Difference between revisions of "Team:CPU CHINA/partsOverview"

 
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     <style>
 
     <style>
 
         #header #title {
 
         #header #title {
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             left: 12%;
 
         }
 
         }
  
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         </div>
 
         </div>
 
         <img class="background" src="https://static.igem.org/mediawiki/2021/c/cf/T--CPU_CHINA--Parts--background.png" alt="">
 
         <img class="background" src="https://static.igem.org/mediawiki/2021/c/cf/T--CPU_CHINA--Parts--background.png" alt="">
−
         <h1 id="title">Parts Overview</h1>
+
         <h1 id="title">PARTS OVERVIEW</h1>
 
         <svg width="100%" height="100%" viewBox="0 0 1920 600" version="1.1"
 
         <svg width="100%" height="100%" viewBox="0 0 1920 600" version="1.1"
 
             style="fill-rule:evenodd;clip-rule:evenodd;stroke-linejoin:round;stroke-miterlimit:2;">
 
             style="fill-rule:evenodd;clip-rule:evenodd;stroke-linejoin:round;stroke-miterlimit:2;">
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                     <path id="凹形遮罩"
 
                     <path id="凹形遮罩"
 
                         d="M1433.18,439.801C1433.18,439.801 1001.08,524.071 607.621,524.374C219.99,524.673 -217.935,439.801 -217.935,439.801L-217.935,944.811L1433.18,944.811L1433.18,439.801Z"
 
                         d="M1433.18,439.801C1433.18,439.801 1001.08,524.071 607.621,524.374C219.99,524.673 -217.935,439.801 -217.935,439.801L-217.935,944.811L1433.18,944.811L1433.18,439.801Z"
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                         style="fill:#FAFAFA;" />
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                         style="fill:#FFFFFF;" />
 
                 </g>
 
                 </g>
 
             </g>
 
             </g>
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             </svg>
 
             </svg>
 
             <nav>
 
             <nav>
−
                 <div class="catalogue-title">Parts Overview</div>
+
                 <div class="catalogue-title">PARTS OVERVIEW</div>
 
                 <ul class="catalogue">
 
                 <ul class="catalogue">
 
                     <li class="num">
 
                     <li class="num">
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                 </ul>
 
                 </ul>
 
             </nav>
 
             </nav>
−
             <img src="https://static.igem.org/mediawiki/2021/b/b2/T--CPU_CHINA--experimentalize.png" alt="">
+
             <img src="https://static.igem.org/mediawiki/2021/3/38/T--CPU_CHINA--flying.png" alt="">
 
         </div>
 
         </div>
−
         <div id="detail" class="clearfix">
+
         <div id="detail" class="clearfix" style="padding-top: 5%;">
  
−
             <p><span> </span><span>This year, among the 30 parts designed, 19 of them are basic parts and the rest are
+
             <p><span> </span><span>This year, among the 31 parts designed, 20 of them are basic parts and the rest are
 
                     composite parts. All of the parts are designed on our own, and most of them have been tested to
 
                     composite parts. All of the parts are designed on our own, and most of them have been tested to
 
                     ensure their reliability. </span></p>
 
                     ensure their reliability. </span></p>
−
             <p><span> </span><strong><span><a href="#">Click here</a> </span></strong><span>
+
             <p><span> </span><strong><span><a href="https://2021.igem.org/Team:CPU_CHINA/Design">Click here</a> </span></strong><span>
 
                     to learn more about our project to understand the purpose of each parts! Click the part number to
 
                     to learn more about our project to understand the purpose of each parts! Click the part number to
 
                     see detailed information of the parts we design!</span></p>
 
                     see detailed information of the parts we design!</span></p>
 
             <div class="section" id="section1">
 
             <div class="section" id="section1">
 
                 <h2 id='basic-parts'><span>Basic Parts</span></h2>
 
                 <h2 id='basic-parts'><span>Basic Parts</span></h2>
−
                 <p><span> </span><span>Among the 19 basic parts designed this year by ourselves, <a href="http://parts.igem.org/Part:BBa_K3853008">BBa_K3853008</a> is our
+
                 <p><span> </span><span>Among the 20 basic parts designed this year by ourselves, <a href="http://parts.igem.org/Part:BBa_K3853008">BBa_K3853008</a> is our
 
