Team:UCL/Project/Biobricks

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<img src="https://static.igem.org/mediawiki/2014/e/e6/UCLBioBricks_Header.png" width="100%" height="auto" alt="BioBricks" />
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<img src="https://static.igem.org/mediawiki/2014/9/98/UCLBiobricksHeaderOran.jpg" width="100%" height="auto" alt="BioBricks" />
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<ul class="tabs">
<ul class="tabs">
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     <li><a href="#view1">Overview</a></li>
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     <li><a href="#view1">UCL iGEM 2014</a></li>
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     <li><a href="#view2">Azoreductase R2</a></li>
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     <li><a href="#view2">Azoreductase</a></li>
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     <li><a href="#view3">Azoreductase 1B6</a></li>
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     <li><a href="#view3">Laccase</a></li>
     <li><a href="#view4">Lignin Peroxidase</a></li>
     <li><a href="#view4">Lignin Peroxidase</a></li>
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     <li><a href="#view5">BsDyP</a></li>
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     <li><a href="#view5">Bacterial Peroxidases</a></li>
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     <li><a href="#view6">PpDyP</a></li>
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     <li><a href="#view6">ispB asRNA</a></li>
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    <li><a href="#view7">Nuclease</a></li>
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<!--- This is the overview section --->
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<div id="view1">
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<div id="view1"><div class="textTitle"><h4>Our BioBricks & how they lead to azo degradation</h4></div><br>
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<a data-tip="true" class="top large" data-tip-content="Here's Tanel doing some pipetting in our lab!" href="javascript:void(0)" style="width: 25%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/c/c9/UCLTANELPIPETTING.JPG" style="max-width: 100%;"></a>
<a data-tip="true" class="top large" data-tip-content="Here's Tanel doing some pipetting in our lab!" href="javascript:void(0)" style="width: 25%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/c/c9/UCLTANELPIPETTING.JPG" style="max-width: 100%;"></a>
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<div class="textTitle"><h4>Overview</h4></div>
 
