Difference between revisions of "Team:Peking/Basic Part"

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                    <div id="logo" style="max-width:0px"><a class="" href="https://2018.igem.org/Team:Peking"><img
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                    src="https://static.igem.org/mediawiki/2018/3/36/T--Peking--Logo.png"></a></div>
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                        <ul class="nav">                          
  
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                            <li class="menu-1"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking">Home</a>
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                            </li>
  
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<div class="column full_size judges-will-not-evaluate">
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                            <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Project</a>
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<h3>★  ALERT! </h3>
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                                <ul class="dropdown-menu">
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Project" class="barfont1">Description</a></li>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Design" class="barfont1">Design</a></li>
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</div>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Demonstrate" class="barfont1">Demonstration</a></li>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Perspective" class="barfont1">Perspective</a></li>
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                                </ul>
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                            </li>
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                            <li class="menu-3"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Model">Modeling</a>
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                            </li>
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                            <li class="menu-4"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Software">Software</a>
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                            </li>
  
  
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<div class="clear"></div>
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                            <li class="menu-6"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Human_Practices">Human Practices</a>
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                            </li>
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                                <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Achievement</a>
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                                    <ul class="dropdown-menu">
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<div class="column full_size">
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                                        <li><a href="https://2018.igem.org/Team:Peking/Judging_Form" class="barfont1">Judging Form</a></li>
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<h1>Basic Parts</h1>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Parts" class="barfont1">Parts</a></li>
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<p>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Improve" class="barfont1">Improvement</a></li>
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A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
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                                        <li><a href="https://2018.igem.org/Team:Peking/InterLab" class="barfont1">InterLab</a></li>
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</p>
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
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</div>
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<div class="column full_size">
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<div class="highlight decoration_background">
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<h3>Note</h3>
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<p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Basic Part award, so put your best part first!</p>
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</div>
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</div>
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<div class="column full_size">
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<h3>Best Basic Part Special Prize</h3>
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<p> To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2018.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
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<br><br>
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<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
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</div>
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                                    </ul>
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                                </li>
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                                <li class="dropdown menu-8"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Lab</a>
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                                    <ul class="dropdown-menu">
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                                        <li><a href="https://2018.igem.org/Team:Peking/Team_Members">Team Members</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Attributions" class="barfont1">Attributions</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Notebook" class="barfont1">Notebook</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Collaborations" class="barfont1">Collaborations</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Safety" class="barfont1">Safety</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Acknowledgement" class="barfont1">Acknowledgement</a></li>
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                                    </ul>
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                                </li>
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                                </div>
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                </div>
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        </div>
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        <!--/Navigation -->
  