                         favorite one, which is the coding sequence of manganese peroxidase derived from
 
                         favorite one, which is the coding sequence of manganese peroxidase derived from
 
                     </span><em><span>Phanerochaete chrysosporium</span></em><span>. The translated product of this part
 
                     </span><em><span>Phanerochaete chrysosporium</span></em><span>. The translated product of this part
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>dCas9</span></td>
 
                                 <td><span>dCas9</span></td>
−
                                 <td><span>GongYu Liu</span></td>
+
                                 <td><span>Gongyu Liu</span></td>
 
                                 <td><span>4104</span></td>
 
                                 <td><span>4104</span></td>
 
                             </tr>
 
                             </tr>
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                             <tr>
 
                             <tr>
 
                                 <td>&nbsp;</td>
 
                                 <td>&nbsp;</td>
−
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853001">BBa_K3853005</a></span></td>
+
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853005">BBa_K3853005</a></span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>SpyCatcher</span></td>
 
                                 <td><span>SpyCatcher</span></td>
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                                 <td><span>DNA</span></td>
 
                                 <td><span>DNA</span></td>
 
                                 <td><span>dsDNA</span></td>
 
                                 <td><span>dsDNA</span></td>
−
                                 <td><span>GongYu Liu</span></td>
+
                                 <td><span>Gongyu Liu</span></td>
 
                                 <td><span>189</span></td>
 
                                 <td><span>189</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>DNA</span></td>
 
                                 <td><span>DNA</span></td>
 
                                 <td><span>gRNA scaffold</span></td>
 
                                 <td><span>gRNA scaffold</span></td>
−
                                 <td><span>GongYu Liu</span></td>
+
                                 <td><span>Gongyu Liu</span></td>
 
                                 <td><span>80</span></td>
 
                                 <td><span>80</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>dCas9-SpyCatcher</span></td>
 
                                 <td><span>dCas9-SpyCatcher</span></td>
−
                                 <td><span>GongYu Liu</span></td>
+
                                 <td><span>Gongyu Liu</span></td>
 
                                 <td><span>4530</span></td>
 
                                 <td><span>4530</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>MnP(E74P)</span></td>
 
                                 <td><span>MnP(E74P)</span></td>
−
                                 <td><span>RuYi Ma</span></td>
+
                                 <td><span>Ruyi Ma</span></td>
 
                                 <td><span>1074</span></td>
 
                                 <td><span>1074</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>MnP(E74M)</span></td>
 
                                 <td><span>MnP(E74M)</span></td>
−
                                 <td><span>RuYi Ma</span></td>
+
                                 <td><span>Ruyi Ma</span></td>
 
                                 <td><span>1074</span></td>
 
                                 <td><span>1074</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>MnP(D182T)</span></td>
 
                                 <td><span>MnP(D182T)</span></td>
−
                                 <td><span>RuYi Ma</span></td>
+
                                 <td><span>Ruyi Ma</span></td>
 
                                 <td><span>1074</span></td>
 
                                 <td><span>1074</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>MnP(S232P)</span></td>
 
                                 <td><span>MnP(S232P)</span></td>
−
                                 <td><span>RuYi Ma</span></td>
+
                                 <td><span>Ruyi Ma</span></td>
 
                                 <td><span>1074</span></td>
 
                                 <td><span>1074</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>MnP(E74L)</span></td>
 
                                 <td><span>MnP(E74L)</span></td>
−
                                 <td><span>RuYi Ma</span></td>
+
                                 <td><span>Ruyi Ma</span></td>
 
                                 <td><span>1074</span></td>
 
                                 <td><span>1074</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>coding</span></td>
 
                                 <td><span>coding</span></td>
 
                                 <td><span>MnP(S78P)</span></td>
 
                                 <td><span>MnP(S78P)</span></td>
−
                                 <td><span>RuYi Ma</span></td>
+
                                 <td><span>Ruyi Ma</span></td>
 
                                 <td><span>1074</span></td>
 
                                 <td><span>1074</span></td>
 
                             </tr>
 
                             </tr>
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                                 <td><span>his-tag</span></td>
 
                                 <td><span>his-tag</span></td>
 
                                 <td><span>Peng Luo</span></td>
 
                                 <td><span>Peng Luo</span></td>
−
                                 <td><span>1074</span></td>
+
                                 <td><span>18</span></td>
 