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<p>We plan to create a complete synthetic azo dye decolourising device in <em>E. coli</em> which incorporates several different independent enzymes that act on azo dyes and their breakdown products. After evaluating their individual breakdown characteristics, we aim to investigate the potential synergistic action of these enzymes in a single synthetic <em>E. coli</em> device and design a <a data-tip="true" class="top large" data-tip-content="Click here to learn more about our bioprocess!" href="https://2014.igem.org/Team:UCL/Science/Bioprocessing"><b>bioprocess</b></a> which could be used to upscale the method to an industrial context. </p>
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<p>We have strove to complete a synthetic azo dye decolourising device in E. coli which incorporates several different independent enzymes that act on azo dyes and their breakdown products to create less toxic chemicals. After evaluating their individual breakdown characteristics, we aim to investigate the potential synergistic action of these enzymes in a single synthetic E. coli device and design a bioprocess which could be used to upscale the method to an industrial context.
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<a data-tip="true" class="top large" data-tip-content="Can you guess which one is the RFP BioBrick?" href="javascript:void(0)" style="width: 20%;float: left;margin-top:2%; margin-right:2%"><img src="https://static.igem.org/mediawiki/2014/c/c0/UCLTANELHOLDINGBIOBRICK.jpg" style="max-width: 100%;"></a>
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</p>
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<p>Ideally, we wanted a Azo-Remediation Chassis (ARC), our BioBrick System, to be assembled as follows:</p><br>
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<div><center><a data-tip="true" class="top large" data-tip-content="Here's our prototype Azo-Remediation Chassis!" href="javascript:void(0)" style="width: 60%;margin-left:1%"><img src="https://static.igem.org/mediawiki/2014/0/07/UCL_Chassis.png" style="max-width: 60%;"></a></center></div><br>
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    <p>A further development on this prototype would be to have Bba_K1336000, the AzoR gene, to be inducibly transcribed by one promoter (say BBa_K314103, the LacI Expression Cassette) such that it is expressed in the reductive step of our azo dye remediation process. This would form a distinct BioBrick Device of "promotor A + AzoR + double terminator". <br>A secondary BioBrick Device (of "promoter B + gene 2 + double terminator") would follow this, where gene 2 would be one of our enzymes that function in the oxidative step of the azo dye remediation process, e.g. laccase or one of the dye decolourising peroxidases. A further tertiary BioBrick Device, with another oxidative enzyme would also be ideal. At least 2 oxidative enzymes are proposed as the enzymes are specialised for different substrates (as described in our <a href="/Team:UCL/Project/Biobricks">BioBrick</a> page. </br> <br>
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<a data-tip="true" class="top large" data-tip-content="Can you guess which one is the RFP BioBrick?" href="javascript:void(0)" style="width: 20%;float: left;margin-top:2%; margin-right:2%"><img src="https://static.igem.org/mediawiki/2014/c/c0/UCLTANELHOLDINGBIOBRICK.jpg" style="max-width: 90%;"></a>
<br>
<br>
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In an industrial setting, these enzymes would work sequentially in a bioreactor with preset dynamic conditions. First, azoreductase will <a data-tip="true" class="top large" data-tip-content="Via a double reduction using NADPH as a cofactor." href="javascript:void(0)"><b>cleave the azo-bond (N=N)</b></a>, producing a series of highly toxic aromatic amines. Then, these compounds will be oxidised by lignin peroxidase, laccase and bacterial peroxidases, completing decolourisation and decreasing <a data-tip="true" class="top large" data-tip-content="To the point that the final products of the process are less toxic than the intact dyes themselves." href="javascript:void(0)"><b>toxicity levels</b></a>.
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<p> In an industrial setting, these enzymes would work sequentially in a bioreactor with preset dynamic conditions. First, azoreductase will cleave the azo-bond (N=N), producing a series of highly toxic aromatic amines. Then, these compounds will be oxidised by lignin peroxidase, laccase and bacterial peroxidases, completing decolourisation and decreasing toxicity levels.
 +
</p><b>toxicity levels</b></a>.
 +
<br><br>
 +
<p> The complementary action of azoreductase, lignin peroxidase, laccase, and bacterial peroxidases will be studied in order to find out the best possible approach of sequential reaction.
 +
To ensure that the process is entirely bio-safe we have designed a xeno-biological modules that ensures that beyond the bioreactor our organism could not survive.
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<br><br><br><br><br><br><br>
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  <font size="2">
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    <table border="1px" width="100%" height="auto">
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        <thead>
 +
            <tr>
 +
                <th>  </th>
 +
                <th> Registry ID </th>
 +
                <th> Gene ID</th>
 +
                <th> Name / Function </th>
 +
                <th> Source </th>
 +
                <th> Size </th>
 +
                <th> Status </th>
 +
            </tr>
 +
        </thead>
