Team:Groningen/Project/SilkAssemblyShop

From 2013.igem.org

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<h2>This is so awesome</h2>
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<h2><i>Bacillus subtilis</i> silk genes collection derived from <i>Argiope aurantia</i> MaSp2</h2>
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<p>
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One of the challenges that the project includes is the production of spider silk. In order to achieve this goal iGEM Groningen designed for you what we call “<b>The <i>Bacillus subtilis</i> silk assembly shop</b>”.
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<br>The 'shop' idea follows those conceptual steps:
 +
<ol><li>Design your own silk protein</li>
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<li>Browse the iGEM Groningen silk subunits collection:</li>
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<div align="center">  <!--you can use left/right or center to align the image-->
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<table  id="normal" width=60%> <!--change the percentage to determine the size of your image-->
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<tr>
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<th rowspan="2">Spider silk <br> subunit</th>
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<th rowspan="2">Biobrick id</hd>
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<th colspan ="3">Construct Features</th>
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</tr>
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<tr>
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<th>RBS</th>
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<th>Strep-tag</th>
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<th>Stop codon</th>
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</tr>
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<tr>
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<th rowspan="2">E1</th>
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<td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1085000">BBa_K1085000</a></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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<td></td>
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</tr>
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<tr>
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<td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1085001">BBa_K1085001</a></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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<td></td>
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<td></td>
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</tr>
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<tr>
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<th rowspan="2">E2</th>
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<td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1085002">BBa_K1085002</a></td>
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<td></td>
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<td></td>
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<td></td>
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</tr>
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<tr>
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<td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1085003">BBa_K1085003</a></td>
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<td></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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<td></td>
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</tr>
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<tr>
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<th rowspan="2">Tail</th>
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<td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1085008">BBa_K1085008</a></td>
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<td></td>
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<td></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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</tr>
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<tr>
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<td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1085009">BBa_K1085009</a></td>
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<td></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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<td></html>[[File:Green_tick.gif | 25px]]<html></td>
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</tr>
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<tr>
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<td colspan="5"><font size="1">table 1: The following silk subunits are: E1 blabla , E2 blabla and Tail blabla.</font></td>
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</tr>
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</table>
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</div>
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<li>Select the subunits you need</li>
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<li>Assemble them together</li></ol>
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At this point the silk product is ready to be produced (<a href="">See production backbone</a>) and employed for the desired purpose.
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</p>
<p>
<p>
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This is so awesome
+
The Groningen team enriched the iGEM database adding several new <i>Bacillus subtilis</i> BioBricks containing spider silk gene subunits. This provides the iGEM community with a new bunch of parts; which, in the future, will help anyone in assembling its own silk protein and customize it with different features.
 +
<br>It is the first time that silk-coding BioBricks suitable for <i>Bacillus subtilis</i> are introduced into the database. Therefore this work marks the starting point for further studies about silk within the <i>Bacillus subtilis</i> chassis inside the iGEM framework.
</p>
</p>
 +
 +
<p>
 +
The advantages shown by our collection are mainly two which can be summarized as follows:
 +
<ol><li><b>Accessible design</b>
 +
The iGEM database provides a lot of basic parts (such as RBS and terminator), but often achieving the desired goal turns out to be really tedious and time consuming, since the creation of a working construct needs to go through a lot of steps. iGEM Groningen took into account this problematic aspect while designing the silk collection, therefore all the silk subunits (each of them coding for the same final protein product) have been created in different versions (see Table 1). Such a design enables the end-user to quickly reach the desired silk protein construct without bothering too much about the molecular issues. This kind of approach helps to make synthetic biology and specifically working with silk protein in <i>Bacilus subtilis</i> production more accessible.</li>
 +
<li><b>Compatibility with BioBrick standards</b>
 +
We are aware that the BioBrick assembly standard is the foundation of the iGEM method, allowing all different laboratories to build on each others work. That is why the silk subunits are compatible with the following standard:
 +
<ul><li>BBF RFC 10</li>
 +
<li>BBF RFC 12</li>
 +
<li>BBF RFC 21</li>
 +
<li>BBF RFC 23</li>
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<li>BBF RFC 25</li>
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<li>BBF RFC 1000</li>
 +
</ul>
 +
<li><b>dealing with repetitiveness</b>
 +
One of the issue while working with the silk protein is the high repetitiveness of the coding sequence. The subunit concept provides us with a smart solution; indeed the molecular steps do not depend anymore on the silk coding sequence itself, but on the universal flanking regions. This
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</li>
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</li>
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</ol>
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</p>
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 +
<!--
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<p>
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The aim of the molecular genetic design is to create a handy toolbox in order to produce any desired combination of silk-like genes which can be expressed in <i>Bacillus subtilis</i> for several purposes. Everything is designed within the RFC[23] standard framework. This enables the user to join together all the different parts creating in-frame fusion silk-like proteins.
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</p>
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-->
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<!--
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<br>What kind of spider silk gene is it
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<br>What are general problems with this gene
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<br>Where did we get it from.
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<br>Codon optimisation, solved the problems.
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-->
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<br>
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<h2>Strep-tag</h2>
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<br>Why this is needed
 +
<br>For what purposes it comes in handy
 +
<br>
 +
<h2>Signal peptide</h2>
 +
<br>Why is it so important.
 +
<br> The use of existing pathway so not lots of trouble
 +
<br>The signal sequences are nice addition to the registry
 +
<br> how the pathway works and how the silk will be secreted
<br>
<br>
</html>
</html>

