Difference between revisions of "Team:BGU ISRAEL/Basic Part"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Awards#Special_Prizes">basic part special prize</a>. </p>
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                    </button>
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                    <a class="navbar-brand" href="https://2016.igem.org/Team:BGU_ISRAEL"><img class="OurLogo" alt="bgu_logo_plasticure" src="https://static.igem.org/mediawiki/2016/b/b2/White_plasticure_for_bar_site.png">
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                        <li class="dropdown" id="HomeB"><a class="dropdown-toggle" href="https://2016.igem.org/Team:BGU_ISRAEL">Home</a>
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                        <li class="dropdown" id="projectB"><a class="dropdown-toggle" href="https://2016.igem.org/Team:BGU_ISRAEL/Project">Project</a>
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                            <ul class="dropdown-menu submenubgu">
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Description">Description</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Design">Design</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Experiments">Experiments</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Results">Results</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Protocols">Protocols</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Notebook">Notebook</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Achievements">Achievements</a></li>
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                            </ul>
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                        </li>
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                        <li class="dropdown" id="teamB"><a href="https://2016.igem.org/Team:BGU_ISRAEL/Team">Team</a>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/TeamMembers">Members</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/MeetUniversity">Meet Our University</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/MeetTown">Meet Our Town</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Collaborations">Collaborations</a></li>
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                            </ul>
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                        </li>
  
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                        <li class="dropdown" id="partsB" style="background-color: #77DD77;"><a class="dropdown-toggle" href="https://2016.igem.org/Team:BGU_ISRAEL/Parts">Parts</a>
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                            <ul class="dropdown-menu submenubgu">
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Parts#Overview">Overview</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Basic_Part">Basic Parts</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/ImprovedParts">Improved Parts</a></li>
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                            </ul>
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                        </li>
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                        <li class="dropdown" id="humanB"><a class="dropdown-toggle" href="https://2016.igem.org/Team:BGU_ISRAEL/Integrated_Practices">Human Practices</a>
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                            <ul class="dropdown-menu submenubgu">
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Integrated_Practices">Integrated Practices</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/PlasticArt">Plastic Art</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/EthicsAndSafety">Ethics & Safety</a></li>
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                            </ul>
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                        </li>
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                        <li class="dropdown" id="attributionsB"><a class="dropdown-toggle" href="https://2016.igem.org/Team:BGU_ISRAEL/Attributions">Attributions</a></li>
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                        <li class="dropdown" id="awardsB"><a class="dropdown-toggle" href="https://2016.igem.org/Team:BGU_ISRAEL/Awards">Awards</a>
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                            <ul class="dropdown-menu submenubgu">
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Entrepreneurship">Entrepreneurship</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Measurements">Measurements</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Proof">Proof Of Concept</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Demonstrate">Demonstrate</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/HP/Silver">HP - Silver</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/HP/Gold">HP - Gold</a></li>
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                                <li><a href="https://2016.igem.org/Team:BGU_ISRAEL/Engagement">Engagements</a></li>
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                            </ul>
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                        </li>
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                    </ul>
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        </nav>
  
