Latest revision as of 16:54, 8 March 2013

iGEM Grenoble 2012

iGEM 2012
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Network details

Our system is divided in three modules:

The detection module

The detection 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

In a recent study a new role of cAMP was described: a synthetic E. coli communication system mediated by extracellular cyclic AMP (publication in progress). This system is involved in bacterial communication. We used this module to allow communications within our bacteria population
As for the previous module you can read here our mathematical model and numerical simulation.

When a bacterium detects S. aureus, it produces several molecules of GFP and even more cAMP. cAMP diffuses through the membrane and activates the amplification loop in neighboring bacteria [14], which triggers in turn the production of GFP and cAMP.
This leads to GFP production by the entire population, triggered by a single bacterium that has 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.

Legend :

Promoter

Ribosom Binding Site

Gene

@@ Line 6: / Line 6: @@
 <section>
 <h1>Network details</h1>
-Our system is divided in two modules:
+Our system is divided in three modules:
-<ul><li>a signaling module
+<ul><li><a href="https://2012.igem.org/Team:Grenoble/Biology/Network#10">a detection module</a></li>
-<li>an amplification module<br/>
+<li><a href="https://2012.igem.org/Team:Grenoble/Biology/Network#20">an amplification module</a></li>
+<li><a href="https://2012.igem.org/Team:Grenoble/Biology/Network#8" >a cell to cell communication module</a></li>
 </section>
-<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#20" class="schema" ><img src="https://static.igem.org/mediawiki/2012/b/b1/Circuit_complet.png" alt="" style="position: relative; top: 34px; left: 5px;"/></a>
-<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#10" class="schema" ><img src="https://static.igem.org/mediawiki/2012/a/a4/Circuit_gre.png" alt="" style="position: relative; top: -450px; left: 8px;"/></a>
-<section style="position: relative; top: -80px;">
+<section>
+<br/>
+<br/>
+<br/>
+<center>
+<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#10" class="schema" ><img src="https://static.igem.org/mediawiki/2012/a/a4/Circuit_gre.png" alt="" style="position: relative; top: -145px; left: 130px;"/></a>
+<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#20" class="schema" ><img src="https://static.igem.org/mediawiki/2012/b/b1/Circuit_complet.png" alt="" style="position: relative; top: -50px; left: 125px;"/></a>
+<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#8" class="schema" ><img src="https://static.igem.org/mediawiki/2012/7/70/Cell_to_cell.png" alt=""
+style="position: relative; top: 123px; left: -436px;"/></a>
+</center>
+</section>
+<section>
-<h2 id="10">The signaling module</h2>
+<h2 id="10">The detection module</h2>
-The signaling module allows our bacteria strain to integrate the input signal = the pathogene presence.<br/>
+The detection module allows our bacteria strain to integrate the input signal = the presence of a pathogene.<br/>
 <br/>
-This is a <a href="https://2012.igem.org/Team:Grenoble/Modeling/Signaling">modelized module</a>.<br/>
+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/>
 <center><img src="https://static.igem.org/mediawiki/2012/e/e1/Signaling_gre.png"/></center>
@@ Line 26: / Line 37: @@
 The idea behind this module comes from the iGEM London Imperial College 2010 Team's work on Parasight <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[1]</a>. <br/>
 <br/>
-<i>Staphylococcus aureus</i> secretes the exfoliative toxin B <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[2]</a> 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.<br/>
+<i>Staphylococcus aureus</i> secretes the exfoliative toxin B <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[2]</a> which cleaves a specific amino-acids sequence (Desmoglein&nbsp;1). This specific sequence can be used as a linker between a membrane protein and a dipeptide.<br/>
 Once <i>S. aureus</i> is present, the linker is cut by the toxin and the dipeptide is released.<br/>
 <br/>
-The dipeptide binds its receptor which was engineered <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> by the team:
+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> is a dipeptide receptor involved in the chemotaxism</li>
+<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> is a histidine kinase involved in the osmoregulation</li>
+<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>
 <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/>
-OmpR phosphorylation's allows the activation of the OmpC promoter<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[10]</a>.
+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 style="position: relative; top: -80px;">
+<section>
 <h2 id="20">Amplification module</h2>
