Team:Toulouse/Parts

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<!--welcome box -->
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<!-- STYLESHEET -->
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<tr>
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<!-- *********** --
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<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<br>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Toulouse/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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</td>
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</tr>
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<tr> <td colspan="3" height="5px"> </td></tr>
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    <link rel="stylesheet" href="https://2013.igem.org/Team:INSA_Toulouse/template/stylesheet?action=raw&amp;ctype=text/css" type="text/css" />
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<!-- end welcome box -->
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<tr>  
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</head>
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-->
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<body >
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<!--main content -->
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<!--navigation menu -->
<!--navigation menu -->
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<td align="center" colspan="3">
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<div style="background-color : transparent" >
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    <div class="Item" style="left :5%;">  
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<tr heigth="75px">  
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        <a class="btHeaderA1" href="https://2014.igem.org/Team:Toulouse">Home</a>
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        </a>
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    </div>
 +
   
 +
    <div class="Item" style="left :15%">  
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        <a class="btHeaderA2" href="https://2014.igem.org/Team:Toulouse/Team">Team</a>
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        <ul class="Item sub-nav" style="top : 125px;">
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            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Team" class="leaf">Our Team</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://igem.org/Team.cgi?year=2014&team_name=Toulouse" class="leaf"> Official Team Profile </a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Team/Contact" class="leaf">Contact</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Team/Gallery" class="leaf">Gallery</a></li>
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        </ul>
 +
    </div>
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    <div class="Item" style=" left :25%"> 
 +
        <a class="btHeaderA3" href="https://2014.igem.org/Team:Toulouse/Project/Overview">Project</a>
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        <ul class="Item sub-nav" style="top : 155px;">
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            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Project/Overview" class="leaf">Overview</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Project/Fixation" class="leaf">Fixation</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Project/Chemotaxis" class="leaf">Chemotaxis</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Project/Fungicides" class="leaf">Fungicides</a></li>
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            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Project/Spreading" class="leaf">Spreading</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Modeling" class="leaf">Modeling</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Parts" class="leaf">Parts</a></li>
 +
        </ul>
 +
    </div>
 +
   
 +
    <div class="Item" style=" left :35%"> 
 +
        <a class="btHeaderA4" href="https://2014.igem.org/Team:Toulouse/Safety">Human </br> Practice</a>
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        <ul class="Item sub-nav" style="top : 149px;">
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Safety" class="leaf">Safety</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Human_Practice/Ethique" class="leaf">Ethique</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Human_Practice/Communication" class="leaf">Communication</a></li>
 +
        </ul>
 +
    </div>
 +
    <div class="Item" style=" left :45%" > 
 +
        <a class="btHeaderA5" href="https://2014.igem.org/Team:Toulouse/Notebook/Calendar">Notebook</a>
 +
        <ul class="Item sub-nav" style="top : 160px;">
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Notebook/Calendar" class="leaf">Calendar</a></li>
 +
<li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Notebook/Project_Monitoring" class="leaf">Project Monitoring</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Notebook/Protocols" class="leaf">Protocols</a></li>
 +
        </ul>
 +
    </div>
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    <div class="Item" style=" left : 55%">
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<a href="https://2014.igem.org/Team:Toulouse"style="color:#000000">Home </a> </td>
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        <a class="btHeaderA6" href="https://2014.igem.org/Team:Toulouse/Attributions">Acknowledgement</a>
 +
        <ul class="Item sub-nav" style="top : 152px;">
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Attributions" class="leaf">Attributions</a></li>
 +
            <li class="sub-nav-item" align="left"><a href="https://2014.igem.org/Team:Toulouse/Sponsors" class="leaf">Sponsors</a></li>
 +
        </ul>
 +
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    <div class="Item" style="left :70%; Z-index:4;" align ="center" width="60px" >
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<a href="https://2014.igem.org/Team:Toulouse/Team"style="color:#000000"> Team </a> </td>
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        <a href="https://2014.igem.org/Main_Page">  
 +
        <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px">
 +
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 +
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 +
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 +
<!--end navigation menu -->
 +
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 +
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 +
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-
<a href="https://igem.org/Team.cgi?year=2014&team_name=Toulouse"style="color:#000000"> Official Team Profile </a></td>
 
-
<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
 
-
<a href="https://2014.igem.org/Team:Toulouse/Project"style="color:#000000"> Project</a></td>
 
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
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<!--TITRE-->
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<a href="https://2014.igem.org/Team:Toulouse/Parts"style="color:#000000"> Parts</a></td>
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<h1 align="center" style="font-size:50px">
 +
Parts
 +
</h1>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
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<br>
-
<a href="https://2014.igem.org/Team:Toulouse/Modeling"style="color:#000000"> Modeling</a></td>
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-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
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<!--Introduction-->
-
<a href="https://2014.igem.org/Team:Toulouse/Notebook"style="color:#000000"> Notebook</a></td>
+
<p>
 +
As the chassis <i>B. subtilis</i> is not as used as <i>E. coli</i>,
 +
it was sometimes hard for us the get or find desired parts.<br>
 +
However, with the collaboration of other iGEM and a synthesis compagny, we managed to obtain or make the following parts:<br>
 +
</p>
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
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<br>
-
<a href="https://2014.igem.org/Team:Toulouse/Safety"style=" color:#000000"> Safety </a></td>
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<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
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<!--SOUS-TITRE-->
-
<a href="https://2014.igem.org/Team:Toulouse/Attributions"style="color:#000000"> Attributions </a></td>
+
<h2 align="center">
 +
Submitted parts
 +
</h2>
 +
<br>
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
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<!--Introduction-->
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</tr>
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<p>
-
</table>
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We have deposed X new BioBrick parts to the Registry.  
 +
All of them were cloned into the standard plasmid pSB1C3, tested and sequenced.<br>
 +
<!--à vérifier et confirmer-->
 +
</p>
-
<!--end navigation menu -->
 