 +
        <tbody>
 +
            <!--Lisbon plasmids-->
 +
            <tr>
 +
                <td>  </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336000">BBa_K1336000</a> </td>
 +
                <td> &nbsp;AzoR </td>
 +
                <td> &nbsp;FMN-dependent NADH-azoreductase 1 </td>
 +
                <td> &nbsp;<em>Pseudomonas putida</em> </td>
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336000">612 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Primers">In Progress</a>]: primers designed </td>
 +
            </tr>
 +
            <tr>
 +
                <td>  </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336001">BBa_K1336001</a> </td>
 +
                <td> &nbsp;1B6 </td>
 +
                <td> &nbsp;AzoR heat-stable mutant</td>
 +
                <td> &nbsp;<em>Pseudomonas putida</em> </td>
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336001">612 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Experiments">In Progress</a>]: to remove 2 illegal PstI sites </td>
 +
            </tr>
 +
            <tr>
 +
                <td>  </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336002">BBa_K1336002</a> </td>
 +
                <td> &nbsp;CotA </td>
 +
                <td> &nbsp;Spore Coat Protein Laccase</td>
 +
                <td> &nbsp;<em>Bacillus subtilis</em> </td>
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336002">1542 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Primers">In Progress</a>]: primers designed </td>
 +
            </tr>
 +
            <tr>
 +
                <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336003">BBa_K1336003</a> </td>
 +
                <td> &nbsp;BsDyP </td>
 +
                <td> &nbsp;Dye Decolourising Peroxidase BSU38260</td>
 +
                <td> &nbsp;<em>Bacillus subtilis</em> </td>
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336003">1251 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Experiments">New BioBrick Part</a>]: submitted </td>
 +
            </tr>
 +
            <tr>
 +
                <td>  </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336004">BBa_K1336004</a> </td>
 +
                <td> &nbsp;PpDyP </td>
 +
                <td> &nbsp;Dye Decolourising Peroxidase PP_3248 </td>
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                <td> &nbsp;<em>Pseudomonas putida</em> </td>
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                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336004">864 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Primers">In Progress</a>]: primers designed </td>
 +
            </tr>
 +
            <tr>
 +
                <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336005">BBa_K1336005</a> </td>
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                <td> &nbsp;ispB RNAi </td>
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                <td> &nbsp;RNAi of Octaprenyl Diphosphate <br>Synthase fragment </td>
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                <td> &nbsp;<em>Escherichia coli, K12 strain</em> </td>
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                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336005">562 bp</a> </td>
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                <td> &nbsp;[<a href="/Team:UCL/Science/Experiment">New BioBrick Part</a>]: submitted </td>
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            </tr>
 +
            <tr>
 +
                <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td>
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                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336006">BBa_K1336006</a> </td>
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                <td> &nbsp;LacIEC+ispB </td>
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                <td> &nbsp;IPTG inducible ispB RNAi </td>
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                <td> &nbsp;<em>Escherichia coli, K12 strain </em> </td>
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                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336006">2208 bp</a> </td>
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                <td> &nbsp;[<a href="/Team:UCL/Science/Experiment">New BioBrick Device</a>]: submitted </td>
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            </tr>
 +
            <tr>
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                <td> <center><img src="https://static.igem.org/mediawiki/2014/e/e0/UCL_Bronze-metal-star.jpg" width="25px"></center> </td>
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                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K1336007">BBa_K1336007</a> </td>
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                <td> &nbsp;LacIEC+BsDyP </td>
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                <td> &nbsp;IPTG inducible BsDyP </td>
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                <td> &nbsp;<em>Bacillus subtilis</em> </td>
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                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K1336007">2895 bp</a> </td>
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                <td> &nbsp;[<a href="/Team:UCL/Science/Experiment">New BioBrick Device</a>]: submitted </td>
 +
            </tr>
 +
            <tr>
 +
                <td>  </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K729006">BBa_K729006</a> </td>
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                <td> &nbsp;CueO </td>