                             </tr>
 
                             </tr>
 
                         </tbody>
 
                         </tbody>
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                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853054">BBa_K3853054</a></span></td>
 
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853054">BBa_K3853054</a></span></td>
 
                                 <td><span>composite</span></td>
 
                                 <td><span>composite</span></td>
−
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-SpyTag-HFB1-AOX1
+
                                 <td><span>R0085-C0012-B2002-his-tag-SpyTag-HFB1-B0012</td>
−
                                        Terminator</span></td>
+
 
                                 <td><span>Peng Luo</span></td>
 
                                 <td><span>Peng Luo</span></td>
−
                                 <td><span>1836</span></td>
+
                                 <td><span>1657</span></td>
 
                             </tr>
 
                             </tr>
 
                             <tr>
 
                             <tr>
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             <div class="section" id="section3">
 
             <div class="section" id="section3">
 
                 <h2 id='part-collection'><strong><span>Part Collection</span></strong></h2>
 
                 <h2 id='part-collection'><strong><span>Part Collection</span></strong></h2>
−
                 <p><span> </span><span>This year, we developed a part collection related to the CRSIPR/dCas9 anchoring
+
                 <p><span> </span><span>This year, we successfully obtained and expressed six manganese peroxidase (MnP) mutants as our part collection. These mutants, including MnP (E74P), MnP (E74M), MnP (D182T), MnP (S232P), MnP (E74L) and MnP(S78P), have the same function, which could all be used to degrade polyethylene (PE). However, they differ from each other on the stability under specific conditions. For example, MnP (E74L) has a higher enzyme activity than wild-type MnP at room temperature, while MnP (E74M) can remain stable at relatively high temperature. By carrying out protein characterization experiments, we could find the MnP mutant which has the best ability to degrade PE.</span>
−
                        system. By introducing SpyTag into the N-terminus of different proteins to develop fusion
+
−
                        proteins,
+
−
                        their connection to dCas9-SpyCatcher and the following sgRNA-guided anchoring on dsDNA can be
+
−
                        realized. The type, quantity and proportion of anchoring components will remarkably affect their
+
−
                        individual function, as well as the overall performance of the complex. It depends on how the
+
−
                        system
+
−
                        designer would like to arrange the dCas9-binding sequence on dsDNA, and how the assembly process
+
−
                        is
+
−
                        conducted through specific order for acquiring expected component array of the complex.</span>
+
−
                </p>
+
−
                <p><span> </span><span> For our part collection, we characterized three different fusion proteins, i.e.
+
−
                        SpyTag-MnP, SpyTag-AAO, SpyTag-HFB1, and uploaded their complete and detailed characterization
+
−
                        data
+
−
                        to the iGEM part registry. We hope these organized information can be instructive for the design
+
−
                        and
+
−
                        charaterization of upcoming teams who wish to adopt these protein-nucleic-acid complex.</span>
+
 
                 </p>
 
                 </p>
 
                 <figure>
 
                 <figure>
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                         <thead>
 
                         <thead>
 
                             <tr>
 
                             <tr>
−
                                <th><span>Peptide segment</span></th>
 
−
                                <th><span>Fusion</span></th>
 
 
                                 <th><span>Part Name</span></th>
 
                                 <th><span>Part Name</span></th>
 
                                 <th><span>Type</span></th>
 
                                 <th><span>Type</span></th>
Line 475: Line 456:
 
                         <tbody>
 
                         <tbody>
 
                             <tr>
 
                             <tr>
−
                                <td rowspan="3"><span>SpyTag</span></td>
+
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853056">BBa_K3853056</a></span></td>
−
                                <td rowspan="3"><span>N-terminal</span></td>
+
−
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853051">BBa_K3853051</a></span></td>
+
 
                                 <td><span>composite</span></td>
 
                                 <td><span>composite</span></td>
−
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-SpyTag-MnP-AOX1
+
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-MnP(E74P)-AOX1
 
                                         Terminator</span></td>
 
                                         Terminator</span></td>
 
                                 <td><span>Peng Luo</span></td>
 
                                 <td><span>Peng Luo</span></td>
−
                                 <td><span>2664</span></td>
+
                                 <td><span>2508</span></td>
 
                             </tr>
 
                             </tr>
 
                             <tr>
 
                             <tr>
−
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853053">BBa_K3853053</a></span></td>
+
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853057">BBa_K3853057</a></span></td>
 