-
</tr>
 
 +
<h3 align="center">
 +
Chemotaxis
 +
</h3>
-
</tr>
+
<!--K1364000 : RBS + Chimio + terminator-->
-
+
<p>
 +
<b>BBa_K1364000:</b> Strong RBS for <i>B. subtilis</i>  
 +
(<a href="http://parts.igem.org/Part:BBa_K780001">K780001</a>)
 +
+ Chemotaxis code
 +
+ Double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>)<br><br>
 +
<b>N-acetylglucosamine based chemotaxis:</b><br>
 +
This part is designed to enable a N-acetylglucosamine
 +
based chemotaxis in <i>Bacillus subtilis</i>.<br><br>
 +
<b>Design:</b><br>
 +
The encoded protein is a chimera of two proteins:<br>
 +
- the methyl accepting Chemotaxis protein (McpA from <i>Bacillus subtilis</i> which is required for taxis towards glucose.<br>
 +
- the N-acetylglucosamine regulated methyl-accepting chemotaxis protein from <i>Vibrio cholerae</i> (VCD).<br>
 +
<br><br>
 +
The chimeric protein contains the intracellular domains of McpA from <i>Bacillus subtilis</i> to enable the transduction of the signal:
 +
these domains correspond to the amino acids 1-37 and 282-610.
 +
The extracellular domain of VCD is inserted between the intracellular regions of McpA
 +
to sense N-acetylglucosamine and corresponds to the amino acids 31-310.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Translation unit<br>
 +
<br>
 +
<b>Tests</b><br>
 +
This part was tested with the protocol Plug and pond.
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
Uniprot:<br>
 +
- <a href="http://www.uniprot.org/uniprot/P39214">McpA</a><br>
 +
- <a href="http://www.uniprot.org/uniprot/C3NYT2">N-acetylglucosamine regulated methyl-accepting chemotaxis protein</a><br>
 +
<!--à compléter-->
 +
</p>
 +
<br>
 +
<!--K1364004 : Promotor Pveg + Chimio-->
 +
<p>
 +
<b>BBa_K1364004:</b> Strong, constitutive promotor of <i>B. subtilis</i>
 +
P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>) + RBS, Chemotaxis code and Double terminator (K1364000)<br>
 +
<br>
 +
<b>N-acetylglucosamine based chemotaxis:</b><br>
 +
This part is designed to enable a N-acetylglucosamine
 +
based chemotaxis in <i>Bacillus subtilis</i>.<br><br>
 +
<b>Design:</b><br>
 +
This expression cassette is designed for the expression of an antifungal peptide,
 +
D4E1 and for its secretion in <i>Bacillus subtilis</i>.
 +
It is composed of the strong, constitutive promotor of <i>B. subtilis</i>
 +
P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>),
 +
strong RBS for <i>B. subtilis</i> (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>),
 +
the open reading frame of D4E1
 +
and a double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>) <br>
 +
<br>
 +
<b>Type</b><br>
 +
Expression cassette<br>
 +
<br>
 +
<b>Tests</b><br>
 +
This part was tested with the protocol Plug and pond.
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
Uniprot:<br>
 +
- <a href="http://www.uniprot.org/uniprot/P39214">McpA</a><br>
 +
- <a href="http://www.uniprot.org/uniprot/C3NYT2">N-acetylglucosamine regulated methyl-accepting chemotaxis protein</a><br>
 +
<!--à compléter-->
 +
</p>
 +
<br>
-
</td>
+
<!--K1364006 : Pveg, RBS, Chimio, Terminator, Pveg, RBS, Binding and Terminator-->
 +
<p>
 +
<b>BBa_K1364006:</b>
 +
P<sub>veg</sub>, RBS, Chemotaxis code, Double terminator(BBa_K1364004)
 +
+ P<sub>veg</sub>, RBS, Binding, Double terminator(BBa_K1364005).<br>
 +
<b>Type</b><br>
 +
Expression cassette<br>
 +
<br>
 +
<b>Tests</b><br>
 +
This part was not tested.
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
See BBa_K1364004 and BBa_1364005.
 +
<!--à compléter + lien-->
 +
</p>
-
<tr> <td colspan="3"  height="15px"> </td></tr>
+
<br>
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
+
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
 +
<h3 align="center">
 +
Binding
 +
</h3>
-
<!--Parts Submitted to the Registry  -->
+
<!--K1364001 : RBS + Binding + Terminator-->
-
<tr><td > <h3> Parts Submitted to the Registry </h3></td>
+
-
<td ></td >
+
-
<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
+
-
</tr>
+
-
<tr>
+
-
<td width="45%"  valign="top">  
+
<p>
<p>
-
An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox.
+
<b>BBa_K1364001:</b> Consensus RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K090505">K090505</a>) + Binding code + Double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>)<br><br>
 +
<b>Binding module:</b><br>
 +
This part is designed to enable the binding of <i>Bacillus subtilis</i>
 +
to the fungi wall made of chitin.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of a Cell Wall Binding (CWB) sequence
 +
and a Chitin Binding Domain (CBD) linked with a 6 amino acids linker.<br>
 +
<br>
 +
The CWB domain has been extracted from LytC (<a href="http://parts.igem.org/Part:BBa_K316030">BBa_K316030</a>) of the iGEM 2010 Imperial College team.<br>
 +
The CBD is composed of the Domain 4 of the GbpA protein of <i>Vibrio cholerae</i>,
 +
a protein reported to mediate bacterial attachment to chitin.
 +
It has been shown that the Domain 4 was essential to bind chitin.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Translation unit<br>
 +
<br>
 +
<b>Tests</b><br>
 +
This part was tested with chitin beeds.
 +
Link ?
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br>
 +
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br>
 +
<!--à compléter-->
 +
</p>
 +
<br>
 +
 +
 +
<h3 align="center">
 +
Fungicides
 +
</h3>
 +
 +
<h4 align="center">
 +
GAFP-1
 +
</h4>
 +
 +
<br>
 +
 +
<!--K1364002 : RBS + GAFP-1-->
<p>
<p>
-
<strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.  
+
<b>BBa_K1364002:</b> Strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>) + GAFP-1<br>
 +
<br>
 +
<b>GAFP-1: Gastrodia anti-fungal protein</b><br>
 +
The <i>Gastrodia</i> anti-fungal protein (GAFP-1) is a mannose-binding lectin
 +
which is able to inhibit the growth of multiples species of plant pathogenic fungi.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of a Strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a> and
 +
the open reading frame of the <i>Gastrodia</i> anti-fungal protein 1 (GAFP-1)
 +
optimized for its expression and its secretion in <i>Bacillus subtilis</i>.
 +
The codon optimization was made thanks to the DNA 2.0 software program.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Composite part<br>
 +
<br>
 +
<b>Tests</b><br>
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br>
 +
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br>
 +
<!--à compléter-->
</p>
</p>
 +
<br>
 +
</p>
 +
 +
<!--K1364007 : RBS + GAFP-1 + Terminator-->
<p>
<p>
-
Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.
+
<b>BBa_K1364007:</b> Strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>) + GAFP-1 + Double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a><br>
 +
<br>
 +
<b>GAFP-1: Gastrodia anti-fungal protein</b><br>
 +
The <i>Gastrodia</i> anti-fungal protein (GAFP-1) is a mannose-binding lectin
 +
which is able to inhibit the growth of multiples species of plant pathogenic fungi.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of a Strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>,
 +
the open reading frame of the <i>Gastrodia</i> anti-fungal protein 1 (GAFP-1)
 +
and a double terminator <a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>.
 +
optimized for its expression and its secretion in <i>Bacillus subtilis</i>.
 +
The codon optimization was made thanks to the DNA 2.0 software program.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Composite part<br>
 +
<br>
 +
<b>Tests</b><br>
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br>
 +
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br>
 +
<!--à compléter-->
</p>
</p>
 +
<br>
 +
<!--K13640008 : Pveg + RBS + GAFP-1 + Terminator-->
 +
<p>
 +
<b>BBa_K1364008:</b>
 +
Strong, constitutive promoter of <i>Bacillus subtilis</i> P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a> +
 +
Strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>) +
 +
GAFP-1 +
 +
Double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a><br>
 +
<br>
 +
<b>GAFP-1: Gastrodia anti-fungal protein</b><br>
 +
The <i>Gastrodia</i> anti-fungal protein (GAFP-1) is a mannose-binding lectin
 +
which is able to inhibit the growth of multiples species of plant pathogenic fungi.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of the strong, constitutive promoter of <i>Bacillus subtilis</i> P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>,
 +
strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>,
 +
the open reading frame of the <i>Gastrodia</i> anti-fungal protein 1 (GAFP-1)
 +
and a double terminator <a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>.
 +
optimized for its expression and its secretion in <i>Bacillus subtilis</i>.
 +
The codon optimization was made thanks to the DNA 2.0 software program.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Expression cassette<br>
 +
<br>
 +
<b>Tests</b><br>
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)<br>
 +
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373<br>
 +
<!--à compléter-->
 +
</p>
-
<h3>When should you put parts into the Registry?</h3>
+
<br>
 +
<h4 align="center">
 +
D4E1
 +
</h4>
 +
 +
<br>
 +
 +
<!--K1364003 : RBS + D4E1 + Terminator-->
<p>
<p>
-
As soon as possible! We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.  
+
<b>BBa_K1364003:</b> Strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>) + D4E1
 +
+ Double terminator (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_B0015">B0015</a><br>
 +
<br>
 +
<b>D4E1</b><br>
 +
D4E1 is a linear synthetic peptide of 17 amino acids
 +
which has shown to have antifungal activities
 +
by complexing with a sterol present in conodial wall of a varety of fungi.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of a Strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>,
 +
the open reading frame of D4E1 and
 +
a Double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>)
 +
optimized for its expression and its secretion in <i>Bacillus subtilis</i>.
 +
This part was optimized for the expression and its secretion in <i>Bacillus subtilis </i>
 +
thanks to the DNA 2.0 software program.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Translation unit<br>
 +
<br>
 +
<b>Tests</b><br>
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
- De Lucca AJ, Bland JM, Grimm C, Jacks TJ, Cary JW, Jaynes JM, Cleveland TE, Walsh TJ. Fungicidal properties, sterol binding, and proteolytic resistance of the synthetic peptide D4E1.<br>
 +
- Can J Microbiol. 1998 Jun;44(6):514-20.<br>
 +
<!--à compléter-->
</p>
</p>
-
</td>
 
