [9], which is a constitutively produced transcriptional activator.
OmpR phosphorylation allows the activation of the ompC promoter [10]. We introduced cyaA (that code for adenyl cyclase) downstream of this promoter.
Amplification module
The amplification module allows our bacteria to amplify the input signal and to produce an output signal = fluorescence.As for the previous module you can read here our mathematical model and numerical simulation.
The activation of the ompC promoter allows the production of Adenyl cyclase [11]. Adenyl cyclase catalyses the conversion of ATP (Adenosine Tri-Phosphate) into cAMP (cyclic Adenosine Mono-Phosphate).
The binding of cAMP to CRP (cAMP Receptor Protein) leads to the production of AraC by activating the pmalT promoter [12].
In the presence of arabinose, AraC and cAMP-CRP, cooperatively activate the paraBAD promoter [13], thus forming an "AND" gate. This allows the production of:
- Adenyl cyclase which reproduces cAMP, forming thus a positive amplification loop
- GFP (Green Fluorescent Protein) = the output signal
Cell to cell communication module
When a bacterium detects S. aureus, it produces a several molecules of GFP and evenmore cAMP. cAMP diffuses through the membrane and activates the amplification loop in all the neighbouring bacteria [14], which triggers the production of GFP and cAMP.This leads to an entire population which produces GFP where only a bacterium detected the pathogen in the first place:
References
- [1] Imperial college 2010's detection module
- [2] Masayuki Amagi, Takayuki Yamaguchi, Yasushi Hanakawa, Koji Nishifuji, Motoyuki Sugai, John R. Stanley. Staphylococcal Exfoliative Toxin B Specifically Cleaves Desmoglein 1. (2002). The Journal of Investigative Dermatology. Vol. 118, No. 5.
- [3] J W Baumgartner, C Kim, R E Brissette, M Inouye, C Park, G L Hazelbauer. (1994). Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensors EnvZ. Journal of Bacteriology. Vol. 176, No. 4.
- [4] Siromi Weerasuriya, Brian M. Schneider, Michael D. Manson. (1998). Chimeric Chemoreceptors in Escherichia coli: Signaling properties of Tar-Tap and Tap-Tar Hybrids. Journal of Bacteriology. Vol. 180, No. 4, p. 914-920.
- [5] Polypeptide: Tap
- [6] Protein: EnvZ sensory histidine kinase
- [7] Michael D. Manson, Volker Blank, Gabriele Brade. (1986). Peptide chemotaxis in E. coli involves the Tap signal transducer and the dipeptide permease. Nature. Vol. 321.
- [8] Sheng Jian Cai, Masayori Inouye. (2002). EnvZ-OmpR Interaction and Osmoregulation in Escherichia coli. The Journal of Biological Chemistry. Vol. 277, No. 27, p.24155-24161.
- [9] ompR expression
- [10] Sumio Maeda, Katsuhiko Takayanagi, Yoshifumi Nishimura, Takemi Maruyama, Kou Sato, and Takeshi Mizuno. (1991). Activation of the Osmoregulated ompC Gene by the OmpR Protein in Escherichia coli: A Study Involving Synthetic OmpR-Binding Sequences. Journal of Biochemistry. 110, 324-327.
- [11] Enzyme: adenyl cyclase
- [12] Transcription Unit: malT
- [13] Transcription Unit: araBAD
- [14] Balagaddé F. K., Song H., Ozaki J., Collins C. H., Barnet M., Arnold F. H., Quake S. R., You L. (2008). A synthetic Escherichia coli predator-prey ecosystem. Molecular Systems Biology. 4:187.