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                <td> &nbsp;Laccase </td>
 +
                <td> &nbsp;<em>Escherichia coli </em> </td>
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K729006">1612 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Experiment">In Progress</a>]: ascertaining identity </td>
 +
            </tr>
 +
            <tr>
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                <td> <center>(<img src="https://static.igem.org/mediawiki/2014/3/36/UCL_Gold-metal-star.jpg" width="25px">)</center> </td>
 +
                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K500000">BBa_K500000</a> </td>
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                <td> &nbsp;LiP </td>
 +
                <td> &nbsp;Lignin Peroxidase </td>
 +
                <td> &nbsp;<em>Phanerochaete chrysosporium</em> </td> <!-- <br>(White-Rot Fungi) -->
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K500000">1116 bp</a> </td> <!--Check size!-->
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Results">Improved Characterisation</a>]: toxicity issues in gene synthesis. <br>&nbsp;[<a href="/Team:UCL/Science/Experiment">In Progress</a>]: to subclone into pSB1C3/pSB3C5. </td>
 +
            </tr>
 +
            <tr>
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                <td> <center><img src="https://static.igem.org/mediawiki/2014/3/36/UCL_Gold-metal-star.jpg" width="25px"></center> </td>
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                <td> &nbsp;<a href="http://parts.igem.org/Part:BBa_K729004">BBa_K729004</a> </td>
 +
                <td> &nbsp;nucB </td>
 +
                <td> &nbsp;Extracellular nuclease </td>
 +
                <td> &nbsp;<em>Staphylococcus aureus</em> </td>
 +
                <td> &nbsp;<a href="/Team:UCL/Science/Sequences#BBa_K729004">561 bp</a> </td>
 +
                <td> &nbsp;[<a href="/Team:UCL/Science/Results">Improved Function</a>] </td>
 +
            </tr>
 +
        </tbody>
 +
    </table>
<br><br>
<br><br>
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The complementary action of azoreductase, lignin peroxidase, laccase, and bacterial peroxidases will be studied in order to find out the best possible approach of sequential reaction, and this core degradation module will be extrapolated to other areas such as BioArt projects and work on <a data-tip="true" class="top large" data-tip-content="Trying to set up the foundations for a synthetic ecology." href="javascript:void(0)"><b>algal-bacterial symbiosis</b></a>.<br><br><br></p>
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</p>
</div>
</div>
<!--- This is the first biobrick --->
<!--- This is the first biobrick --->
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<div id="view2"><div class="textTitle"><h4><a name="BBa_K1336000"><span>Azoreductase R2 (BBa_K1336000)</span></a></h4></div>
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<div id="view2"><div class="textTitle"><h4>Azoreductase (<a href="http://parts.igem.org/Part:BBa_K1336000">BBa_K1336000</a>)</h4></div><br>
<!-- This is the biobrick image -->
<!-- This is the biobrick image -->
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<img class="alignright" src="https://static.igem.org/mediawiki/2014/d/dd/BBa_K1336000.png" alt="" width=30%>
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<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/d/dd/BBa_K1336000.png" style="max-width: 100%;"></a>
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<p>This non-specific enzyme was isolated from <em>Bacillus subtilis</em>, although it is also found in other bacterial species, including those inhabiting the human intestine. It starts the <strong>degradation of azo dyes by cleaving the azo bond</strong>, composed of two nitrogens linked by a double bond (N=N), which is characteristic of all azo dyes. The products of this cleavage varies greatly among different dyes, but are generally aromatic amines. This azo cleavage does not only occur with azo dyes, but also with other molecules like Sulfasalazine, a drug that is broken down in the gut to release compounds that fight bowel disease and arthritis. We will isolate this enzyme from <em>B. subtilis</em> and convert it to BioBrick format via polymerase chain reaction (PCR).</p>
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<p>This enzyme was isolated from Bacillus subtilis, although it is also found in other bacterial species. It
 +
starts the degradation of azo dyes by reductively cleaving the azo bond.
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</p>
 +
<p>This azo cleavage, does not only occur with azo dyes, but also with other molecules like Sulfasalazine. We isolated this enzyme from B. subtilis and converted it to BioBrick format via polymerase chain reaction (PCR). However the site directed mutagenesis did not successfully remove the illegal restriction sites and therefore we could not characterise the effects.
 +
</p>
 +
<div class="textTitle"><h4>Azoreductase 1B6 (<a href="http://parts.igem.org/Part:BBa_K1336001">BBa_K1336001</a>)</h4></div><br>
 +
<!-- This is the biobrick image -->
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<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/5/5d/UCLBBAzo1b6.png" style="max-width: 100%;"></a>
 +
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
 +
<p>Another azoreductase that we will be using is isolated from Pseudomonas aeruginosa. It functions in the same way as Azoreductase R1 - cleaving the azo bond - but it is intended to work complementary with it, in order to cover a wider spectrum of dyes more efficiently.
 +
</p>
 +
 
