Revision as of 23:53, 24 September 2012

iGEM Grenoble 2012

iGEM 2012
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Network details

Our system is divided in two modules:

a signaling module
an amplification module

The signaling module

The signaling module allows our bacteria strain to integrate the input signal = the pathogene presence.

This is a modelized 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 its receptor which was engineered [3] [4] by the team:

the extracellular part of Tap [5] is a dipeptide receptor involved in the chemotaxism
the intracellular part of EnvZ [6] is 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's allows the activation of the OmpC promoter[10].

Amplification module

The amplification module allows our bacteria to amplify the input signal and to produce an output signal = fluorescence.

This is also one of our module of modeling.

Internal amplification

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 (C-reactive 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 an amplification loop
GFP (Green Fluorescent Protein) = our output signal

External amplification

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.

@@ Line 7: / Line 7: @@
 <h1>Network details</h1>
 Our system is divided in two modules:
-<ul><li>signaling module
+<ul><li>a signaling module
-<li>amplification module<br/>
+<li>an amplification module<br/>
 </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>
@@ Line 15: / Line 15: @@
 <section style="position: relative; top: -80px;">
-<h2 id="10">Signaling module</h2>
+<h2 id="10">The signaling module</h2>
-The signaling module allows our bacterial strain to integrate the input signal = the pathogene presence.<br/>
+The signaling module allows our bacteria strain to integrate the input signal = the pathogene presence.<br/>
 <br/>
-This is also <a href="https://2012.igem.org/Team:Grenoble/Modeling/Signaling">one of our module of modeling</a>.<br/>
+This is a <a href="https://2012.igem.org/Team:Grenoble/Modeling/Signaling">modelized module </a>.<br/>
 <br/>
 <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 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 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:
-<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> is 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> is 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 href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[9]</a>, a transcriptional activator which is constitutively produced.<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/>
-Once OmpR is phosphorylated, it allows the activation of the OmpC promoter<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[10]</a>.
+OmpR phosphorylation's allows the activation of the OmpC promoter<a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[10]</a>.
 </section>
 <section style="position: relative; top: -80px;">
@@ Line 42: / Line 42: @@
 <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/>
@@ Line 49: / Line 49: @@
 <center><img src="https://static.igem.org/mediawiki/2012/f/fc/Amplifcation1.png"/></center>
 <br/>
-The activation of the OmpC promoter by phosphorylated OmpR allows the production of Adenyl cyclase <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[11]</a>. Adenyl cyclase is an enzyme which catalyse the conversion of ATP (Adenosine Tri-Phosphate) to 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/>
-cAMP binds to CRP (C-reactive protein) and then this complex allows 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 (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/>
-In the presence of arabinose, AraC, with cAMP-CRP, activates the pAraBAD promoter <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[13]</a>, 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 an amplification loop
 <li>GFP (Green Fluorescent Protein) = our output signal
 </ul>
 <br/>
 <h3 id="8">External amplification</h3>
-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 <a href="https://2012.igem.org/Team:Grenoble/Biology/Network#30">[14]</a> which can thus produce a lot of GFP and cAMP.<br/>
+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/>
-The result is an entire population which produce GFP whereas only one bacterium has detected the pathogen in the first place:<br/>
+This leads to an entire population which produces GFP where only a bacterium 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 72: / Line 72: @@
 <h2 id="30">References</h2>
 <ul>
-<li><b>[1]</b> <a href="https://2010.igem.org/Team:Imperial_College_London/Modules/Detection" target="_blank">Imperial college 2011's detection module</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> <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>