Team:Grenoble/Biology/Network

From 2012.igem.org

(Difference between revisions)
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<h1>Network details</h1>
<h1>Network details</h1>
Our system is divided in two modules:
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>
</section>
<a href="http://2012.igem.org/Team:Grenoble/Biology/Network#20" class="schema" ><img src="http://2012.igem.org/wiki/images/b/b1/Circuit_complet.png" alt="" style="position: relative; top: 34px; left: 5px;"/></a>
<a href="http://2012.igem.org/Team:Grenoble/Biology/Network#20" class="schema" ><img src="http://2012.igem.org/wiki/images/b/b1/Circuit_complet.png" alt="" style="position: relative; top: 34px; left: 5px;"/></a>
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<section style="position: relative; top: -80px;">
<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/>
<br/>
-
This is also <a href="http://2012.igem.org/Team:Grenoble/Modeling/Signaling">one of our module of modeling</a>.<br/>
+
This is a <a href="http://2012.igem.org/Team:Grenoble/Modeling/Signaling">modelized module </a>.<br/>
<br/>
<br/>
<center><img src="http://2012.igem.org/wiki/images/e/e1/Signaling_gre.png"/></center>
<center><img src="http://2012.igem.org/wiki/images/e/e1/Signaling_gre.png"/></center>
<br/>
<br/>
-
The idea of this module is du to the iGEM London Imperial College 2010 Team work on Parasight <a href="http://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="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[1]</a>. <br/>
<br/>
<br/>
-
<i>Staphylococcus aureus</i> secretes an enzyme, exfoliative toxin B <a href="http://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="http://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/>
<br/>
-
The dipeptide binds to his receptor which is an engineered <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[3]</a> <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[4]</a> receptor:  
+
The dipeptide binds its receptor which was engineered <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[3]</a> <a href="http://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="http://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="http://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="http://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="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[6]</a> is a histidine kinase involved in the osmoregulation</li>
</ul>
</ul>
<br/>
<br/>
-
Once the dipeptide is bound to the Tap part <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[7]</a>, the EnvZ part allows the phosphorylation of OmpR <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[8]</a> <a href="http://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="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[7]</a>, the intracellular EnvZ part allows the phosphorylation of OmpR <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[8]</a> <a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[9]</a>, which is a constitutively produced transcriptional activator.<br/>
<br/>
<br/>
-
Once OmpR is phosphorylated, it allows the activation of the OmpC promoter<a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[10]</a>.
+
OmpR phosphorylation's allows the activation of the OmpC promoter<a href="http://2012.igem.org/Team:Grenoble/Biology/Network#30">[10]</a>.
</section>
</section>
<section style="position: relative; top: -80px;">
<section style="position: relative; top: -80px;">
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<h2 id="20">Amplification module</h2>
<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/>
<br/>
This is also <a href="http://2012.igem.org/Team:Grenoble/Modeling/Amplification">one of our module of modeling</a>.<br/>
This is also <a href="http://2012.igem.org/Team:Grenoble/Modeling/Amplification">one of our module of modeling</a>.<br/>
Line 49: Line 49:
<center><img src="http://2012.igem.org/wiki/images/f/fc/Amplifcation1.png"/></center>
<center><img src="http://2012.igem.org/wiki/images/f/fc/Amplifcation1.png"/></center>
<br/>
<br/>
-
The activation of the OmpC promoter by phosphorylated OmpR allows the production of Adenyl cyclase <a href="http://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="http://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/>
<br/>
<center><img src="http://2012.igem.org/wiki/images/c/c7/AND.png"/></center>
<center><img src="http://2012.igem.org/wiki/images/c/c7/AND.png"/></center>
<br/>
<br/>
-
cAMP binds to CRP (C-reactive protein) and then this complex allows the production of AraC by activating the pMalT promoter <a href="http://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="http://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="http://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="http://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
<li>GFP (Green Fluorescent Protein) = our output signal
</ul>
</ul>
<br/>
<br/>
<h3 id="8">External amplification</h3>
<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="http://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="http://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/>
<br/>
<center><img src="http://2012.igem.org/wiki/images/b/bf/Img_com.png" /></center>
<center><img src="http://2012.igem.org/wiki/images/b/bf/Img_com.png" /></center>
Line 72: Line 72:
<h2 id="30">References</h2>
<h2 id="30">References</h2>
<ul>
<ul>
-
<li><b>[1]</b> <a href="http://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="http://2010.igem.org/Team:Imperial_College_London/Modules/Detection" target="_blank">Imperial college 2010's detection module</a></li>
<br/>
<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>
<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>

Revision as of 23:53, 24 September 2012

iGEM Grenoble 2012

Project

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