Team:Bordeaux/Parts

From 2014.igem.org

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We decided to provide the registry with just a few parts but as documented as possible (in terms either of experiment or design and literature). These parts encode  proteins based on consensus sequences of natural proteins. They are synthetic proteins (not existing in nature), used in a context of "white biotechnology" as biomaterials with specific properties unravelled from the nature.
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[[File:Bdx2014 resilin 2.jpg|center|300px]]<br>
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[https://2014.igem.org/Team:Bordeaux/Parts/BBa_K1317001 BBa_K1317001]<br>
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This part is the coding sequence for the resilin like polypeptide. This sequence was assembled from a consensus of the proresilin exon 1 from Drosophila melanogaster. This protein, in insects, allows resistance and elasticity used for jumping, flapping... The synthetic gene encodes a synthetic protein "resilin-like". The repeated aminoacids allow to retrieve these properties of resistance, resilience and elasticity, but with a minimal pattern of the original protein, which is more suited for downstream applications. It can be used to produce wire presenting these properties after wet-spinning.<br><br>
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[[File:Bdx2014 spider.jpg|center|300px]]<br>
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[https://2014.igem.org/Team:Bordeaux/Parts/BBa_K1317002 BBa_K1317002]<br>
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This part is the coding sequence for the silk like polypeptide. This sequence was assembled from a consensus of the MaSp1 from spiders. This protein, in spiders, allows resistance and elasticity used for spinning the webs. The synthetic gene encodes a synthetic protein "silk-like". The repeated aminoacids allow to retrieve these properties of resistance, resilience and elasticity, but with a minimal pattern of the original protein, which is more suited for downstream applications. It can be used to produce wire presenting these properties after wet-spinning.<br> <br>
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[[File:Bdx2014 elastin.jpg|center|300px]]<br>
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[https://2014.igem.org/Team:Bordeaux/Parts/BBa_K1317003 BBa_K1317003]<br>
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This part is made with a consensus of the natural elastin sequence. Elastin is a protein involved in maintaining shape and elasticity of several tissues like skin. It has a high elasticity and resilience as a polymer.
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In our project, the consensus sequence allows the use of a minimal pattern of the protein while keeping these particular properties. In an iGEM spirit the consensus itself can be used as a brick to vary length and nature of the polymers with our other biobricks (BBa_K1317001, BBa_K1317002).
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The basic length of a polymer is 20 monomers. The coding sequence can be repeated easily using our improvement of the biobrick assembly system to get rid of the Stop Codon. After variation of the length different properties are attributed to the part. For example it can be used as a fusion tag to purify easily any fuse protein thanks to the thermal cycling purification.
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ELP indeed have this particularity to solubilize at lower temperature. If it is used in a protein mixture (a lysate for example) after a few cycles of thermal cycling (from 4°C to 50°C), the pure fuse protein is obtained.
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This part can be used as a purification tag for easy, quick and column-free purification or as coding sequence for a polymer usable to get fiber with good elasticity and resilience. The polymer is biocompatible, biodegradable and could be used as a tool for surgery or other health applications.<br><br>
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<b>The part provided to the registry encodes for ELP20. Throughout all the experiments, if two copies are used it will be ELP40, and if three copies are used it will be ELP60.</b> <br> <br>
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[https://2014.igem.org/Team:Bordeaux/Parts/BBa_K1317004 BBa_K1317004]<br>
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The ELP presents specific properties: it precipitates at high temperature. This property can be used for thermal cycling purification for instance. By successive cycles of temperature, ELP can be purified from a mix of proteins. This special property has been used to create a composite part for the iGEM registry. It is a proof of concept of the use of this part as a tool for protein purification by fusing ELP to another protein. The protein used as an example is RFP, to ease vizualisation of the process.<br> <br>
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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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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Bordeaux/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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[https://2014.igem.org/Team:Bordeaux/Parts/Assembly_improvement Improvement of the Biobrick standard assembly]<br>
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In order to get rid of the stop codon in a coding sequence, to fuse properly proteins, we proposed an improvement of the assembly system by using the restriction site NheI.<br>
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{{:Team:Bordeaux/Pied}}
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<a href="https://2014.igem.org/Team:Bordeaux"style="color:#000000">Home </a> </td>
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<a href="https://2014.igem.org/Team:Bordeaux/Team"style="color:#000000"> Team </a> </td>
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<a href="https://igem.org/Team.cgi?year=2014&team_name=Bordeaux"style="color:#000000"> Official Team Profile </a></td>
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<a href="https://2014.igem.org/Team:Bordeaux/Project"style="color:#000000"> Project</a></td>
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<a href="https://2014.igem.org/Team:Bordeaux/Parts"style="color:#000000"> Parts</a></td>
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<a href="https://2014.igem.org/Team:Bordeaux/Modeling"style="color:#000000"> Modeling</a></td>
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<a href="https://2014.igem.org/Team:Bordeaux/Notebook"style="color:#000000"> Notebook</a></td>
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<a href="https://2014.igem.org/Team:Bordeaux/Safety"style=" color:#000000"> Safety </a></td>
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<a href="https://2014.igem.org/Team:Bordeaux/Attributions"style="color:#000000"> Attributions </a></td>
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<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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<tr><td > <h3> Parts Submitted to the Registry </h3></td>
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<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
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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. 
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<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.
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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.
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<h3>When should you put parts into the Registry?</h3>
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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.
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<td > </td>
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The information needed to initially create a part on the Registry is:
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<li>Part Name</li>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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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.
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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.
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<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
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Any parts your team has created will appear in this table below:</td></tr>
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<groupparts>iGEM013 Bordeaux</groupparts>
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Latest revision as of 03:06, 18 October 2014

