Latest revision as of 16:54, 8 March 2013

iGEM Grenoble 2012

iGEM 2012
main page

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>signaling module
+<ul><li><a href="https://2012.igem.org/Team:Grenoble/Biology/Network#10">a detection module</a></li>
-<li>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/bb/Circuit2.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: -488px; left: 5px;"/></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>
-<h2 id="10">Signaling module</h2>
+<section>
-The signaling module allows our bacterial strain to integrate the input signal = the pathogene presence.<br/>
+<h2 id="10">The detection module</h2>
+The detection module allows our bacteria strain to integrate the input signal = the presence of a pathogene.<br/>
+<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/>
-This is also <a href="https://2012.igem.org/Team:Grenoble/Modeling/Signaling">one of our module of modeling</a>.
 <center><img src="https://static.igem.org/mediawiki/2012/e/e1/Signaling_gre.png"/></center>
 <br/>
-The idea of this module is du to the iGEM London Imperial College 2010 Team work on Parasight <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[1]</a>. <br/>
+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 an enzyme, exfoliative toxin B <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[2]</a> which cut 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 protease 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/>
-The dipeptide binds to his receptor which is an 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> receptor:
+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 is 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>
+<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 is 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>
+<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 is bound to the Tap part <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[7]</a>, the EnvZ part allows the phosphorylation of OmpR <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[8]</a>, a transcriptional activator.
+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 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 bacterial strain 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/>
-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/>
-Once OmpR is phosphorylated, it allows the production of adenyl cyclase by activating the OmpC promoter <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[9]</a>.<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/>
-Adenyl cyclase is an enzyme which catalyse the conversion of ATP (Adenosine Tri-Phosphate) to cAMP (cyclic Adenosine Mono-Phosphate).<br/>
 <br/>
 <center><img src="https://static.igem.org/mediawiki/2012/c/c7/AND.png"/></center>
 <br/>
-cAMP binds to CRP (C-reactive protein) and then this complex allows the production of AraC by activating the pMalT promoter.<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, with cAMP-CRP, activates the pAraBAD promoter, forming thus an "AND" gate, which allow 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 reproduce 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 one bacterium detecte <i>S. aureus</i>, it produces a lot of GFP and cAMP. cAMP can diffuse through the membrane and activates the amplification loop in all the neighbourings bacteria which can thus produce a lot of GFP and cAMP.<br/>
+<h2 id="8">Cell to cell communication module</h2>
-The result is an entire population which produce GFP whereas only one bacterium has 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 68: / Line 83: @@
 </section>
 <br/>
-<section style="position: relative; top: -80px;">
+<section>
 <h2 id="30">References</h2>
 <ul>
-<li><b>[1]</b> <a href="https://2010.igem.org/Team:Imperial_College_London/Modules/Detection">https://2010.igem.org/Team:Imperial_College_London/Modules/Detection</a></li>
+<li><b>[1]</b> <a href="https://2010.igem.org/Team:Imperial_College_London/Modules/Detection" target="_blank">Imperial college 2010's detection module</a></li>
 <br/>
-<li><b>[2]</b> Masayuki Amagi, Takayuki Yamaguchi, Yasushi Hanakawa, Koji Nishifuji, Motoyuki Sugai, John R. Stanley. Staphylococcal Exfoliative Toxin B Specifically Cleaves Desmoglein 1. (2002). <i>The Journal of Investigative Dermatology</i>. Vol. 118, No. 5.</li>
+<li><b>[2]</b> <a href="http://www.nature.com/jid/journal/v118/n5/full/5601482a.html" target="_blank">Masayuki Amagi, Takayuki Yamaguchi, Yasushi Hanakawa, Koji Nishifuji, Motoyuki Sugai, John R. Stanley. Staphylococcal Exfoliative Toxin B Specifically Cleaves Desmoglein 1. (2002). <i>The Journal of Investigative Dermatology</i>. Vol. 118, No. 5.</a></li>
 <br/>
-<li><b>[3]</b> 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.</li>
+<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> 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.</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">Polypeptide: Tap</a></li>
+<li><b>[5]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10987" target="_blank">Polypeptide: Tap</a></li>
 <br/>
-<li><b>[6]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10269">Protein: EnvZ sensory histidine kinase</a></li>
+<li><b>[6]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10269" target="_blank">Protein: EnvZ sensory histidine kinase</a></li>
 <br/>
-<li><b>[7]</b> Michael D. Manson, Volker Blank, Gabriele Brade. (1986). Peptide chemotaxis in <i>E. coli</i> involves the Tap signal transducer and the dipeptide permease. <i>Nature</i>. Vol. 321.</li>
+<li><b>[7]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/3520334" target="_blank">Michael D. Manson, Volker Blank, Gabriele Brade. (1986). Peptide chemotaxis in <i>E. coli</i> involves the Tap signal transducer and the dipeptide permease. <i>Nature</i>. Vol. 321.</a></li>
 <br/>
-<li><b>[8]</b> Sheng Jian Cai, Masayori Inouye. (2002). EnvZ-OmpR Interaction and Osmoregulation in <i>Escherichia coli</i>. <i>The Journal of Biological Chemistry</i>. Vol. 277, No. 27, p.24155-24161.</li>
+<li><b>[8]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/11973328" target="_blank">Sheng Jian Cai, Masayori Inouye. (2002). EnvZ-OmpR Interaction and Osmoregulation in <i>Escherichia coli</i>. <i>The Journal of Biological Chemistry</i>. Vol. 277, No. 27, p.24155-24161.</a></li>
 <br/>
-<li><b>[9]</b> Sumio Maeda, Katsuhiko Takayanagi, Yoshifumi Nishimura, Takemi Maruyama, Kou Sato, and Takeshi Mizuno. (1991). Activation of the Osmoregulated <i>ompC</i> Gene by the OmpR Protein in <i>Escherichia coli</i>: A Study Involving Synthetic OmpR-Binding Sequences. <i>Journal of Biochemistry</i>. 110, 324-327.</li>
+<li><b>[9]</b> <a href="http://ecoliwiki.net/colipedia/index.php/ompR:Expression" target="_blank">ompR expression</a></li>
+<br/>
+<li><b>[10]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/1769957" target="_blank">Sumio Maeda, Katsuhiko Takayanagi, Yoshifumi Nishimura, Takemi Maruyama, Kou Sato, and Takeshi Mizuno. (1991). Activation of the Osmoregulated <i>ompC</i> Gene by the OmpR Protein in <i>Escherichia coli</i>: A Study Involving Synthetic OmpR-Binding Sequences. <i>Journal of Biochemistry</i>. 110, 324-327.</a></li>
+<br/>
+<li><b>[11]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10170" target="_blank">Enzyme: adenyl cyclase</a></li>
+<br/>
+<li><b>[12]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00091" target="_blank">Transcription Unit: malT</a></li>
+<br/>
+<li><b>[13]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00214" target="_blank">Transcription Unit: araBAD</a></li>
+<br/>
+<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>