-
<td > </td>
+
<br>
-
<td width="45%" valign="top">
+
 +
<!--K1364009 : Pveg + RBS + D4E1 + Terminator-->
<p>
<p>
-
The information needed to initially create a part on the Registry is:
+
<b>BBa_K1364009:</b> Strong, constitutive promotor of <i>B. subtilis</i>
 +
P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>)
 +
+ RBS, D4E1 code and Double terminator (K1364003)<br>
 +
<b>D4E1</b><br>
 +
D4E1 is a linear synthetic peptide of 17 amino acids
 +
which has shown to have antifungal activities
 +
by complexing with a sterol present in conodial wall of a varety of fungi.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of the strong, constitutive promotor of <i>B. subtilis</i>
 +
P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>),
 +
a strong RBS (<a href="http://parts.igem.org/Part:BBa_K780002">K780002</a>),
 +
the open reading frame of D4E1 and
 +
a double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>).
 +
This part was optimized for the expression and its secretion in <i>Bacillus subtilis </i>
 +
thanks to the DNA 2.0 software program.<br>
 +
<br>
 +
<b>Type</b><br>
 +
Expression cassette<br>
 +
<br>
 +
<b>Tests</b><br>
 +
Link ?<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
- De Lucca AJ, Bland JM, Grimm C, Jacks TJ, Cary JW, Jaynes JM, Cleveland TE, Walsh TJ. Fungicidal properties, sterol binding, and proteolytic resistance of the synthetic peptide D4E1.<br>
 +
- Can J Microbiol. 1998 Jun;44(6):514-20.<br>
 +
<!--à compléter-->
</p>
</p>
-
<ol>
 
