(53 intermediate revisions by 6 users not shown) | |||
Line 1: | Line 1: | ||
{{TU_Darmstadt}}{{TU_Darmstadt/Bootstrap}}{{TU_Darmstadt/CSS}}{{TU_Darmstadt/Homepage/SVG_HEADER}}{{TU_Darmstadt/NavBar}}{{TU_Darmstadt/Parts/Banner}}{{TU_Darmstadt/Homeboy}} | {{TU_Darmstadt}}{{TU_Darmstadt/Bootstrap}}{{TU_Darmstadt/CSS}}{{TU_Darmstadt/Homepage/SVG_HEADER}}{{TU_Darmstadt/NavBar}}{{TU_Darmstadt/Parts/Banner}}{{TU_Darmstadt/Homeboy}} | ||
+ | |||
+ | |||
+ | |||
+ | |||
<html> | <html> | ||
<div class="container-fluid"> | <div class="container-fluid"> | ||
Line 6: | Line 10: | ||
<div class="sidenav"> | <div class="sidenav"> | ||
− | <a href="# | + | <a href="#Basic_Parts">Basic Parts</a> |
− | <a href="# | + | <a href="#Composite_Parts">Composite Parts</a> |
− | <a href="# | + | <a href="#Registry_Parts">Registry Parts</a> |
− | + | ||
− | + | ||
</div> | </div> | ||
</div> | </div> | ||
Line 16: | Line 18: | ||
<div class="col-lg-12 col-xl-8"> | <div class="col-lg-12 col-xl-8"> | ||
+ | <a class="anchor" id="scroll"></a> | ||
<br> | <br> | ||
<div class="TFcontainer"> | <div class="TFcontainer"> | ||
<div class="containertext" id=Chapter1 > | <div class="containertext" id=Chapter1 > | ||
− | <b>Due to | + | <b>Due to COVID-19 </b> we were <b> not able to test </b> any of our designed parts in the lab. Nevertheless, we registered our basic parts, so <b> future teams </b> are easily able to characterize them. For our <b> Composite Parts we only uploaded one</b> for which we can provide modeling data. We refrained from uploading the others to the registry as there exists no primary literature on them, but we still provide schematic images on them. We did not submit any parts for the special prizes Best Basic Part and Best Composite Part. Parts we submit for the <b>medal criterion contribution</b> are also marked with <b>this symbol:</b> ♥. |
</div> | </div> | ||
</div> | </div> | ||
− | < | + | <a class="anchor" id="Basic_Parts"></a> |
+ | <h2>Basic Parts</h2> | ||
+ | <div class="headlinebar"> | ||
+ | </div> | ||
<div class="TFcontainer"> | <div class="TFcontainer"> | ||
− | <div class="containertext" | + | <div class="containertext"> |
− | <b> | + | |
− | + | All <b>basic parts</b> we implemented into the design of our constructs are listed in the table below. | |
− | + | ||
</div> | </div> | ||
</div> | </div> | ||
Line 42: | Line 47: | ||
<tr> | <tr> | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429000" target="_blank">BBa_K3429000</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429000" target="_blank">BBa_K3429000</a></th> | ||
− | <td> | + | <td>Promoter</td> |
− | <td> | + | <td>P<sub><i>grac</sub></i> promoter</td> |
<td>170</td> | <td>170</td> | ||
</tr> | </tr> | ||
Line 55: | Line 60: | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429002" target="_blank">BBa_K3429002</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429002" target="_blank">BBa_K3429002</a></th> | ||
<td>Coding Sequence</td> | <td>Coding Sequence</td> | ||
− | <td> | + | <td>Superfolder Green Fluorescent Protein (sfGFP)</td> |
<td>712</td> | <td>712</td> | ||
</tr> | </tr> | ||
Line 61: | Line 66: | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429003" target="_blank">BBa_K3429003</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429003" target="_blank">BBa_K3429003</a></th> | ||
<td>Coding Sequence</td> | <td>Coding Sequence</td> | ||
− | <td>Protein Linker for fusion proteins | + | <td>Protein Linker for fusion proteins: ARGGGGSGGGGSGS</td> |
<td>42</td> | <td>42</td> | ||
</tr> | </tr> | ||
Line 67: | Line 72: | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429004" target="_blank">BBa_K3429004</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429004" target="_blank">BBa_K3429004</a></th> | ||
<td>Terminator</td> | <td>Terminator</td> | ||
− | <td>trpA | + | <td><i>trpA</i> terminator</td> |
− | <td>24</td> | + | <td>24</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429005" target="_blank">BBa_K3429005</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429005" target="_blank">BBa_K3429005</a></th> | ||
<td>Coding Sequence</td> | <td>Coding Sequence</td> | ||
− | <td>Ribosomal Protein S2 (rpsB) | + | <td>Ribosomal Protein S2 (rpsB)</i></td> |