 The amplification module allows our bacteria to amplify the input signal and to produce an output signal = fluorescence.<br/>
 <br/>
-This is also <a href="https://2012.igem.org/Team:Grenoble/Modeling/Amplification">one of our module of modeling</a>.<br/>
+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/>
-<br/>
-<h3>Internal amplification</h3>
 <center><img src="https://static.igem.org/mediawiki/2012/f/fc/Amplifcation1.png"/></center>
 <br/>
-The activation of the OmpC promoter allows the production of Adenyl cyclase <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[11]</a>. Adenyl cyclase catalyses the conversion of ATP (Adenosine Tri-Phosphate) into cAMP (cyclic Adenosine Mono-Phosphate).<br/>
+The activation of the ompC promoter allows the production of Adenyl cyclase <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[11]</a>. Adenyl cyclase catalyses the conversion of ATP (Adenosine Tri-Phosphate) into cAMP (cyclic Adenosine Mono-Phosphate).<br/>
 <br/>
 <center><img src="https://static.igem.org/mediawiki/2012/c/c7/AND.png"/></center>
 <br/>
-The binding of cAMP to CRP (C-reactive 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/>
+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 an amplification loop
+<ul><li>Adenyl cyclase which reproduces cAMP, forming thus a positive amplification loop
-<li>GFP (Green Fluorescent Protein) = our output signal
+<li>GFP (Green Fluorescent Protein) = the output signal
 </ul>
-<br/>
+</section>
-<h3 id="8">External amplification</h3>
+<section>
-When a bacterium detects <i>S. aureus</i>, 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 <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[14]</a>, which triggers the production of GFP and cAMP.<br/>
+<h2 id="8">Cell to cell communication module</h2>
-This leads to an entire population which produces GFP where only a bacterium detected the pathogen in the first place:<br/>
+In a recent study a new role of cAMP was described: a synthetic <i>E. coli</i> communication system mediated by extracellular cyclic AMP (<a href="http://cellule-et-futur.fr/">publication in progress</a>). This system is involved in bacterial communication.
+We used this module to allow communications within our bacteria population<br/>
+As for the previous module you can read <a href="https://2012.igem.org/Team:Grenoble/Modeling/Amplification/Quorum">here</a> our mathematical model and numerical simulation.<br/><br/>
+When a bacterium detects <i>S. aureus</i>, it produces several molecules of GFP and even more cAMP. cAMP diffuses through the membrane and activates the amplification loop in neighboring bacteria <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[14]</a>, which triggers in turn the production of GFP and cAMP.<br/>
+This leads to GFP production by the entire population, triggered by a single bacterium that has detected the pathogen in the first place:<br/>
 <br/>
 <center><img src="https://static.igem.org/mediawiki/2012/b/bf/Img_com.png" /></center>
@@ Line 69: / Line 83: @@
 </section>
 <br/>
-<section style="position: relative; top: -80px;">
+<section>
 <h2 id="30">References</h2>
 <ul>
@@ Line 78: / Line 93: @@
 <li><b>[3]</b> <a href="http://jb.asm.org/content/176/4/1157.full.pdf+html" target="_blank">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. <i>Journal of Bacteriology</i>. Vol. 176, No. 4.</a></li>
 <br/>
-<li><b>[4]</b> <a ref="http://www.ncbi.nlm.nih.gov/pubmed/9473047" target="_blank">Siromi Weerasuriya, Brian M. Schneider, Michael D. Manson. (1998). Chimeric Chemoreceptors in <i>Escherichia coli</i>: Signaling properties of Tar-Tap and Tap-Tar Hybrids. <i>Journal of Bacteriology</i>. Vol. 180, No. 4, p. 914-920. </a></li>
+<li><b>[4]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9473047" target="_blank">Siromi Weerasuriya, Brian M. Schneider, Michael D. Manson. (1998). Chimeric Chemoreceptors in <i>Escherichia coli</i>: Signaling properties of Tar-Tap and Tap-Tar Hybrids. <i>Journal of Bacteriology</i>. Vol. 180, No. 4, p. 914-920. </a></li>
 <br/>
 <li><b>[5]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10987" target="_blank">Polypeptide: Tap</a></li>
@@ Line 100: / Line 115: @@
 <li><b>[14]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18414488" target="_blank">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. <i>Molecular Systems Biology</i>. 4:187.</a></li>
 </ul>
+</section>
+<div class="index" style="width: 130px; position: fixed; top: 260px; right: 30px;">
+	<center>Legend :</center>
+	<div style="border: solid 2px black; border-radius: 10px; padding-top: 10px;">
+	<center><img src="https://static.igem.org/mediawiki/2012/c/c2/Promoter_gre.png" alt="" /><center>
+	<center>Promoter</center><br/>
+	<center><img src="https://static.igem.org/mediawiki/2012/7/7d/RBS_gre.png" alt="" /></center>
+	<center>Ribosom Binding Site</center><br/>
+	<center><img src="https://static.igem.org/mediawiki/2012/c/cf/Gene_gre.png" alt="" /></center>
+	<center>Gene</center><br/>
+	</div>
+</div>
 </div>
 </body>