-
<li>Part Name</li>
+
<br>
-
<li>Part type</li>
+
-
<li>Creator</li>
+
-
<li>Sequence</li>
+
-
<li>Short Description (60 characters on what the DNA does)</li>
+
-
<li>Long Description (Longer description of what the DNA does)</li>
+
-
<li>Design considerations</li>
+
-
</ol>
+
 +
<h4 align="center">
 +
EcAMP-1
 +
</h4>
 +
 +
<!--K1364010 : Pveg RBS + EcAMP -->
<p>
<p>
-
We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part.  
+
<b>BBa_K1364010:</b> Constitutive promoter P<sub>veg</sub> and
 +
strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K733013">K733013</a>)
 +
+ EcAMP-1 (<a href="http://parts.igem.org/Part:BBa_K1162001">K1162001</a>)
 +
<br>
 +
<b>EcAMP-1</b><br>
 +
EcAMP-1 is an antimicrobial peptide of 37 amino acids
 +
originated from the specie <i>Echinochloa crus-galli</i>,  
 +
a type of wild grass.
 +
This peptide has a particular structure : it is helical because of two disulfide bonds.<br>
 +
EcAMP-1 has shown to have antifungal activities. Its mode of action may be the prevention of hyphae elongation.<br>
 +
This part was added to the Registry by the iGEM Utah State team in 2013.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of the constitutive promoter P<sub>veg</sub> and
 +
strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K733013">K733013</a>) and
 +
the open reading frame of EcAMP-1.<br>
 +
The EcAMP-1 part was codon optimized for <i>E. coli</i> by the iGEM Utah State team
 +
and thanks to the Life Technologies GeneArt software program.
 +
<br>
 +
<b>Type</b><br>
 +
Composite part<br>
 +
<br>
 +
<b>Tests</b><br>
 +
The electrophoresis and PCR tests were OK.<br>
 +
<!--à compléter avec les tests--><br>
 +
<b>References</b><br>
 +
<br>
 +
<!--à compléter : demander à emeline-->
</p>
</p>
 +
<br>
 +
 +
<!--K1364011 : Pveg RBS + EcAMP + Double term-->
<p>
<p>
-
You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry"> Add a Part to the Registry</a> link.
+
<b>BBa_K1364011:</b> Constitutive promoter P<sub>veg</sub> and
 +
strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K733013">K733013</a>)
 +
+ EcAMP-1 (<a href="http://parts.igem.org/Part:BBa_K1162001">K1162001</a>)
 +
+ Double terminator (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_B0015">B0015</a>)
 +
<br>
 +
<b>EcAMP-1</b><br>
 +
EcAMP-1 is an antimicrobial peptide of 37 amino acids
 +
originated from the specie <i>Echinochloa crus-galli</i>,
 +
a type of wild grass.
 +
This peptide has a particular structure : it is helical because of two disulfide bonds.<br>
 +
EcAMP-1 has shown to have antifungal activities. Its mode of action may be the prevention of hyphae elongation.<br>
 +
This part was added to the Registry by the iGEM Utah State team in 2013.<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is composed of the constitutive promoter P<sub>veg</sub> and
 +
strong RBS for <i>B. subtilis</i>
 +
(<a href="http://parts.igem.org/Part:BBa_K733013">K733013</a>),
 +
the open reading frame of EcAMP-1 and
 +
a double terminator (<a href="http://parts.igem.org/Part:BBa_B0015">B0015</a>).<br>
 +
The EcAMP-1 part was codon optimized for <i>E. coli</i> by the iGEM Utah State team
 +
and thanks to the Life Technologies GeneArt software program.
 +
<br>
 +
<b>Type</b><br>
 +
Expression cassette<br>
 +
<br>
 +
<b>Tests</b><br>
 +
The test does not work yet.<br>
 +
<!--à compléter avec les tests-->
 +
<br>
 +
<b>References</b><br>
 +
<br>
 +
<!--à compléter : demander à emeline-->
</p>
</p>
-
</td>
 
