Difference between revisions of "Team:UPMC-Paris/Description"

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<h1>Overview :</h1>
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<p><h3><i>BBa_K2180001 : Zinc Operator - CzrA Repressor Binding Site</i></h3></p>
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<p>Some parts were used to complete our project. Some of these parts where used from the Registry, others were designed and cloned for this project. In the following section, we are presenting all parts we used and designed.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180001">http://parts.igem.org/Part:BBa_K2180001</a></p><p> Biobrick based on a previous biobrick made by the iGEM09_Newcastle Team (2009-10-14) :</p>
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<div class="image" id="Parts1"></div>
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<p><a href="http://parts.igem.org/Part:BBa_K174015">http://parts.igem.org/Part:BBa_K174015</a></p>
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<div class="image" id="Parts2"></div>
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<p>We add two restriction sites: SacII before and PacI after the regulatory region in order to use it in our project. They allow us to replace a regulatory region with another regulatory region.</p>
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<h1>Our parts collection :</h1>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180002 : Fructose Operator - FruR Binding Site</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180002">http://parts.igem.org/Part:BBa_K2180002</a></p><p> The sequence of the regulatory region comes from this site : <a href="http://regprecise.lbl.gov/RegPrecise/regulon.jsp?regulon_id=12681">http://regprecise.lbl.gov/RegPrecise/regulon.jsp?regulon_id=12681</a></p><p> We add two restriction sites: SacII before and PacI after the regulatory region in order to use it in our project. They allow us to replace a regulatory region with another regulatory region. The regulatory region is composed by two FruR binding sites wich are derepressed in the presence of fructose.</p>
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<groupparts>iGEM2016 UPMC-Paris</groupparts>
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<p>&nbsp;</p>
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</center>
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<p><h3><i>BBa_K2180003 : Sucrose Operator - DegU Binding Site </i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180003">http://parts.igem.org/Part:BBa_K2180003</a></p><p> The sequence of the regulatory region comes from this site&nbsp;: <a href="http://www.prodoric.de/site.php?site_acc=SI002871">http://www.prodoric.de/site.php?site_acc=SI002871</a></p><p> We add two restriction sites SacII before and PacI after the regulatory region in order to use it in our project. They allow us to replace a regulatory region with another regulatory region. The regulatory region is composed by two DegU binding (one forward, one reverse) sites wich are derepressed in the presence of sucrose.</p>
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<p>We designed a biobricks collection that can be used in B. subtilis as biosensors.</p>
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<p>&nbsp;</p>
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<p>In our collection, promoters and operators can be easily changed depending on the detection requirements.  
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<p><h3><i>BBa_K2180004 : LacI + LVA for B. subtilis</i></h3></p>
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<a href="https://2016.igem.org/Team:UPMC-Paris/Basic_Part">Basic parts:</a> Here we present LacI-LVA and PiBlue for B. subtilis a high sensitive regulator and a blue pigment, respectively.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180004">http://parts.igem.org/Part:BBa_K2180004</a></p>
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<p>In addition we designed different promoters/operators, based on Registred parts or using literature.</p>
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<p>The sequence is based on a previous IGEM part made by the group Antiquity (2003-01-31) coding for LacI + LVA for E. coli:</p>
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<p><a href="https://2016.igem.org/Team:UPMC-Paris/Composite_Part">Composite parts :</a> Here we present our parts composed by our basic parts.</p>
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<p><a href="http://parts.igem.org/Part:BBa_C0012">http://parts.igem.org/Part:BBa_C0012</a></p>
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<p>Coding sequence of LacI protein + LVA (rapid degradation tail) wich improve the switch time and make it more sensitive.</p>
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<p>We had to improve the codon usage for B. subtilis</p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180005 : Blue Pigment for B. subtilis</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180005">http://parts.igem.org/Part:BBa_K2180005</a></p>
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<p>Biobrick based on a previous biobrick made by the Team iGEM11_Uppsala-Sweden &nbsp; (2011-09-18) :</p>
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<p><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K592009">http://parts.igem.org/wiki/index.php?title=Part:BBa_K592009</a></p>
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<p>This sequence is coding for a blue pigment we use in our detection system as reporter.</p>
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<p>We had to improve the codon usage for B. subtilis.</p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180006 : Promoter LacO for B. subtilis</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180006">http://parts.igem.org/Part:BBa_K2180006</a></p>