 +
<p>Like the previous azoreductase, this BioBrick will be constructed using PCR. A promoter and a ribosomal binding site (RBS) will then be added to create a functioning composite device.
 +
<p>
 +
 
 +
<p>AzoR creates two or more aromatic amines (dependent on the number of azo bonds in the molecule) which are carcinogens. This is therefore only the first step of degradation. Some useful aromatic amines will be filtered off and sold as feedstock products for the fragrance industry which is further explained in the bioprocessing pages.
 +
</p>
 +
 
 +
<img src="https://static.igem.org/mediawiki/2014/0/0b/SSAzoReductase.png">
 +
<br>
</div>
</div>
<!--- This is the second biobrick --->
<!--- This is the second biobrick --->
-
<div id="view3"><div class="textTitle"><h4>Azoreductase 1B6 (BBa_K1336001)</h4></div>
+
<div id="view3"><div class="textTitle"><h4>Spore Coat Protein Laccase (<a href="http://parts.igem.org/Part:BBa_K1336002">BBa_K1336002</a>)</h4></div><br>
 +
<!-- This is the biobrick image -->
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/f/f6/UCL_BBa_K1336002.png" style="max-width: 100%;"></a>
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
-
<p>Another azoreductase that we will be using is isolated from <em>Pseudomonas aeruginosa</em>. It functions in the same way as Azoreductase R1 -  cleaving the azo bond - but it is intended to work complementary with it, in order to cover a wider spectrum of dyes more efficiently. Like the previous azoreductase, this BioBrick will be constructed using PCR. A promoter and a ribosomal binding site(RBS) will then be added to create a functioning composite device. </p>
+
<p>The laccase enzyme is a very non-specific oxidising enzyme. We intend to use it in concert with and as a second step to the azo reductase action to create no toxic products. Laccase will:
 +
<ul>
 +
<li>
 +
Break down azo bonds in specific azo dyes to non-toxic compounds
 +
</li>
 +
<li>Polymerise non-specific azoreductase breakdown products to filterable, non toxic compounds
 +
</li>
 +
<li>Oxidise specific azoreductase breakdown products to non-toxic compounds.
 +
</li>
 +
</ul>
 +
<p>The spanning range of reactions that take place in laccase are largely due to the unspecific copper mediated oxidising active site. Known reaction products are below, however these are known to break down further in ways not yet tested via NMR.  
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2014/4/4e/SSlaccase1.png">
 +
<img src="https://static.igem.org/mediawiki/2014/e/eb/SSLaccase2.png">
 +
<p>Despite laccase’s unspecific active site, it cannot break down sulphonated dyes and hence oxidation of those must be left for the peroxidases (see next tab.)
 +
</p><br>
</div>
</div>
<!--- This is the third biobrick --->
<!--- This is the third biobrick --->
-
<div id="view4"><div class="textTitle"><h4><a name="BBa_K1336003"><span>Lignin Peroxidase (BBa_K1336003)</span></a></h4></div>
+
<div id="view4"><div class="textTitle"><h4>Lignin Peroxidase (<a href="http://parts.igem.org/Part:BBa_K500000">BBa_K500000</a>)</h4></div><br>
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/f/f1/UCL_BBa_K500000.png" style="max-width: 95%;margin-top:-15%;"></a>
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
-
<p>Usually found in white-rot fungi species, its main function in nature is to participate in lignin-degrading processes by these organisms. However, it has also been found to <strong>play a role in azo dye degradation and decolourisation, by oxidative processes</strong>. This enzyme, like laccase, would be incorporated in the second step of the reaction to oxidise the products of the azo bond cleavage, in order to achieve greater detoxification. The sequence for the enzyme will be ordered and synthesised, including the BioBrick prefix and suffix. Again, it will function together with a promoter and a RBS.</p>
+
<p>Usually found in white-rot fungi species, its main function in nature is to participate in lignin-degrading processes by these organisms. However, it has also been found to play a role in <a data-tip="true" class="top large" data-tip-content="Using oxidative processes." href="javascript:void(0)"><b>azo dye degradation and decolourisation</b></a>. <br><br>This enzyme, like laccase, would be incorporated in the second step of the reaction to oxidise the products of the azo bond cleavage, in order to achieve greater detoxification. The sequence for the enzyme will be ordered and synthesised, including the BioBrick prefix and suffix. Again, it will function together with a promoter and a RBS.</p><br>
</div>
</div>
<!--- This is the fourth biobrick --->
<!--- This is the fourth biobrick --->
-
<div id="view5"><div class="textTitle"><h4><a name="BBa_K1336004"><span><em>Bacillus subtilis</em> dye-decolorizing peroxidase (BsDyP) (BBa_K1336004)</span></a></h4></div>
+
<div id="view5"><div class="textTitle"><h4><em>Bacillus subtilis</em> dye-decolorizing peroxidase (BsDyP) (<a href="http://parts.igem.org/Part:BBa_K1336003">BBa_K1336003</a>)</h4></div><br>
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/7/78/UCLBBLigningperoxidase.png" style="max-width: 95%;margin-top:-20%;"></a>
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
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-