<td>721</td> | <td>721</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429006" target="_blank">BBa_K3429006</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429006" target="_blank">BBa_K3429006</a></th> | ||
− | <td> | + | <td>Promoter</td> |
− | <td> | + | <td>P<sub><i>degQ</sub></i> promoter</td> |
<td>192</td> | <td>192</td> | ||
</tr> | </tr> | ||
Line 85: | Line 90: | ||
<td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429007" target="_blank">BBa_K3429007</a></th> | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429007" target="_blank">BBa_K3429007</a></th> | ||
<td>Terminator</td> | <td>Terminator</td> | ||
− | <td> | + | <td><i>degQ</i> terminator</td> |
<td>36</td> | <td>36</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td scope="row"><a href="http://parts.igem.org/Part: | + | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429011" target="_blank">BBa_K3429011</a>♥</th> |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<td>Coding Sequence</td> | <td>Coding Sequence</td> | ||
<td>Laccase CotA</td> | <td>Laccase CotA</td> | ||
Line 107: | Line 100: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429012" target="_blank">BBa_K3429012</a></th> | + | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K3429012" target="_blank">BBa_K3429012</a>♥</th> |
<td>Coding Sequence</td> | <td>Coding Sequence</td> | ||
<td>Blue copper oxidase CueO</td> | <td>Blue copper oxidase CueO</td> | ||
− | <td> | + | <td>1551</td> |
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
− | + | <a class="anchor" id="Composite_Parts"></a> | |
− | < | + | <h2>Composite Parts</h2> |
− | < | + | <div class="headlinebar"> |
+ | </div> | ||
+ | <a class="anchor" id="invitro_Characterization"></a> | ||
+ | <h4> For <i>in vitro</i> Characterization </h4> | ||
<div class="TFcontainer"> | <div class="TFcontainer"> | ||
<div class="containertext" id=Chapter1 > | <div class="containertext" id=Chapter1 > | ||
− | For purification and <a href="https://2020.igem.org/Team:TU_Darmstadt/Project/ | + | For purification and <a href="https://2020.igem.org/Team:TU_Darmstadt/Project/Pharmaceutical_Degradation#Experimentalapproach" target="_blank"><i>in vitro</i> characterization</a> of our enzymes we <b> designed the following Composite Parts </b>: <i>cotA</i>, <i> cueO</i>, and <i> ereB</i>. All of these Composite Parts contain a strep-tag for purification and are optimized for <I> E. coli</I>. |
</div> | </div> | ||
</div> | </div> | ||
<br> | <br> | ||
+ | <div class="containerimg" id=Chapter2> | ||
<figure> | <figure> | ||
− | < | + | <a href="https://static.igem.org/mediawiki/2020/5/58/T--TU_Darmstadt--Composite_Pharmies.png" target="_blank"><img style="width:800px;" src="https://static.igem.org/mediawiki/2020/5/58/T--TU_Darmstadt--Composite_Pharmies.png" alt="figure"></a> |
− | <figcaption id="Figure#">Figure 1: Composite parts for <i> in vitro</i> characterization of our enzymes </figcaption> | + | <figcaption id="Figure#"><b>Figure 1:</b> Composite parts for <i>in vitro</i> characterization of our enzymes. Composite parts formed by T7 promoter, <i>lac</i> operator, the respective enzyme (including purification tag), and T7 terminator. Composite parts would have been introduced into the pET24(+) expression vector.</figcaption> |
</figure> | </figure> | ||
− | + | </div> | |
− | < | + | <a class="anchor" id="Immobilization"></a> |
+ | <h4> For Immobilization on our Biofilm </h4> | ||
+ | <div class="TFcontainer"> | ||
+ | <div class="containertext" id=Chapter1 > | ||
+ | The following parts were designed for immobilization of our enzymes on the <a href="https://2020.igem.org/Team:TU_Darmstadt/Project/Biofilm#Displaying_Enzymes" target="_blank">TasA matrix protein</a> of our <i>B. subtilis </i> biofilm. In these composite parts the <b> enzymes are genetically fused to TasA</b>. We <a href="https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling" target="_blank">modeled</a> the structure of the TasA-EreB fusion protein via MD simulation to see whether the enzyme remains stable (<a href="http://parts.igem.org/Part:BBa_K3429013" target="_blank">BBa_K3429013</a>♥). | ||
+ | </div> | ||
+ | </div> | ||
+ | <br> | ||
+ | <div class="containerimg" id=Chapter2> | ||
+ | <figure> | ||