-
</tr>
 
-
<tr> <td colspan="3" height="15px"> </td></tr>
+
<h4 align="center">
 +
Fungicide operons
 +
</h4>
-
<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
+
<!--K1364012 : RBS + GAFP + RBS + D4E1 + Terminator-->
 +
<p>
 +
<b>BBa_K1364012:</b>  
 +
RBS and GAFP-1 (K1364002) + RBS, D4E1 and double terminator (K1364003)<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is designed for the co-expression of two different peptides
 +
with anti-fungal activities : D4E1 and GAFP-1.
 +
It is composed of the translation unit with D4E1 (BBa_K1364002)
 +
and the composite part with GAFP-1 (BBa_K1364003).<br>
 +
<br>
 +
<b>Type</b><br>
 +
Translation unit<br>
 +
<br>
 +
<b>Tests</b><br>
 +
<br>
 +
<!--à compléter avec les tests-->
 +
<br>
 +
<b>References</b><br>
 +
See BBa_K1364002 and BBa_K1364003.<br>
 +
<!--à compléter-->
 +
</p>
 +
<br>
 +
 +
<!--K1364013 : Pveg + RBS + GAFP + RBS + D4E1 + Terminator-->
 +
<p>
 +
<b>BBa_K1364013:</b>
 +
Strong, constitutive promotor of <i>B. subtilis</i>
 +
P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>)
 +
+ RBS, GAFP-1, RBS, D4E1 and double terminator (K1364012).<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part is designed for the co-expression of two different peptides
 +
with anti-fungal activities : D4E1 and GAFP-1.
 +
It is composed of the strong, constitutive promotor of <i>B. subtilis</i>
 +
P<sub>veg</sub> (<a href="http://parts.igem.org/wiki/index.php/Part:BBa_K823003">K823003</a>)
 +
and the translation unit with GAFP-1 and D4E1 (BBa_K1364012).<br>
 +
<br>
 +
<b>Type</b><br>
 +
Expression cassette<br>
 +
<br>
 +
<b>Tests</b><br>
 +
<br>
 +
<!--à compléter avec les tests-->
 +
<br>
 +
<b>References</b><br>
 +
See BBa_K1364002 and BBa_K1364003.<br>
 +
<!--à compléter-->
 +
</p>
-
<tr><td width="45%" colspan="3" valign="top">
+
<br>
-
Any parts your team has created will appear in this table below:</td></tr>
+
 
 +
<!--K1364014 : Pveg RBS spoVG + EcAMP + RBS +  GAFP + RBS + D4E1 + Terminator-->
 +
<p>
 +
<b>BBa_K1364014:</b>
 +
Promotor P<sub>veg</sub> RBS spoVG, EcAMP-1 (BBa_K1364010)
 +
+ RBS, GAFP-1, RBS, D4E1 and double terminator (BBa_K1364012)<br>
 +
<br>
 +
<b>Design:</b><br>
 +
This part contains the three fungicides on the same operon.
 +
It is composed of the composite part with EcAMP--1 (BBa_K1364010)
 +
and the translation unit with GAFP-1 and D4E1 (BBa_K1364012).<br>
 +
<br>
 +
<b>Type</b><br>
 +
??<br>
 +
<br>
 +
<b>Tests</b><br>
 +
<br>
 +
<!--à compléter avec les tests-->
 +
<br>
 +
<b>References</b><br>
 +
See BBa_K1364010, BBa_K1364002 and BBa_K1364003.<br>
 +
<!--à compléter-->
 +
</p>
 +
 
 +
<br>
 +
 
 +
<!--SOUS-TITRE-->
 +
<h2 align="center">
 +
Used parts
 +
</h2>
 +
 
 +
<br>
 +
 
 +
<!--Table-->
 +
<p>
 +
<table border="1" width="100%" height="20%" id="Chassis">
 +
<!--1ere ligne-->
 +
<tr>
 +
<td><b>BioBrick</b></td>
 +
<td><b>Description</b></td>
 +
<td><b>Origine</b></td>
 +
<td><b>Module(s)</b></td>
 +
</tr>
 +
<!--2eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K733013">K733013</a></td>
 +
<td>P<sub>veg</sub> (<a href="http://parts.igem.org/Part:BBa_K316001">K316001</a>) + RBS-SpoVG (<a href="http://parts.igem.org/Part:BBa_K143021">K143021</a>) : Constitutive promotor P<sub>veg</sub> and strong RBS for <i>B. subtilis</i></td>
 +
<td>2014 Kit plate 1, 7H</td>
 +
<td>Fungicides (EcAMP)</td>
 +
</tr>
 +
<!--3eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K823003">K823003</a></td>
 +
<td>P<sub>veg</sub> : strong, constitutive promotor of <i>B. subtilis</i></td>
 +
<td>2014 Kit plate 1, 20G</td>
 +
<td>Fungicides (D4E1 GAFP-1)<br>Chemotaxis<br>Binding</td>
 +
</tr>
 +
<!--4eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K823002">K823002</a></td>
 +
<td>P<sub>lepA</sub> : constitutive promotor of <i>B. subtilis</i>.
 +
<br>It is the promotor of the lepA gene of <i>B. subtilis</i></td>
 +
<td>2014 Kit plate 1, 20E</td>
 +
<td>Fungicides (D4E1)<br>Chemotaxis<br>Binding</td>
 +
</tr>
 +
<!--5eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K606061">K606061</a></td>
 +
<td>SpoVG RBS for <i>B. subtilis</i>
 +
<br>Strong ribosome binding site from subtilis. Works fine in <i>E. coli</i></td>
 +
<td>2014 Kit plate 1, 15A</td>
 +
<td>Optional</td>
 +
</tr>
 +
<!--6eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K316027">K316027</a></td>
 +
<td><i>B. subtilis</i> transformation vector with LacI, targets amyE locus.</td>
 +
<td>2014 Kit plate 1, 2N</td>
 +
<td>Fungicides<br>Chemotaxis<br>Binding</td>
 +
</tr>
 +
<!--7eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_B0015">B0015</a></td>
 +
<td>Double terminator (<a href="http://parts.igem.org/Part:BBa_B0010">BBa_B0010</a> + <a href="http://parts.igem.org/Part:BBa_B0012">BBa_B0012</a>)</td>
 +
<td>2014 Kit plate 3, 3F</td>
 +
<td>Fungicides (GAFP-1, EcAMP-1)</td>
 +
</tr>
 +
<!--8eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K780000">K780000</a></td>
 +
<td>Terminator for <i>B. subtilis</i></td>
 +
<td>Sent by the Warsaw iGEM team</td>
 +
<td></td>
 +
</tr>
 +
<!--9eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K780001">K780001</a></td>
 +
<td>Strong RBS for <i>B. subtilis</i></td>
 +
<td>Sent by the Warsaw iGEM team</td>
 +
<td></td>
 +
</tr>
 +
<!--10eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K780002">K780002</a></td>
 +
<td>Strong RBS for <i>B. subtilis</i></td>
 +
<td>Sent by the Warsaw iGEM team</td>
 +
<td></td>
 +
</tr>
 +
<!--11eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K780003">K780003</a></td>
 +
<td>Strong constitutive promotor for <i>B. subtilis</i></td>
 +
<td>Sent by the Warsaw iGEM team</td>
 +
<td>Fungicides<br>Chemotaxis<br>Binding</td>
 +
</tr>
 +
<!--12eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K1162001">K1162001</a></td>
 +
<td>EcAMP-1</td>
 +
<td>Sent by the Utah State iGEM team</td>
 +
<td>Fungicides (EcAMP-1)</td>
 +
</tr>
 +
<!--13eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K823023">K823023</a></td>
 +
<td>Empty backbone vector pSB<sub>BS</sub>1C for integration into <i>B. subtilis</i>
 +
<br>It integrates in the amyE locus</td>
 +
<td>Sent by the Munich iGEM team</td>
 +
<td>Fungicides<br>Chemotaxis<br>Binding</td>
 +
</tr>
 +
<!--14eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K823022">K823022</a></td>
 +
<td>Empty backbone vector pSB<sub>BS</sub>4S for integration into<i>B. subtilis</i>
 +
<br>It integrates in the thrC locus</td>
 +
<td>Sent by the Munich iGEM team</td>
 +
<td>Fungicides<br>Chemotaxis<br>Binding</td>
 +
</tr>
 +
<!--15eme ligne-->
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K823021">K823021</a></td>
 +
<td>Reporter vector pSB<sub>BS</sub>1C-lacZ for <i>B. subtilis</i></td>
 +
<td>Sent by the Munich iGEM team</td>
 +
<td>Fungicides<br>Chemotaxis<br>Binding</td>
 +
</tr>
</table>
</table>
-
</html>
+
</p>
-
<groupparts>iGEM013 Toulouse</groupparts>
+
<br>
 +
 