<p>Found in <em>B. subtilis</em>, the physiological function of this newly discovered enzyme is still unclear, although it has <strong>shown effectiveness in degrading lignin and azo dyes</strong>, which makes it useful for us. It is not as effective as PpDyP for most compounds, but very efficient in degrading ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid)). The BioBrick will be constructed via PCR.</p>
+
<p>Found in <em>B. subtilis</em>, the physiological function of this newly discovered enzyme is still unclear, although it has shown effectiveness in degrading lignin and azo dyes, which makes it useful for us. It is not as effective as PpDyP for most compounds, but very efficient in degrading ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid)). <br><br>The BioBrick will be constructed via PCR.</p><br><br>
 +
<div class="textTitle"><h4><em>Pseudomonas putida</em> MET94 dye-decolorizing peroxidase (PpDyP) (<a href="http://parts.igem.org/Part:BBa_K1336004">BBa_K1336004</a>)</h4></div><br>
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/a/ad/UCLBBBsdyp.png" style="max-width: 95%;margin-top:-20%;"></a>
 +
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
 +
<p>This enzyme is found in <em>P. putida</em>. Although it is relatively novel, and has not yet been studied in detail, it seem to be an extremely versatile and powerful biocatalyst; it oxidises a wide <a data-tip="true" class="top large" data-tip-content="Such as azo dyes, anthraquinones, phenolic compounds, manganese or veratryl alcohol." href="javascript:void(0)"><b>variety of substrates</b></a> very efficiently. This will broaden the <a data-tip="true" class="top large" data-tip-content="Going further just azo dyes!" href="javascript:void(0)"><b>spectrum of action</b></a> of our decolourising device, and thus being able to degrade other toxic compounds typically found in industrial wastewaters. <br><br>This BioBrick will be constructed via PCR.</p><br>
</div>
</div>
<!--- This is the fifth biobrick --->
<!--- This is the fifth biobrick --->
-
<div id="view6"><div class="textTitle"><h4><a name="BBa_K1336005"><span><em>Pseudomonas putida</em> MET94 dye-decolorizing peroxidase (PpDyP) (BBa_K1336005)</span></a></h4></div>
+
<div id="view6"><div class="textTitle"><h4>Octaprenyl Diphosphate Synthase (ispB) (<a href="http://parts.igem.org/Part:BBa_K1336005">BBa_K1336005</a>)</h4></div><br>
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/9/9c/UCLBBPpdyp.png" style="max-width: 95%;margin-top:-15%;"></a>
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
-
<p>This enzyme is found in <em>P. putida</em>. Although it is relatively novel, and has not yet been studied in detail, it seem to be an extremely versatile and powerful biocatalyst; it <strong>oxidises a wide variety of substrates very efficiently, like azo dyes, anthraquinones, phenolic compounds, manganese or veratryl alcohol</strong>. This will broaden the spectrum of action of our decolourising device, going further just azo dyes, and thus being able to degrade other toxic compounds typically found in industrial wastewaters. BioBrick will be constructed via PCR.</p>
+
<p>Octaprenyl diphosphate synthase is a crucial enzyme in the E. coli metabolism, being responsible for the synthesis of the side chains of isoprene quinones.
 +
<br><br>In order to knock down this gene, an anti-sense RNA sequence was designed in BioBick format via PCR. This would allow us to, in the future, develop through bio-directed evolution an <em>E. coli</em> strain completely dependent on certain synthetic compounds, such as azo-dyes.</p><br><br>
</div>
</div>
 +
<!--- This is the fifth biobrick --->
 +
<div id="view7"><div class="textTitle"><h4>Extracellular Nuclease (nucB) (<a href="http://parts.igem.org/Part:BBa_K729004">BBa_K729004</a>)</h4></div><br>
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/e/ec/UCL_BBa_K729004.png" style="max-width: 95%;margin-top:-15%;"></a>
 +
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
 +
<p>This part, submitted by the 2012 UCL iGEM team, was tested in the presence of azo-dye contaminants as a safety approach involving the degradation of extracellular DNA, and thus inhibiting DNA transfer between our synthetic organism and other bacterial species present in the environment.
 +
<br><br><br> More information on the characterisation of this part can be found in the results page.</p><br>
</div>
</div>
 +
<div id="view8"><div class="textTitle"><h4>SpyGFP (<a href="http://parts.igem.org/Part:BBa_K239009">BBa_K239009</a>)</h4></div><br>
 +
<a data-tip="true" class="top large" data-tip-content="This diagram explains the basic construct of the BioBrick, the only part that changes is the selected function itself." href="javascript:void(0)" style="width: 30%;float: right;margin-left:2%"><img src="https://static.igem.org/mediawiki/2014/e/ec/UCL_BBa_K729004.png" style="max-width: 95%;margin-top:-15%;"></a>
 +
<!-- This is the main text. Anything in a <p>TEXT</p> is a paragraph and will be spaced appropriately-->
 +
<p>This part, developed by the 2012 UCL iGEM team, was designed to function as a stress-sensor, producing GFP when exposed to shear stress.
 +
<br><br>We aimed to re-purpose this sensor, testing whether the presence of the azo-dyes in the medium was detected by the cells as "stress", with a subsequent production of GFP.
 +
<br><br><br>
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Latest revision as of 03:58, 18 October 2014

