Team:Grenoble/Biology/Network

From 2012.igem.org

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<h2 id="30">References</h2>
<h2 id="30">References</h2>
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<li><b>[1]</b> <a href="http://2010.igem.org/Team:Imperial_College_London/Modules/Detection">Imperial college 2011's detection module</a></li>
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<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>
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<li><b>[2]</b> <a href="http://www.nature.com/jid/journal/v118/n5/full/5601482a.html" 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>
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<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>
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<li><b>[3]</b> <a href="http://jb.asm.org/content/176/4/1157.full.pdf+html" 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>
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<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>
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<li><b>[4]</b> <a ref="http://www.ncbi.nlm.nih.gov/pubmed/9473047"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>
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<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>
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<li><b>[5]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10987">Polypeptide: Tap</a></li>
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<li><b>[5]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10987" target="_blank">Polypeptide: Tap</a></li>
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<li><b>[6]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10269">Protein: EnvZ sensory histidine kinase</a></li>
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<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>
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<li><b>[7]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/3520334"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>
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<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>
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<li><b>[8]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/11973328"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>
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<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>
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<li><b>[9]</b> <a href="http://ecoliwiki.net/colipedia/index.php/ompR:Expression">ompR expression</a></li>
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<li><b>[9]</b> <a href="http://ecoliwiki.net/colipedia/index.php/ompR:Expression" target="_blank">ompR expression</a></li>
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<li><b>[10]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/1769957"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>
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<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>
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<li><b>[11]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10170">Enzyme: adenyl cyclase</a></li>
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<li><b>[11]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10170" target="_blank">Enzyme: adenyl cyclase</a></li>
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<li><b>[12]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00091">Transcription Unit: malT</a></li>
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<li><b>[12]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00091" target="_blank">Transcription Unit: malT</a></li>
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<li><b>[13]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00214">Transcription Unit: araBAD</a></li>
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<li><b>[13]</b> <a href="http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00214" target="_blank">Transcription Unit: araBAD</a></li>
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<li><b>[14]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18414488"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>
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<li><b>[14]</b> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18414488" target="_blank">alagaddé 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>
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Revision as of 23:06, 24 September 2012

iGEM Grenoble 2012

Project

Network details

Our system is divided in two modules:
  • signaling module
  • amplification module

Signaling module

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

This is also one of our module of modeling.

The idea of this module is du to the iGEM London Imperial College 2010 Team work on Parasight [1].

Staphylococcus aureus secretes an enzyme, exfoliative toxin B [2] 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.
Once S. aureus is present, the linker is cut by the protease and the dipeptide is released.

The dipeptide binds to his receptor which is an engineered [3] [4] receptor:
  • the extracellular part is the extracellular part of Tap [5], a dipeptide receptor involved in the chemotaxism
  • the intracellular part is the intracellular part of EnvZ [6], a histidine kinase involved in the osmoregulation

Once the dipeptide is bound to the Tap part [7], the EnvZ part allows the phosphorylation of OmpR [8] [9], a transcriptional activator which is constitutively produced.

Once OmpR is phosphorylated, it allows the production of adenyl cyclase by activating the OmpC promoter [10]

Amplification module

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

This is also one of our module of modeling.

Internal amplification


Adenyl cyclase [11] is an enzyme which catalyse the conversion of ATP (Adenosine Tri-Phosphate) to cAMP (cyclic Adenosine Mono-Phosphate).


cAMP binds to CRP (C-reactive protein) and then this complex allows the production of AraC by activating the pMalT promoter [12].
In the presence of arabinose, AraC, with cAMP-CRP, activates the pAraBAD promoter [13], forming thus an "AND" gate, which allow the production of:
  • adenyl cyclase which reproduce cAMP, forming thus an amplification loop
  • GFP (Green Fluorescent Protein) = our output signal

External amplification

When one bacterium detecte S. aureus, it produces a lot of GFP and cAMP. cAMP can diffuse through the membrane and activates the amplification loop in all the neighbourings bacteria [14] which can thus produce a lot of GFP and cAMP.
The result is an entire population which produce GFP whereas only one bacterium has detected the pathogen in the first place:


References