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<p>The part is made of a previous IGEM part made by the team iGEM12_LMU-Munich&nbsp;&nbsp; (2012-07-16) :</p>
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<p><a href="http://parts.igem.org/Part:BBa_K823002">http://parts.igem.org/Part:BBa_K823002</a></p>
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<p>We add two LacI binding sites (Gilbert and Maxam, PNAS, 1973)</p>
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<p>This part is made of PlepA promoter, two LacI binding sites and a RBS. There is a PacI restriction site before LacI binding sites and a SacII restriction site after them. They allows us to remplace the LacI binding sites by another operating sequence. A SalI restriction sites is presents before the PlepA sequence and a NdeI restriction site after the RBS that may be used to insert the whole sequence. We use this part in our project to promote the pigment expression under the control of LacI.</p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180007 : Promoter Fur for B. subtilis</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180007">http://parts.igem.org/Part:BBa_K2180007</a></p>
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<p>This part is based on a previous IGEM part made by the Team iGEM12_LMU-Munich &nbsp;(2012-07-16) : <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K823000">http://parts.igem.org/wiki/index.php?title=Part:BBa_K823000</a></p><p> We add the Fur Box site (Baichoo and Helmann, J. Bacteriol., 2002) in order to make this promoter inactive in the absence of Iron.</p>
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<p>This part is made of PliaG promoter, a fur (Ferric Uptake Regulator) binding site and a RBS. There is a ClaI restriction site before the Fur Box (Fur Binding Site) and a PscI restriction site after. They allows us to remplace Fur Box by another operating sequence. A BamHI restriction sites is present before the PliaG sequence and a NcoI restriction site after the RBS that may be used to insert the whole sequence. We use this part in our project to promote the LacI + LVA expression under the control of Fur. We had to check the compatibility of the promoter with the Fur Box.</p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180008 : Double terminator</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180008">http://parts.igem.org/Part:BBa_K2180008</a></p>
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<p>This part is based on a previous iGEM part made by the Team Antiquity (2003-07-17) :</p>
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<p><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_B0015">http://parts.igem.org/wiki/index.php?title=Part:BBa_B0015</a></p><p> This is a double terminator we use in our project for the pigment production. He is made of a transcriptional terminator in forward and reverse direction. We add a BmtI restriction site before the first terminator (forward) and an AvrII restriction site after the second terminator (reverse).</p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180009 : LacI + LVA + Promoter + Terminator</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180009">http://parts.igem.org/Part:BBa_K2180009</a></p><p> This is the assembly of our basic parts BBa_K2180004, BBa_K2180007 and BBa_K2180008</p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180010 : Cadmium Operator - MntR Binding Site</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180010">http://parts.igem.org/Part:BBa_K2180010</a></p>
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<p>Biobrick based on a previous biobrick made by the iGEM09_Cornell Team (2009-08-10) :</p>
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<p><a href="http://partsregistry.org/Part:BBa_K285103:Design">http://partsregistry.org/Part:BBa_K285103:Design</a></p>
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<p>We add two restriction sites: SacII before and PacI after the regulatory region in order to use it in our project. They allow us to replace a regulatory region with another regulatory region. This Region allow MntR to bind to DNA and repress transcription. In the presence of Cadmium transcription is derepressed because of the fixation of cadmium to MntR.</p>
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<p><i>*Other metallic ions may bind to MntR.</i></p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180011 : Cadmium Operator - ArsR Binding Site</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K2180011">http://parts.igem.org/Part:BBa_K2180011</a></p>
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<p>Biobrick based on a previous biobrick made by the iGEM09_Newcastle Team (2009-10-14) :</p>
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<p><a href="http://parts.igem.org/Part:BBa_K174015">http://parts.igem.org/Part:BBa_K174015</a></p>
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<p>We add two restriction sites: SacII before and PacI after the regulatory region in order to use it in our project. They allow us to replace a regulatory region with another regulatory region. This Region allows ArsR to bind to DNA and repress transcription. In the presence of Heavy Metals such as Arsenic or Cadmium transcription is derepressed because of the fixation to ArsR.</p>
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<p><i>*Other metalic ions may bind to ArsR.</i></p>
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<p>&nbsp;</p>
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<p><h3><i>BBa_K2180012 : Blue Pigment+ PLacO + Double terminator</i></h3></p>
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<p><a href="http://parts.igem.org/Part:BBa_K21800102">http://parts.igem.org/Part:BBa_K21800102</a></p>
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<p>This is the assembly of our parts BBa_K2180005, BBa_K2180006 and BBa_K2180008</p>
 
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Revision as of 01:51, 15 October 2016