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        <!-- Page Title======================================================================== -->
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        <div id="page-title">
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            <div class="row">
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                <div class="twelve columns centered text-center">
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                    <h1>Parts</h1>
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                    <p class="title1" style="text-align:center"></p>
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                </div>
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            </div>
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        </div>
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        <!-- Page Title End-->
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        <div id="page-content" class="row page">
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            <div id="primary" class="twelve columns">
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                <section>
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                    <div class="row">
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                            <div id="page-wrap">
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                                <div id="sidebar" style="color:#000000">
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                                    <h4><a href="https://2018.igem.org/Team:Peking/Part_Collection">Part&nbsp;Collection</a></h4>
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                                    <h4><a href="https://2018.igem.org/Team:Peking/Basic_Part">Basic&nbsp;Part</a></h4>
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                                    <h4><a href="https://2018.igem.org/Team:Peking/Composite_Part">Composite&nbsp;Part</a></h4>
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                                </div>
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                            </div>
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                        </div>
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                        <div class="nine columns">
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                            <div class="texttitle"><a id="favor"></a>Favorite Parts</div>
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                            <h3 class="classic-title">Schematic diagram</h3>
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                            <hr style="border:2px dashed; height:2px" color="#666666">
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                            <figure>
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                                <p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2018/d/df/T--Peking--parts0.png" alt=""/></p>
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                                <figcaption style="text-align:center;">
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                                    Figure. 1 Schematic diagram of most parts submitted by Peking iGEM 2018.
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                                </figcaption>
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                            </figure>
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                            <h3 class="classic-title"><a href="http://parts.igem.org/Part:BBa_K2601010">BBa_K2601010</a></h3>
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                            <hr style="border:2px dashed; height:2px" color="#666666">
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                            <figure>
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                                <p style="text-align:center;"><img src=" https://static.igem.org/mediawiki/2018/1/1f/T--Peking--parts1.png" alt=""/></p>
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                                <figcaption style="text-align:center;">
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                                  Figure. 2 Schematic diagram of BBa_K2601010
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                                </figcaption>
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                            </figure>
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                            <p class="lead add-bottom" style="color:#5E5656">We combined Frb, yEGFP and HOTag6 togethor in <a href="http://parts.igem.org/Part:BBa_K2601010">BBa_K2601010</a>. Frb can interact with FKBP after adding rapamycin, which makes the RapaSPOT formation controllable. We constructed yeast strains with FKBP-mCherry-HOTag3 and Frb-yEGFP-HOTag6 and used 10 μM rapamycin to induce SPOT formation. Minutes after adding rapamycin, granules appeared and became larger gradually.</p>
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                            <br/>
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<h3 class="classic-title"><a href="http://parts.igem.org/Part:BBa_K2601011">BBa_K2601011</a></h3>
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                            <hr style="border:2px dashed; height:2px" color="#666666">
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                            <figure>
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                                <p style="text-align:center;"><div align="center"><img src=" https://static.igem.org/mediawiki/2018/8/87/T--Peking--parts2.jpeg" alt=""/></p></div>
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                                <figcaption style="text-align:center;">
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                                    Figure. 3 Schematic diagram of BBa_K2601011
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                                </figcaption>
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                            </figure>
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                            <p class="lead add-bottom" style="color:#5E5656">To make our SPOT a reaction hub, we fused the enzymes of β-carotene synthase system, CrtI, CrtE and CrtYB into Frb-HOTag6 backbone. In the presence of rapamycin, FKBP-yEGFP-HOTag3 and Frb-enzyme-HOTag6 can condense into aggregates. And if the yeast contains SPOT, there will be more β-carotene producted. Meanwhile, we wondered if we can load enzymes onto SPOT mediated by indirected connection. We fused CFP to anti-GFP nanobody as the demonstration of our design and we observed the co-localization of the blue and green fluorescence as expected.  </p>
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                            <br/>
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                            <h3 class="classic-title"><a href="http://parts.igem.org/Part:BBa_K2601012">BBa_K2601012</a></h3>
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                            <hr style="border:2px dashed; height:2px" color="#666666">
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                            <figure>
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                                <div align="center"><p style="text-align:center;"><img  src="https://static.igem.org/mediawiki/2018/3/36/T--Peking--parts3.png" alt=""/></p></div>
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                                <figcaption style="text-align:center;">
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                                    Figure. 4 Schematic diagram of BBa_K2601012.
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                                </figcaption>
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                            </figure>
 +
                            <p class="lead add-bottom" style="color:#5E5656">In the biobrick  <a href="http://parts.igem.org/Part:BBa_K2601012">BBa_K2601012</a>, we fused SUMO, yEGFP and HOTag3 together. SUMO is the interaction module which can bind SIM spontaneously, while HOTag3 can introduce multivalence. These two features are necessary for SPOT formation. We expressed SUMO-yEGFP-HOTag3 and SIM-mCherry-HOTag6 in one yeast strain, and we observed the colocalization of yEGFP and mCherry in two different fluorescence channels, which confirms our hypothesis that the two components could form synthetic organelles. </p>
 +
                           
 +
                           
 +
                           
 +
                         
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                            <br/>
 +
                            <a id="table"></a>
 +
                            <div class="texttitle">Part Table</div>
 +
                           