We decided to provide the registry with just a few parts but as documented as possible (in terms either of experiment or design and literature). These parts encode proteins based on consensus sequences of natural proteins. They are synthetic proteins (not existing in nature), used in a context of "white biotechnology" as biomaterials with specific properties unravelled from the nature.

Bdx2014 resilin 2.jpg

BBa_K1317001
This part is the coding sequence for the resilin like polypeptide. This sequence was assembled from a consensus of the proresilin exon 1 from Drosophila melanogaster. This protein, in insects, allows resistance and elasticity used for jumping, flapping... The synthetic gene encodes a synthetic protein "resilin-like". The repeated aminoacids allow to retrieve these properties of resistance, resilience and elasticity, but with a minimal pattern of the original protein, which is more suited for downstream applications. It can be used to produce wire presenting these properties after wet-spinning.

Bdx2014 spider.jpg

BBa_K1317002
This part is the coding sequence for the silk like polypeptide. This sequence was assembled from a consensus of the MaSp1 from spiders. This protein, in spiders, allows resistance and elasticity used for spinning the webs. The synthetic gene encodes a synthetic protein "silk-like". The repeated aminoacids allow to retrieve these properties of resistance, resilience and elasticity, but with a minimal pattern of the original protein, which is more suited for downstream applications. It can be used to produce wire presenting these properties after wet-spinning.

Bdx2014 elastin.jpg

BBa_K1317003
This part is made with a consensus of the natural elastin sequence. Elastin is a protein involved in maintaining shape and elasticity of several tissues like skin. It has a high elasticity and resilience as a polymer. In our project, the consensus sequence allows the use of a minimal pattern of the protein while keeping these particular properties. In an iGEM spirit the consensus itself can be used as a brick to vary length and nature of the polymers with our other biobricks (BBa_K1317001, BBa_K1317002). The basic length of a polymer is 20 monomers. The coding sequence can be repeated easily using our improvement of the biobrick assembly system to get rid of the Stop Codon. After variation of the length different properties are attributed to the part. For example it can be used as a fusion tag to purify easily any fuse protein thanks to the thermal cycling purification. ELP indeed have this particularity to solubilize at lower temperature. If it is used in a protein mixture (a lysate for example) after a few cycles of thermal cycling (from 4°C to 50°C), the pure fuse protein is obtained. This part can be used as a purification tag for easy, quick and column-free purification or as coding sequence for a polymer usable to get fiber with good elasticity and resilience. The polymer is biocompatible, biodegradable and could be used as a tool for surgery or other health applications.

The part provided to the registry encodes for ELP20. Throughout all the experiments, if two copies are used it will be ELP40, and if three copies are used it will be ELP60.

BBa_K1317004
The ELP presents specific properties: it precipitates at high temperature. This property can be used for thermal cycling purification for instance. By successive cycles of temperature, ELP can be purified from a mix of proteins. This special property has been used to create a composite part for the iGEM registry. It is a proof of concept of the use of this part as a tool for protein purification by fusing ELP to another protein. The protein used as an example is RFP, to ease vizualisation of the process.

Improvement of the Biobrick standard assembly
In order to get rid of the stop codon in a coding sequence, to fuse properly proteins, we proposed an improvement of the assembly system by using the restriction site NheI.

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