+ | <a href="https://static.igem.org/mediawiki/2020/1/1d/T--TU_Darmstadt--Composite_Filmies.png" target="_blank"><img style="width:800px;" src="https://static.igem.org/mediawiki/2020/1/1d/T--TU_Darmstadt--Composite_Filmies.png"></a> | ||
+ | <figcaption id="Figure#"><b>Figure 2:</b> Composite parts for immobilization on biofilm matrix. TasA fusion proteins are flanked by the P<sub>grac</sub> promoter, <i>lacO</i> operator, and <i>trpA</i> terminator. Composite parts would have been introduced into the pSEVA3b67Rb shuttle vector.</figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | <a class="anchor" id="Kill_Switch"></a> | ||
+ | <h4> For our Kill Switch </h4> | ||
<div class="TFcontainer"> | <div class="TFcontainer"> | ||
<div class="containertext" id=Chapter1 > | <div class="containertext" id=Chapter1 > | ||
− | + | For our <a href="https://2020.igem.org/Team:TU_Darmstadt/Project/Kill_Switch#FinalKillSwitch" target="_blank">kill switch</a>, we combined already <a href="#Registry_Parts">existing iGEM parts</a> with genetic elements of the <i> B. subtilis</i> <a href="https://2020.igem.org/Team:TU_Darmstadt/Background#Quorum%20Sensing" target="_blank">quorum sensing system</a>. Thus, generating a novel kill switch variant. | |
</div> | </div> | ||
</div> | </div> | ||
<br> | <br> | ||
<div class="containerimg" id=Chapter2> | <div class="containerimg" id=Chapter2> | ||
− | + | <figure> | |
− | + | <a href="https://static.igem.org/mediawiki/2020/4/46/T--TU_Darmstadt--Switchies_Part.svg" target="_blank"><img style="width:800px;" src="https://static.igem.org/mediawiki/2020/4/46/T--TU_Darmstadt--Switchies_Part.svg"></a> | |
− | <figcaption id="Figure#">Figure | + | <figcaption id="Figure#"><b>Figure 3: </b> Composite parts for the kill switch. The essential gene rpsB is under control of the Pveg or PdegQ promoter. Because of the orientation of the lox 66 and lox 71 recombination sites, the sequence between them can be inverted by the Cre recombinase. The gene for the Cre recombinase is under control of the xylose induced PxylA promoter.</figcaption> |
</figure> | </figure> | ||
</div> | </div> | ||
− | < | + | <a class="anchor" id="Registry_Parts"></a> |
− | < | + | <h2>Registry Parts</h2> |
− | + | <div class="headlinebar"> | |
− | + | </div> | |
− | < | + | |
<br> | <br> | ||
<div class="TFcontainer"> | <div class="TFcontainer"> | ||
− | <div class="containertext" | + | <div class="containertext">For our project design we <b>took advantage of the iGEM registry</b> and took several parts from it. The parts are listed in the table below. For the well characterized part <a href="http://parts.igem.org/Part:BBa_K1159000" target="_blank">BBa_K1159000</a> from iGEM TU Munich 2013 we <b>generated the missing <a href="https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#EreB_CM" target="_blank">modelling data</a></b>. For <a href="http://parts.igem.org/Part:BBa_K1680007" target="_blank"> BBa_K1680007</a> we provide <b>further literature information</b>. |
− | + | ||
</div> | </div> | ||
</div> | </div> | ||
+ | |||
Line 163: | Line 174: | ||
<th scope="col">Description</th> | <th scope="col">Description</th> | ||
<th scope="col">Length in bp</th> | <th scope="col">Length in bp</th> | ||
+ | <th scope="col">Part created by</th> | ||
</tr> | </tr> | ||
</thead> | </thead> | ||
<tbody> | <tbody> | ||
− | + | <tr> | |
− | + | <td scope="row"><a href=" http://parts.igem.org/Part:BBa_K733002" target="_blank"> BBa_K733002</a></th> | |
− | <td></td> | + | <td> Promoter </td> |
− | <td></td> | + | <td> P<sub><i>XylA</sub></i> promoter </td> |
− | <td></td> | + | <td>1387</td> |
+ | <td> iGEM HKUST Hong Kong 2012</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td scope="row"><a href="" target="_blank"></a></th> | + | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K823003" target="_blank"> BBa_K823003</a></th> |
− | <td></td> | + | <td> Promoter </td> |
− | <td></td> | + | <td>P</i><sub>veg</sub></i> promoter</td> |
− | <td></td> | + | <td>237</td> |
+ | <td> iGEM LMU Munich 2012</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K1680007" target="_blank">BBa_K1680007</a>♥</th> | ||
+ | <td>Coding Sequence</td> | ||
+ | <td>Cre recombinase</td> | ||
+ | <td>1029</td> | ||
+ | <td>iGEM Tuebingen 2015</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td scope="row"><a href="" target="_blank"></a></th> | + | <td scope="row"><a href="http://parts.igem.org/Part:BBa_I718016" target="_blank">BBa_I718016</a></th> |