Revision as of 10:37, 3 October 2013

Silk Assembly Shop

Bacillus subtilis silk genes collection derived from Argiope aurantia MaSp2

One of the challenges that the project includes is the production of spider silk. In order to achieve this goal iGEM Groningen designed for you what we call “The Bacillus subtilis silk assembly shop”.
The 'shop' idea follows those conceptual steps:

  1. Design your own silk protein
  2. Browse the iGEM Groningen silk subunits collection:
    3. Spider silk
    subunit    		 Biobrick id Construct Features
    RBS Strep-tag Stop codon
    E1 BBa_K1085000 25px 25px
    BBa_K1085001 25px
    E2 BBa_K1085002
    BBa_K1085003 25px
    Tail BBa_K1085008 25px
    BBa_K1085009 25px 25px
    table 1: The following silk subunits are: E1 blabla , E2 blabla and Tail blabla.
  3. Select the subunits you need
  4. Assemble them together
At this point the silk product is ready to be produced (See production backbone) and employed for the desired purpose.

The Groningen team enriched the iGEM database adding several new Bacillus subtilis BioBricks containing spider silk gene subunits. This provides the iGEM community with a new bunch of parts; which, in the future, will help anyone in assembling its own silk protein and customize it with different features.
It is the first time that silk-coding BioBricks suitable for Bacillus subtilis are introduced into the database. Therefore this work marks the starting point for further studies about silk within the Bacillus subtilis chassis inside the iGEM framework.

The advantages shown by our collection are mainly two which can be summarized as follows:

  1. Accessible design The iGEM database provides a lot of basic parts (such as RBS and terminator), but often achieving the desired goal turns out to be really tedious and time consuming, since the creation of a working construct needs to go through a lot of steps. iGEM Groningen took into account this problematic aspect while designing the silk collection, therefore all the silk subunits (each of them coding for the same final protein product) have been created in different versions (see Table 1). Such a design enables the end-user to quickly reach the desired silk protein construct without bothering too much about the molecular issues. This kind of approach helps to make synthetic biology and specifically working with silk protein in Bacilus subtilis production more accessible.
  2. Compatibility with BioBrick standards We are aware that the BioBrick assembly standard is the foundation of the iGEM method, allowing all different laboratories to build on each others work. That is why the silk subunits are compatible with the following standard:
    • BBF RFC 10
    • BBF RFC 12
    • BBF RFC 21
    • BBF RFC 23
    • BBF RFC 25
    • BBF RFC 1000
  3. dealing with repetitiveness One of the issue while working with the silk protein is the high repetitiveness of the coding sequence. The subunit concept provides us with a smart solution; indeed the molecular steps do not depend anymore on the silk coding sequence itself, but on the universal flanking regions. This


Strep-tag


Why this is needed
For what purposes it comes in handy

Signal peptide


Why is it so important.
The use of existing pathway so not lots of trouble
The signal sequences are nice addition to the registry
how the pathway works and how the silk will be secreted

Retrieved from "http://2013.igem.org/Team:Groningen/Project/SilkAssemblyShop"