                                 <td><span>composite</span></td>
 
                                 <td><span>composite</span></td>
−
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-SpyTag-AAO-AOX1
+
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-MnP(E74M)-AOX1
 
                                         Terminator</span></td>
 
                                         Terminator</span></td>
 
                                 <td><span>Peng Luo</span></td>
 
                                 <td><span>Peng Luo</span></td>
−
                                 <td><span>3309</span></td>
+
                                 <td><span>2508</span></td>
 
                             </tr>
 
                             </tr>
 
                             <tr>
 
                             <tr>
−
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853054">BBa_K3853054</a></span></td>
+
                                 <td><span><a href="http://parts.igem.org/Part:BBa_K3853058">BBa_K3853058</a></span></td>
 
                                 <td><span>composite</span></td>
 
                                 <td><span>composite</span></td>
−
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-SpyTag-HFB1-AOX1
+
                                 <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-MnP(D182T)-AOX1
 
                                         Terminator</span></td>
 
                                         Terminator</span></td>
 
                                 <td><span>Peng Luo</span></td>
 
                                 <td><span>Peng Luo</span></td>
−
                                 <td><span>1836</span></td>
+
                                 <td><span>2508</span></td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><span><a href="http://parts.igem.org/Part:BBa_K3853059">BBa_K3853059</a></span></td>
 +
                                <td><span>composite</span></td>
 +
                                <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-MnP(S232P)-AOX1
 +
                                        Terminator</span></td>
 +
                                <td><span>Peng Luo</span></td>
 +
                                <td><span>2508</span></td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><span><a href="http://parts.igem.org/Part:BBa_K3853060">BBa_K3853060</a></span></td>
 +
                                <td><span>composite</span></td>
 +
                                <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-MnP(E74L)-AOX1
 +
                                        Terminator</span></td>
 +
                                <td><span>Peng Luo</span></td>
 +
                                <td><span>2508</span></td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><span><a href="http://parts.igem.org/Part:BBa_K3853061">BBa_K3853061</a></span></td>
 +
                                <td><span>composite</span></td>
 +
                                <td><span>P</span><sub><span>AOX1</span></sub><span>-α-factor-his-tag-MnP(S78P)-AOX1
 +
                                        Terminator</span></td>
 +
                                <td><span>Peng Luo</span></td>
 +
                                <td><span>2508</span></td>
 
                             </tr>
 
                             </tr>
 
                         </tbody>
 
                         </tbody>
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                <h4>Contact us</h4>
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            <h4>Contact us</h4>
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+
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Latest revision as of 03:41, 22 October 2021

This year, among the 31 parts designed, 20 of them are basic parts and the rest are composite parts. All of the parts are designed on our own, and most of them have been tested to ensure their reliability.

Click here to learn more about our project to understand the purpose of each parts! Click the part number to see detailed information of the parts we design!

Basic Parts

Among the 20 basic parts designed this year by ourselves, BBa_K3853008 is our favorite one, which is the coding sequence of manganese peroxidase derived from Phanerochaete chrysosporium. The translated product of this part enables our multi-enzyme complex to degrade polyethylene efficiently. Besides, many other basic parts have also been designed to construct our project.

Favorite Part Name Type Description Designer Length
  BBa_K3853000 coding MnP Peng Luo 1074
  BBa_K3853001 coding AAO Peng Luo 1719
  BBa_K3853002 coding HFB1 Peng Luo 246
  BBa_K3853003 coding dCas9 Gongyu Liu 4104
  BBa_K3853004 coding SpyTag Peng Luo 39
  BBa_K3853005 coding SpyCatcher Peng Luo 351
  BBa_K3853006 DNA dsDNA Gongyu Liu 189
  BBa_K3853007 DNA gRNA scaffold Gongyu Liu 80
♥ BBa_K3853008 coding his-tag-SpyTag-MnP Peng Luo 1248
  BBa_K3853009 coding his-tag-SpyTag-AAO Peng Luo 1893
  BBa_K3853010 coding his-tag-SpyTag-HFB1 Peng Luo 420
  BBa_K3853011 coding dCas9-SpyCatcher Gongyu Liu 4530
  BBa_K3853012 coding sfGFP Peng Luo 720
  BBa_K3853013 coding MnP(E74P) Ruyi Ma 1074
  BBa_K3853014 coding MnP(E74M) Ruyi Ma 1074
  BBa_K3853015 coding MnP(D182T) Ruyi Ma 1074
  BBa_K3853016 coding MnP(S232P) Ruyi Ma 1074
  BBa_K3853017 coding MnP(E74L) Ruyi Ma 1074
  BBa_K3853018 coding MnP(S78P) Ruyi Ma 1074
  BBa_K3853019 coding his-tag Peng Luo 18

 

Composite Parts

A series of composite parts have been designed by us this year, and most of them are used for the assembly of the PE-degrading complex in our project throughout the season.