Goodbye Azodye UCL iGEM 2014

BioBricks

Our BioBricks & how they lead to azo degradation


We have strove to complete a synthetic azo dye decolourising device in E. coli which incorporates several different independent enzymes that act on azo dyes and their breakdown products to create less toxic chemicals. After evaluating their individual breakdown characteristics, we aim to investigate the potential synergistic action of these enzymes in a single synthetic E. coli device and design a bioprocess which could be used to upscale the method to an industrial context.

Ideally, we wanted a Azo-Remediation Chassis (ARC), our BioBrick System, to be assembled as follows:



A further development on this prototype would be to have Bba_K1336000, the AzoR gene, to be inducibly transcribed by one promoter (say BBa_K314103, the LacI Expression Cassette) such that it is expressed in the reductive step of our azo dye remediation process. This would form a distinct BioBrick Device of "promotor A + AzoR + double terminator".
A secondary BioBrick Device (of "promoter B + gene 2 + double terminator") would follow this, where gene 2 would be one of our enzymes that function in the oxidative step of the azo dye remediation process, e.g. laccase or one of the dye decolourising peroxidases. A further tertiary BioBrick Device, with another oxidative enzyme would also be ideal. At least 2 oxidative enzymes are proposed as the enzymes are specialised for different substrates (as described in our BioBrick page.


In an industrial setting, these enzymes would work sequentially in a bioreactor with preset dynamic conditions. First, azoreductase will cleave the azo-bond (N=N), producing a series of highly toxic aromatic amines. Then, these compounds will be oxidised by lignin peroxidase, laccase and bacterial peroxidases, completing decolourisation and decreasing toxicity levels.

toxicity levels.

The complementary action of azoreductase, lignin peroxidase, laccase, and bacterial peroxidases will be studied in order to find out the best possible approach of sequential reaction. To ensure that the process is entirely bio-safe we have designed a xeno-biological modules that ensures that beyond the bioreactor our organism could not survive.