 +
 
 +
<!--SOUS-TITRE-->
 +
<h2 align="center">
 +
Other parts
 +
</h2>
 +
 
 +
<br>
 +
 
 +
 
 +
 
 +
<!-- footer -->
 +
<center>
 +
<div id="Footer" >
 +
<table align="center" style="width : 100%; background-color:transparent;" bgColor="#99FF99">
 +
    <td width="5px"></td>
 +
    <td style="width: 35px;" align="center">
 +
        <a href="https://www.facebook.com/iGEM.Toulouse.2014?ref_type=bookmark"><img src="https://static.igem.org/mediawiki/2013/f/fc/Insa-toulouse2013-iconfacebook.png" alt="Facebook" /></a>
 +
        <br> <br>
 +
        <a href="https://twitter.com/iGEM_Toulouse"><img src="https://static.igem.org/mediawiki/2013/7/7b/Insa-toulouse2013-icontwitter.png" alt="Twitter" /></a>
 +
        <br>
 +
    </td>
 +
    <td width="15px"></td>
 +
    <td>
 +
        <p><b> iGEM Toulouse</b><br><address>
 +
        INSA Toulouse <br>135, Avenue de Rangueil <br>
 +
        31400 TOULOUSE <br></address>
 +
        <br>e-mail: <span><a href="mailto:igemtoulouse2014@gmail.com"> igemtoulouse2014@gmail.com</a></span></p>
 +
    </td>
 +
    <td align="right">
 +
        <a href="https://2013.igem.org/Main_Page">
 +
            <img style="width:170px" src="https://static.igem.org/mediawiki/igem.org/1/17/IGEM_basic_Logo_white_stylized.png"/img>
 +
        </a>
 +
    </td>
 +
  </table>
 +
</div>
 +
</center>
 +
</div>
 +
</html>

Latest revision as of 13:29, 11 September 2014

header background

Parts


As the chassis B. subtilis is not as used as E. coli, it was sometimes hard for us the get or find desired parts.
However, with the collaboration of other iGEM and a synthesis compagny, we managed to obtain or make the following parts:


Submitted parts


We have deposed X new BioBrick parts to the Registry. All of them were cloned into the standard plasmid pSB1C3, tested and sequenced.

Chemotaxis

BBa_K1364000: Strong RBS for B. subtilis (K780001) + Chemotaxis code + Double terminator (B0015)

N-acetylglucosamine based chemotaxis:
This part is designed to enable a N-acetylglucosamine based chemotaxis in Bacillus subtilis.

Design:
The encoded protein is a chimera of two proteins:
- the methyl accepting Chemotaxis protein (McpA from Bacillus subtilis which is required for taxis towards glucose.
- the N-acetylglucosamine regulated methyl-accepting chemotaxis protein from Vibrio cholerae (VCD).


The chimeric protein contains the intracellular domains of McpA from Bacillus subtilis to enable the transduction of the signal: these domains correspond to the amino acids 1-37 and 282-610. The extracellular domain of VCD is inserted between the intracellular regions of McpA to sense N-acetylglucosamine and corresponds to the amino acids 31-310.

Type
Translation unit

Tests
This part was tested with the protocol Plug and pond. Link ?

References
Uniprot:
- McpA
- N-acetylglucosamine regulated methyl-accepting chemotaxis protein


BBa_K1364004: Strong, constitutive promotor of B. subtilis Pveg (K823003) + RBS, Chemotaxis code and Double terminator (K1364000)

N-acetylglucosamine based chemotaxis:
This part is designed to enable a N-acetylglucosamine based chemotaxis in Bacillus subtilis.