To achieve this assembly, we designed fusion enzymes and proteins containing SpyTag and fusion deactivated CRISPR-associated protein 9 (dCas9) containing SpyCatcher, enabling the incubation-induced connection of multi-protein complexes via covalent bond formation mediated by the two Spy domains. Subsequently, these multi-protein complexes could anchor to designated positions on the designed double-stranded DNA (dsDNA) template through the guidance of dCas9-combined sgRNAs.

Our favorite composite part is BBa_K3853051 , which contains the sequence of manganese peroxidase (MnP) for polyethylene degradation, and the sequence of SpyTag for multi-domain complex formation, as well as sequences of AOX1 promoter and AOX1 terminator, enabling its efficient inducible expression in Pichia pastoris.

Favorite Part Name Type Description Designer Length
  BBa_K3853050 composite PAOX1-α-factor-sfGFP-AOX1 Terminator Peng Luo 2136
♥ BBa_K3853051 composite PAOX1-α-factor-his-tag-SpyTag-MnP-AOX1 Terminator Peng Luo 2664
  BBa_K3853053 composite PAOX1-α-factor-his-tag-SpyTag-AAO-AOX1 Terminator Peng Luo 3309
  BBa_K3853054 composite R0085-C0012-B2002-his-tag-SpyTag-HFB1-B0012 Peng Luo 1657
  BBa_K3853055 composite R0085-C0012-B2002-his-tag-dCas9-SpyCatcher-B0012 Peng Luo 5758
  BBa_K3853056 composite PAOX1-α-factor-his-tag-MnP(E74P)-AOX1 Terminator Peng Luo 2508
  BBa_K3853057 composite PAOX1-α-factor-his-tag-MnP(E74M)-AOX1 Terminator Peng Luo 2508
  BBa_K3853058 composite PAOX1-α-factor-his-tag-MnP(D182T)-AOX1 Terminator Peng Luo 2508
  BBa_K3853059 composite PAOX1-α-factor-his-tag-MnP(S232P)-AOX1 Terminator Peng Luo 2508
  BBa_K3853060 composite PAOX1-α-factor-his-tag-MnP(E74L)-AOX1 Terminator Peng Luo 2508
  BBa_K3853061 composite PAOX1-α-factor-his-tag-MnP(S78P)-AOX1 Terminator Peng Luo 2508

 

Part Collection

This year, we successfully obtained and expressed six manganese peroxidase (MnP) mutants as our part collection. These mutants, including MnP (E74P), MnP (E74M), MnP (D182T), MnP (S232P), MnP (E74L) and MnP(S78P), have the same function, which could all be used to degrade polyethylene (PE). However, they differ from each other on the stability under specific conditions. For example, MnP (E74L) has a higher enzyme activity than wild-type MnP at room temperature, while MnP (E74M) can remain stable at relatively high temperature. By carrying out protein characterization experiments, we could find the MnP mutant which has the best ability to degrade PE.

Part Name Type Description Designer Length
BBa_K3853056 composite PAOX1-α-factor-his-tag-MnP(E74P)-AOX1 Terminator Peng Luo 2508
BBa_K3853057 composite PAOX1-α-factor-his-tag-MnP(E74M)-AOX1 Terminator Peng Luo 2508
BBa_K3853058 composite PAOX1-α-factor-his-tag-MnP(D182T)-AOX1 Terminator Peng Luo 2508
BBa_K3853059 composite PAOX1-α-factor-his-tag-MnP(S232P)-AOX1 Terminator Peng Luo 2508
BBa_K3853060 composite PAOX1-α-factor-his-tag-MnP(E74L)-AOX1 Terminator Peng Luo 2508
BBa_K3853061 composite PAOX1-α-factor-his-tag-MnP(S78P)-AOX1 Terminator Peng Luo 2508