 +
                            <div class="highlight" align="center" >
 +
                              <table cellpadding="3" cellspacing="0" style="width: 60%;margin:auto">
 +
<tr>
 +
<td width="30%">BBa_</td>
 +
<td align="right">Part</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601000">K2601000</a></td>
 +
<td align="right">Promoter-tet07</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601001">K2601001</a></td>
 +
<td align="right">Promoter-PDH3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601002">K2601002</a></td>
 +
<td align="right">SUMO</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601003">K2601003</a></td>
 +
<td align="right">SIM</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601004">K2601004</a></td>
 +
<td align="right">HOTag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601005">K2601005</a></td>
 +
<td align="right">HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601007">K2601007</a></td>
 +
<td align="right">Frb-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601008">K2601008</a></td>
 +
<td width="570%" align="right">FKBP-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601010">K2601010</a></td>
 +
<td align="right">Frb-yEGFP-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601011">K2601011</a></td>
 +
<td align="right">FKBP-yEGFP-HOTag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601012">K2601012</a></td>
 +
<td align="right">SUMO-yEGFP-HOtag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601021">K2601021</a></td>
 +
<td align="right">Tet07-Frb-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601023">K2601023</a></td>
 +
<td align="right">PDH3-Frb-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601025">K2601025</a></td>
 +
<td align="right">Tet07-FKBP-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601026">K2601026</a></td>
 +
<td align="right">TEF1-FKBP-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601027">K2601027</a></td>
 +
<td align="right">PDH3-FKBP-yEGFP</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601032">K2601032</a></td>
 +
<td align="right">Tet07-Frb-yEGFP-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601033">K2601033</a></td>
 +
<td align="right">TEF1-Frb-yEGFP-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601034">K2601034</a></td>
 +
<td align="right">PDH3-Frb-yEGFP-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601037">K2601037</a></td>
 +
<td align="right">TEF1-FKBP-yEGFP-HOTag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601038">K2601038</a></td>
 +
<td align="right">PDH3-FKBP-yEGFP-HOTag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601040">K2601040</a></td>
 +
<td align="right">Tet07-SUMO-yEGFP-HOtag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601041">K2601041</a></td>
 +
<td align="right">TEF1-SUMO-yEGFP-HOtag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601042">K2601042</a></td>
 +
<td align="right">PDH3-SUMO-yEGFP-HOtag3</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601054">K2601054</a></td>
 +
<td align="right">PDH3-Frb-crtE-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601056">K2601056</a></td>
 +
<td align="right">Tet07-Frb-crtYB-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601058">K2601058</a></td>
 +
<td align="right">PDH3-Frb-crtYB-HOTag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601060">K2601060</a></td>
 +
<td align="right">SIM-crtE-Hotag6</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K2601061">K2601061</a></td>
 +
<td align="right">SIM-crtYB-Hotag6</td>
 +
</tr>
 +
</table>
 +
                            </div>
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                            <a id="collection"></a>
 +
                            <div class="texttitle">Part Collection</div>
 +
                            <p class="lead add-bottom" style="color:#5E5656">2018 Peking iGEM team members devoted themselves to constructing a part collection that can drive phase separation. We have not only submitted all of new basic HOTag parts, but also provided multiple composite parts combining HOTags with other protein-protein interaction modules and fluorescent reporters. The basic part, HOTag3, is a homo-oligomeric short peptide containing only 30 amino acids. It has high stoichiometry, forming hexamer spontaneously. The HOTag3, together with another tetrameric HOTag6, can robustly drive phase separation upon protein-protein interaction. Protein-protein interaction is achieved by our dimerization parts, including FKBP/Frb and SUMO/SIM. Functions of all the parts were thoroughly tested. Some thermodynamic and kinetic properties of the parts were characterized as well. We believe the HOTag is useful tool for other iGEM teams to investigate protein phase separation and design synthetic organelles.</p>
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Revision as of 13:13, 17 October 2018

Parts

Favorite Parts

Schematic diagram

Figure. 1 Schematic diagram of most parts submitted by Peking iGEM 2018.