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        <div class="container-fluid">
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            <div class="row">
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                <div class="PartColor">
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                    <p>Basic Part</p>
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                </div>
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            </div>
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        </div>
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        <div class="container-fluid">
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                <div class="col-lg-8">
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                    <p class="bigAssHeader">Protocatechuate Degradation Pathway</p>
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                    <hr>
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                    <div class="row protoText">
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                        <div class="col-lg-6">
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                            <p>
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                                <i>Pseudomonas putida</i> is a bacterium capable of utilizing protocatechuate, a toxic molecule for most bacteria. The protocatechuate degradation pathway converts protocatechuate into 3-oxoadipate, which is further metabolized by the bacteria and enters the TCA cycle. <br>
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                                We chose to submit the genes encoding the enzymes in this pathway.
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                                We also characterized the utilization of protocatechuate by bacterium using M9 minimal medium with protocatechuate as a sole carbon source.
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                                We have not been able to submit the pcaB gene, encoding the 3-Carboxymuconate Cycloisomerase, since the sequence contained 4 PstI restriction cut sites, which we did not have time to alter using point mutations.
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                            </p> 
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                        </div>
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                        <div class="col-lg-6">
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                            <img class="partPutipic" src="https://static.igem.org/mediawiki/2016/9/9e/Puti_biobricksBGU2016.png">
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                        </div>
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                    </div>
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                    <table class="table table-bordered">
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                        <thead>
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                            <tr>
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                                <th>Part Name</th>
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                                <th>Type</th>
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                                <th>Description</th>
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                                <th>Designer</th>
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                                <th>Length</th>
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                            </tr>
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                        </thead>
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                        <tbody>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091000">BBa_K2091000</a></td>
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                                <td>Coding</td>
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                                <td>Protocatechuate 3,4-dioxygenase Alpha Subunit</td>
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                                <td>B. Vaknin</td>
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                                <td>606</td>
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                            </tr>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091001">BBa_K2091001</a></td>
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                                <td>Coding</td>
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                                <td>Protocatechuate 3,4-dioxygenase Beta Subunit</td>
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                                <td>B. Vaknin</td>
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                                <td>720</td>
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                            </tr>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091002">BBa_K2091002</a></td>
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                                <td>Coding</td>
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                                <td>4-Carboxymuconolactone Decarboxylase</td>
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                                <td>B. Vaknin</td>
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                                <td>393</td>
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                            </tr>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091003">BBa_K2091003</a></td>
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                                <td>Coding</td>
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                                <td>3-Oxoadipate enol-lactonase</td>
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                                <td>B. Vaknin</td>
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                                <td>792</td>
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                            </tr>
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                        </tbody>
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                    </table>
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                </div>
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            </div>
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        </div>
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        <div class="container-fluid">
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            <div class='row  lightgold'>
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                <div class="col-lg-2"></div>
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                <div class="col-lg-8">
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                    <p class="bigAssHeader">LC-Cutinase Protein Variants</p>
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                    <hr>
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                    <div class="row CutiText">
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                        <div class="col-lg-6">
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                            <p>
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                                LC-cutinase is an enzyme found to have the ability to degrade PET. We have chosen to improve this enzyme using rational mutagenesis. 4 mutant variants of the LC-cutinase protein were produced using the PROSS algorithm and one Codon-optimized version of the protein was designed using the Genome Compiler software. <br>
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                                We have tested and characterized these proteins using kinetic trials, bacterial growth assays and scanning electron microscopy imaging. <br>
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                            </p> 
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                        </div>
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                        <div class="col-lg-6">
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                            <img class="partCutipic" src="https://static.igem.org/mediawiki/2016/0/00/Cuti_design_BGU2016.png">
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                        </div>
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                    <table class='table table-bordered'>
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                        <thead>
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                            <tr>
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                                <th>Part Name</th>
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                                <th>Type</th>
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                                <th>Description</th>
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                                <th>Designer</th>
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                                <th>Length</th>
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                            </tr> 
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                        </thead>
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                        <tbody>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091004">BBa_K2091004</a></td>
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                                <td>Coding</td>
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                                <td>LC-Cutinase Codon Optimized</td>
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                                <td>I. Bariah, E. Zajfman, I. Segal</td>
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                                <td>948</td>
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                            </tr>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091005">BBa_K2091005</a></td>
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                                <td>Coding</td>
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                                <td>LC-Cutinase Variant F4</td>
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                                <td>I. Bariah, E. Zajfman, I. Segal</td>
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                                <td>948</td>
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                            </tr>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091006">BBa_K2091006</a></td>
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                                <td>Coding</td>
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                                <td>LC-Cutinase Variant F7</td>
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                                <td>I. Bariah, E. Zajfman, I. Segal</td>
 +
                                <td>948</td>
 +
                            </tr>
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                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091007">BBa_K2091007</a></td>
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                                <td>Coding</td>
 +
                                <td>LC-Cutinase Variant R4</td>
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                                <td>I. Bariah, E. Zajfman, I. Segal</td>
 +
                                <td>948</td>
 +
                            </tr>
 +
                            <tr>
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                                <td><a href="http://parts.igem.org/Part:BBa_K2091008">BBa_K2091008</a></td>
 +
                                <td>Coding</td>
 +
                                <td>LC-Cutinase Variant R7</td>
 +
                                <td>I. Bariah, E. Zajfman, I. Segal</td>
 +
                                <td>948</td>
 +
                            </tr>
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                        </tbody>
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                    </table>
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                </div>
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            </div>
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        </div>
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        <a href="#" class="back-to-top">
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            <img src='https://static.igem.org/mediawiki/2016/5/52/Arrow_for_site.png'>
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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                    <h4>Address:</h4>
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                    <p>
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                        Ben-Gurion University of the Negev<br>
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                        Ben Gurion 1, Beer Sheva 8410501, Israel
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                    <h5>
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                        <b><u>Mail:</u></b> igembgu2016@gmail.com
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<p>
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                    </h5>
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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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                    <h4>Connect With Us!</h4>
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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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Latest revision as of 14:55, 19 October 2016

PlastiCure

Basic Part

Protocatechuate Degradation Pathway

Pseudomonas putida is a bacterium capable of utilizing protocatechuate, a toxic molecule for most bacteria. The protocatechuate degradation pathway converts protocatechuate into 3-oxoadipate, which is further metabolized by the bacteria and enters the TCA cycle.
We chose to submit the genes encoding the enzymes in this pathway. We also characterized the utilization of protocatechuate by bacterium using M9 minimal medium with protocatechuate as a sole carbon source. We have not been able to submit the pcaB gene, encoding the 3-Carboxymuconate Cycloisomerase, since the sequence contained 4 PstI restriction cut sites, which we did not have time to alter using point mutations.

Part Name Type Description Designer Length
BBa_K2091000 Coding Protocatechuate 3,4-dioxygenase Alpha Subunit B. Vaknin 606
BBa_K2091001 Coding Protocatechuate 3,4-dioxygenase Beta Subunit B. Vaknin 720
BBa_K2091002 Coding 4-Carboxymuconolactone Decarboxylase B. Vaknin 393
BBa_K2091003 Coding 3-Oxoadipate enol-lactonase B. Vaknin 792

LC-Cutinase Protein Variants

LC-cutinase is an enzyme found to have the ability to degrade PET. We have chosen to improve this enzyme using rational mutagenesis. 4 mutant variants of the LC-cutinase protein were produced using the PROSS algorithm and one Codon-optimized version of the protein was designed using the Genome Compiler software.
We have tested and characterized these proteins using kinetic trials, bacterial growth assays and scanning electron microscopy imaging.

Part Name Type Description Designer Length
BBa_K2091004 Coding LC-Cutinase Codon Optimized I. Bariah, E. Zajfman, I. Segal 948
BBa_K2091005 Coding LC-Cutinase Variant F4 I. Bariah, E. Zajfman, I. Segal 948
BBa_K2091006 Coding LC-Cutinase Variant F7 I. Bariah, E. Zajfman, I. Segal 948
BBa_K2091007 Coding LC-Cutinase Variant R4 I. Bariah, E. Zajfman, I. Segal 948
BBa_K2091008 Coding LC-Cutinase Variant R7 I. Bariah, E. Zajfman, I. Segal 948

Address:

Ben-Gurion University of the Negev
Ben Gurion 1, Beer Sheva 8410501, Israel

Mail: igembgu2016@gmail.com

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