− | <td></td> | + | <td>Recombination Site</td> |
− | <td></td> | + | <td>lox66 site</td> |
− | <td></td> | + | <td>34</td> |
+ | <td>iGEM Paris 2007</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td scope="row"><a href="" target="_blank"></a></th> | + | <td scope="row"><a href="http://parts.igem.org/Part:BBa_I718017" target="_blank">BBa_I718017</a></th> |
− | <td></td> | + | <td>Recombination Site</td> |
− | <td></td> | + | <td>lox71 site</td> |
− | <td></td> | + | <td>34</td> |
+ | <td>iGEM Paris 2007</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td scope="row"><a href="http://parts.igem.org/Part:BBa_K1159000" target="_blank">BBa_K1159000</a>♥ </th> | ||
+ | <td>Coding Sequence</td> | ||
+ | <td>Erythromycin Esterase Type II (EreB) in RFC[25]</td> | ||
+ | <td>1254</td> | ||
+ | <td>iGEM TU Munich 2013</td> | ||
</tr> | </tr> | ||
</tbody> | </tbody> | ||
Line 196: | Line 226: | ||
</div> | </div> | ||
</html> | </html> | ||
+ | |||
+ | |||
+ | |||
+ | |||
{{TU_Darmstadt/Footer}} | {{TU_Darmstadt/Footer}} |
Latest revision as of 13:24, 26 October 2020
Due to COVID-19 we were not able to test any of our designed parts in the lab. Nevertheless, we registered our basic parts, so future teams are easily able to characterize them. For our Composite Parts we only uploaded one for which we can provide modeling data. We refrained from uploading the others to the registry as there exists no primary literature on them, but we still provide schematic images on them. We did not submit any parts for the special prizes Best Basic Part and Best Composite Part. Parts we submit for the medal criterion contribution are also marked with this symbol: ♥.
Basic Parts
All basic parts we implemented into the design of our constructs are listed in the table below.
Part(BBa_) | Type | Description | Length in bp |
---|---|---|---|
BBa_K3429000 | Promoter | Pgrac promoter | 170 |
BBa_K3429001 | Coding Sequence | TasA matrix protein | 783 |
BBa_K3429002 | Coding Sequence | Superfolder Green Fluorescent Protein (sfGFP) | 712 |
BBa_K3429003 | Coding Sequence | Protein Linker for fusion proteins: ARGGGGSGGGGSGS | 42 |
BBa_K3429004 | Terminator | trpA terminator | 24 |
BBa_K3429005 | Coding Sequence | Ribosomal Protein S2 (rpsB) | 721 |
BBa_K3429006 | Promoter | PdegQ promoter | 192 |
BBa_K3429007 | Terminator | degQ terminator | 36 |
BBa_K3429011♥ | Coding Sequence | Laccase CotA | 1542 |
BBa_K3429012♥ | Coding Sequence | Blue copper oxidase CueO | 1551 |
Composite Parts
For in vitro Characterization
For purification and in vitro characterization of our enzymes we designed the following Composite Parts : cotA, cueO, and ereB. All of these Composite Parts contain a strep-tag for purification and are optimized for E. coli.
For Immobilization on our Biofilm
The following parts were designed for immobilization of our enzymes on the TasA matrix protein of our B. subtilis biofilm. In these composite parts the enzymes are genetically fused to TasA. We modeled the structure of the TasA-EreB fusion protein via MD simulation to see whether the enzyme remains stable (BBa_K3429013♥).
For our Kill Switch
For our kill switch, we combined already existing iGEM parts with genetic elements of the B. subtilis quorum sensing system. Thus, generating a novel kill switch variant.
Registry Parts
For our project design we took advantage of the iGEM registry and took several parts from it. The parts are listed in the table below. For the well characterized part BBa_K1159000 from iGEM TU Munich 2013 we generated the missing modelling data. For BBa_K1680007 we provide further literature information.
Part(BBa_) | Type | Description | Length in bp | Part created by |
---|---|---|---|---|
BBa_K733002 | Promoter | PXylA promoter | 1387 | iGEM HKUST Hong Kong 2012 |
BBa_K823003 | Promoter | Pveg promoter | 237 | iGEM LMU Munich 2012 |
BBa_K1680007♥ | Coding Sequence | Cre recombinase | 1029 | iGEM Tuebingen 2015 |
BBa_I718016 | Recombination Site | lox66 site | 34 | iGEM Paris 2007 |
BBa_I718017 | Recombination Site | lox71 site | 34 | iGEM Paris 2007 |
BBa_K1159000♥ | Coding Sequence | Erythromycin Esterase Type II (EreB) in RFC[25] | 1254 | iGEM TU Munich 2013 |