Design:
This expression cassette is designed for the expression of an antifungal peptide, D4E1 and for its secretion in Bacillus subtilis. It is composed of the strong, constitutive promotor of B. subtilis Pveg (K823003), strong RBS for B. subtilis (K780002), the open reading frame of D4E1 and a double terminator (B0015)

Type
Expression cassette

Tests
This part was tested with the protocol Plug and pond. Link ?

References
Uniprot:
- McpA
- N-acetylglucosamine regulated methyl-accepting chemotaxis protein


BBa_K1364006: Pveg, RBS, Chemotaxis code, Double terminator(BBa_K1364004) + Pveg, RBS, Binding, Double terminator(BBa_K1364005).
Type
Expression cassette

Tests
This part was not tested.
References
See BBa_K1364004 and BBa_1364005.


Binding

BBa_K1364001: Consensus RBS for B. subtilis (K090505) + Binding code + Double terminator (B0015)

Binding module:
This part is designed to enable the binding of Bacillus subtilis to the fungi wall made of chitin.

Design:
This part is composed of a Cell Wall Binding (CWB) sequence and a Chitin Binding Domain (CBD) linked with a 6 amino acids linker.

The CWB domain has been extracted from LytC (BBa_K316030) of the iGEM 2010 Imperial College team.
The CBD is composed of the Domain 4 of the GbpA protein of Vibrio cholerae, a protein reported to mediate bacterial attachment to chitin. It has been shown that the Domain 4 was essential to bind chitin.

Type
Translation unit

Tests
This part was tested with chitin beeds. Link ?
References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373


Fungicides

GAFP-1


BBa_K1364002: Strong RBS for B. subtilis (K780002) + GAFP-1

GAFP-1: Gastrodia anti-fungal protein
The Gastrodia anti-fungal protein (GAFP-1) is a mannose-binding lectin which is able to inhibit the growth of multiples species of plant pathogenic fungi.

Design:
This part is composed of a Strong RBS (K780002 and the open reading frame of the Gastrodia anti-fungal protein 1 (GAFP-1) optimized for its expression and its secretion in Bacillus subtilis. The codon optimization was made thanks to the DNA 2.0 software program.

Type
Composite part

Tests
Link ?

References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373


BBa_K1364007: Strong RBS for B. subtilis (K780002) + GAFP-1 + Double terminator (B0015

GAFP-1: Gastrodia anti-fungal protein
The Gastrodia anti-fungal protein (GAFP-1) is a mannose-binding lectin which is able to inhibit the growth of multiples species of plant pathogenic fungi.

Design:
This part is composed of a Strong RBS (K780002, the open reading frame of the Gastrodia anti-fungal protein 1 (GAFP-1) and a double terminator B0015. optimized for its expression and its secretion in Bacillus subtilis. The codon optimization was made thanks to the DNA 2.0 software program.

Type
Composite part

Tests
Link ?

References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373


BBa_K1364008: Strong, constitutive promoter of Bacillus subtilis Pveg (K823003 + Strong RBS for B. subtilis (K780002) + GAFP-1 + Double terminator (B0015

GAFP-1: Gastrodia anti-fungal protein
The Gastrodia anti-fungal protein (GAFP-1) is a mannose-binding lectin which is able to inhibit the growth of multiples species of plant pathogenic fungi.

Design:
This part is composed of the strong, constitutive promoter of Bacillus subtilis Pveg (K823003, strong RBS (K780002, the open reading frame of the Gastrodia anti-fungal protein 1 (GAFP-1) and a double terminator B0015. optimized for its expression and its secretion in Bacillus subtilis. The codon optimization was made thanks to the DNA 2.0 software program.

Type
Expression cassette

Tests
Link ?

References
- Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, et al. (2012)
- The Vibrio cholerae Colonization Factor GbpA Possesses a Modular Structure that Governs Binding to Different Host Surfaces. PLoS Pathog 8(1): e1002373. doi:10.1371/journal.ppat.1002373


D4E1


BBa_K1364003: Strong RBS for B. subtilis (K780002) + D4E1 + Double terminator (B0015

D4E1
D4E1 is a linear synthetic peptide of 17 amino acids which has shown to have antifungal activities by complexing with a sterol present in conodial wall of a varety of fungi.

Design:
This part is composed of a Strong RBS (K780002, the open reading frame of D4E1 and a Double terminator (B0015) optimized for its expression and its secretion in Bacillus subtilis. This part was optimized for the expression and its secretion in Bacillus subtilis thanks to the DNA 2.0 software program.

Type
Translation unit

Tests
Link ?

References
- De Lucca AJ, Bland JM, Grimm C, Jacks TJ, Cary JW, Jaynes JM, Cleveland TE, Walsh TJ. Fungicidal properties, sterol binding, and proteolytic resistance of the synthetic peptide D4E1.
- Can J Microbiol. 1998 Jun;44(6):514-20.


BBa_K1364009: Strong, constitutive promotor of B. subtilis Pveg (K823003) + RBS, D4E1 code and Double terminator (K1364003)
D4E1
D4E1 is a linear synthetic peptide of 17 amino acids which has shown to have antifungal activities by complexing with a sterol present in conodial wall of a varety of fungi.

Design:
This part is composed of the strong, constitutive promotor of B. subtilis Pveg (K823003), a strong RBS (K780002), the open reading frame of D4E1 and a double terminator (B0015). This part was optimized for the expression and its secretion in Bacillus subtilis thanks to the DNA 2.0 software program.

Type
Expression cassette

Tests
Link ?