BBa_K2601010

Figure. 2 Schematic diagram of BBa_K2601010

We combined Frb, yEGFP and HOTag6 togethor in BBa_K2601010. Frb can interact with FKBP after adding rapamycin, which makes the RapaSPOT formation controllable. We constructed yeast strains with FKBP-mCherry-HOTag3 and Frb-yEGFP-HOTag6 and used 10 μM rapamycin to induce SPOT formation. Minutes after adding rapamycin, granules appeared and became larger gradually.


BBa_K2601011

Figure. 3 Schematic diagram of BBa_K2601011

To make our SPOT a reaction hub, we fused the enzymes of β-carotene synthase system, CrtI, CrtE and CrtYB into Frb-HOTag6 backbone. In the presence of rapamycin, FKBP-yEGFP-HOTag3 and Frb-enzyme-HOTag6 can condense into aggregates. And if the yeast contains SPOT, there will be more β-carotene producted. Meanwhile, we wondered if we can load enzymes onto SPOT mediated by indirected connection. We fused CFP to anti-GFP nanobody as the demonstration of our design and we observed the co-localization of the blue and green fluorescence as expected.


BBa_K2601012

Figure. 4 Schematic diagram of BBa_K2601012.

In the biobrick BBa_K2601012, we fused SUMO, yEGFP and HOTag3 together. SUMO is the interaction module which can bind SIM spontaneously, while HOTag3 can introduce multivalence. These two features are necessary for SPOT formation. We expressed SUMO-yEGFP-HOTag3 and SIM-mCherry-HOTag6 in one yeast strain, and we observed the colocalization of yEGFP and mCherry in two different fluorescence channels, which confirms our hypothesis that the two components could form synthetic organelles.


Part Table
BBa_ Part
K2601000 Promoter-tet07
K2601001 Promoter-PDH3
K2601002 SUMO
K2601003 SIM
K2601004 HOTag3
K2601005 HOTag6
K2601007 Frb-yEGFP
K2601008 FKBP-yEGFP
K2601010 Frb-yEGFP-HOTag6
K2601011 FKBP-yEGFP-HOTag3
K2601012 SUMO-yEGFP-HOtag3
K2601021 Tet07-Frb-yEGFP
K2601023 PDH3-Frb-yEGFP
K2601025 Tet07-FKBP-yEGFP
K2601026 TEF1-FKBP-yEGFP
K2601027 PDH3-FKBP-yEGFP
K2601032 Tet07-Frb-yEGFP-HOTag6
K2601033 TEF1-Frb-yEGFP-HOTag6
K2601034 PDH3-Frb-yEGFP-HOTag6
K2601037 TEF1-FKBP-yEGFP-HOTag3
K2601038 PDH3-FKBP-yEGFP-HOTag3
K2601040 Tet07-SUMO-yEGFP-HOtag3
K2601041 TEF1-SUMO-yEGFP-HOtag3
K2601042 PDH3-SUMO-yEGFP-HOtag3
K2601054 PDH3-Frb-crtE-HOTag6
K2601056 Tet07-Frb-crtYB-HOTag6
K2601058 PDH3-Frb-crtYB-HOTag6
K2601060 SIM-crtE-Hotag6
K2601061 SIM-crtYB-Hotag6
Part Collection

2018 Peking iGEM team members devoted themselves to constructing a part collection that can drive phase separation. We have not only submitted all of new basic HOTag parts, but also provided multiple composite parts combining HOTags with other protein-protein interaction modules and fluorescent reporters. The basic part, HOTag3, is a homo-oligomeric short peptide containing only 30 amino acids. It has high stoichiometry, forming hexamer spontaneously. The HOTag3, together with another tetrameric HOTag6, can robustly drive phase separation upon protein-protein interaction. Protein-protein interaction is achieved by our dimerization parts, including FKBP/Frb and SUMO/SIM. Functions of all the parts were thoroughly tested. Some thermodynamic and kinetic properties of the parts were characterized as well. We believe the HOTag is useful tool for other iGEM teams to investigate protein phase separation and design synthetic organelles.