References
- De Lucca AJ, Bland JM, Grimm C, Jacks TJ, Cary JW, Jaynes JM, Cleveland TE, Walsh TJ. Fungicidal properties, sterol binding, and proteolytic resistance of the synthetic peptide D4E1.
- Can J Microbiol. 1998 Jun;44(6):514-20.


EcAMP-1

BBa_K1364010: Constitutive promoter Pveg and strong RBS for B. subtilis (K733013) + EcAMP-1 (K1162001)
EcAMP-1
EcAMP-1 is an antimicrobial peptide of 37 amino acids originated from the specie Echinochloa crus-galli, a type of wild grass. This peptide has a particular structure : it is helical because of two disulfide bonds.
EcAMP-1 has shown to have antifungal activities. Its mode of action may be the prevention of hyphae elongation.
This part was added to the Registry by the iGEM Utah State team in 2013.

Design:
This part is composed of the constitutive promoter Pveg and strong RBS for B. subtilis (K733013) and the open reading frame of EcAMP-1.
The EcAMP-1 part was codon optimized for E. coli by the iGEM Utah State team and thanks to the Life Technologies GeneArt software program.
Type
Composite part

Tests
The electrophoresis and PCR tests were OK.

References


BBa_K1364011: Constitutive promoter Pveg and strong RBS for B. subtilis (K733013) + EcAMP-1 (K1162001) + Double terminator (B0015)
EcAMP-1
EcAMP-1 is an antimicrobial peptide of 37 amino acids originated from the specie Echinochloa crus-galli, a type of wild grass. This peptide has a particular structure : it is helical because of two disulfide bonds.
EcAMP-1 has shown to have antifungal activities. Its mode of action may be the prevention of hyphae elongation.
This part was added to the Registry by the iGEM Utah State team in 2013.

Design:
This part is composed of the constitutive promoter Pveg and strong RBS for B. subtilis (K733013), the open reading frame of EcAMP-1 and a double terminator (B0015).
The EcAMP-1 part was codon optimized for E. coli by the iGEM Utah State team and thanks to the Life Technologies GeneArt software program.
Type
Expression cassette

Tests
The test does not work yet.

References

Fungicide operons

BBa_K1364012: RBS and GAFP-1 (K1364002) + RBS, D4E1 and double terminator (K1364003)

Design:
This part is designed for the co-expression of two different peptides with anti-fungal activities : D4E1 and GAFP-1. It is composed of the translation unit with D4E1 (BBa_K1364002) and the composite part with GAFP-1 (BBa_K1364003).

Type
Translation unit

Tests


References
See BBa_K1364002 and BBa_K1364003.


BBa_K1364013: Strong, constitutive promotor of B. subtilis Pveg (K823003) + RBS, GAFP-1, RBS, D4E1 and double terminator (K1364012).

Design:
This part is designed for the co-expression of two different peptides with anti-fungal activities : D4E1 and GAFP-1. It is composed of the strong, constitutive promotor of B. subtilis Pveg (K823003) and the translation unit with GAFP-1 and D4E1 (BBa_K1364012).

Type
Expression cassette

Tests


References
See BBa_K1364002 and BBa_K1364003.


BBa_K1364014: Promotor Pveg RBS spoVG, EcAMP-1 (BBa_K1364010) + RBS, GAFP-1, RBS, D4E1 and double terminator (BBa_K1364012)

Design:
This part contains the three fungicides on the same operon. It is composed of the composite part with EcAMP--1 (BBa_K1364010) and the translation unit with GAFP-1 and D4E1 (BBa_K1364012).

Type
??

Tests


References
See BBa_K1364010, BBa_K1364002 and BBa_K1364003.


Used parts


BioBrick Description Origine Module(s)
K733013 Pveg (K316001) + RBS-SpoVG (K143021) : Constitutive promotor Pveg and strong RBS for B. subtilis 2014 Kit plate 1, 7H Fungicides (EcAMP)
K823003 Pveg : strong, constitutive promotor of B. subtilis 2014 Kit plate 1, 20G Fungicides (D4E1 GAFP-1)
Chemotaxis
Binding
K823002 PlepA : constitutive promotor of B. subtilis.
It is the promotor of the lepA gene of B. subtilis		 2014 Kit plate 1, 20E Fungicides (D4E1)
Chemotaxis
Binding
K606061 SpoVG RBS for B. subtilis
Strong ribosome binding site from subtilis. Works fine in E. coli		 2014 Kit plate 1, 15A Optional
K316027 B. subtilis transformation vector with LacI, targets amyE locus. 2014 Kit plate 1, 2N Fungicides
Chemotaxis
Binding
B0015 Double terminator (BBa_B0010 + BBa_B0012) 2014 Kit plate 3, 3F Fungicides (GAFP-1, EcAMP-1)
K780000 Terminator for B. subtilis Sent by the Warsaw iGEM team
K780001 Strong RBS for B. subtilis Sent by the Warsaw iGEM team
K780002 Strong RBS for B. subtilis Sent by the Warsaw iGEM team
K780003 Strong constitutive promotor for B. subtilis Sent by the Warsaw iGEM team Fungicides
Chemotaxis
Binding
K1162001 EcAMP-1 Sent by the Utah State iGEM team Fungicides (EcAMP-1)
K823023 Empty backbone vector pSBBS1C for integration into B. subtilis
It integrates in the amyE locus		 Sent by the Munich iGEM team Fungicides
Chemotaxis
Binding
K823022 Empty backbone vector pSBBS4S for integration intoB. subtilis
It integrates in the thrC locus		 Sent by the Munich iGEM team Fungicides
Chemotaxis
Binding
K823021 Reporter vector pSBBS1C-lacZ for B. subtilis Sent by the Munich iGEM team Fungicides
Chemotaxis
Binding


Other parts


Retrieved from "http://2014.igem.org/Team:Toulouse/Parts"