Registry ID Gene ID Name / Function Source Size Status
 BBa_K1336000  AzoR  FMN-dependent NADH-azoreductase 1  Pseudomonas putida  612 bp  [In Progress]: primers designed
 BBa_K1336001  1B6  AzoR heat-stable mutant  Pseudomonas putida  612 bp  [In Progress]: to remove 2 illegal PstI sites
 BBa_K1336002  CotA  Spore Coat Protein Laccase  Bacillus subtilis  1542 bp  [In Progress]: primers designed
 BBa_K1336003  BsDyP  Dye Decolourising Peroxidase BSU38260  Bacillus subtilis  1251 bp  [New BioBrick Part]: submitted
 BBa_K1336004  PpDyP  Dye Decolourising Peroxidase PP_3248  Pseudomonas putida  864 bp  [In Progress]: primers designed
 BBa_K1336005  ispB RNAi  RNAi of Octaprenyl Diphosphate
Synthase fragment
 Escherichia coli, K12 strain  562 bp  [New BioBrick Part]: submitted
 BBa_K1336006  LacIEC+ispB  IPTG inducible ispB RNAi  Escherichia coli, K12 strain  2208 bp  [New BioBrick Device]: submitted
 BBa_K1336007  LacIEC+BsDyP  IPTG inducible BsDyP  Bacillus subtilis  2895 bp  [New BioBrick Device]: submitted
 BBa_K729006  CueO  Laccase  Escherichia coli  1612 bp  [In Progress]: ascertaining identity
()
 BBa_K500000  LiP  Lignin Peroxidase  Phanerochaete chrysosporium  1116 bp  [Improved Characterisation]: toxicity issues in gene synthesis.
 [In Progress]: to subclone into pSB1C3/pSB3C5.
 BBa_K729004  nucB  Extracellular nuclease  Staphylococcus aureus  561 bp  [Improved Function]


Azoreductase (BBa_K1336000)


This enzyme was isolated from Bacillus subtilis, although it is also found in other bacterial species. It starts the degradation of azo dyes by reductively cleaving the azo bond.

This azo cleavage, does not only occur with azo dyes, but also with other molecules like Sulfasalazine. We isolated this enzyme from B. subtilis and converted it to BioBrick format via polymerase chain reaction (PCR). However the site directed mutagenesis did not successfully remove the illegal restriction sites and therefore we could not characterise the effects.

Azoreductase 1B6 (BBa_K1336001)


Another azoreductase that we will be using is isolated from Pseudomonas aeruginosa. It functions in the same way as Azoreductase R1 - cleaving the azo bond - but it is intended to work complementary with it, in order to cover a wider spectrum of dyes more efficiently.

Like the previous azoreductase, this BioBrick will be constructed using PCR. A promoter and a ribosomal binding site (RBS) will then be added to create a functioning composite device.

AzoR creates two or more aromatic amines (dependent on the number of azo bonds in the molecule) which are carcinogens. This is therefore only the first step of degradation. Some useful aromatic amines will be filtered off and sold as feedstock products for the fragrance industry which is further explained in the bioprocessing pages.


Spore Coat Protein Laccase (BBa_K1336002)


The laccase enzyme is a very non-specific oxidising enzyme. We intend to use it in concert with and as a second step to the azo reductase action to create no toxic products. Laccase will:

  • Break down azo bonds in specific azo dyes to non-toxic compounds
  • Polymerise non-specific azoreductase breakdown products to filterable, non toxic compounds
  • Oxidise specific azoreductase breakdown products to non-toxic compounds.

The spanning range of reactions that take place in laccase are largely due to the unspecific copper mediated oxidising active site. Known reaction products are below, however these are known to break down further in ways not yet tested via NMR.

Despite laccase’s unspecific active site, it cannot break down sulphonated dyes and hence oxidation of those must be left for the peroxidases (see next tab.)


Lignin Peroxidase (BBa_K500000)


Usually found in white-rot fungi species, its main function in nature is to participate in lignin-degrading processes by these organisms. However, it has also been found to play a role in azo dye degradation and decolourisation.

This enzyme, like laccase, would be incorporated in the second step of the reaction to oxidise the products of the azo bond cleavage, in order to achieve greater detoxification. The sequence for the enzyme will be ordered and synthesised, including the BioBrick prefix and suffix. Again, it will function together with a promoter and a RBS.


Bacillus subtilis dye-decolorizing peroxidase (BsDyP) (BBa_K1336003)


Found in B. subtilis, the physiological function of this newly discovered enzyme is still unclear, although it has shown effectiveness in degrading lignin and azo dyes, which makes it useful for us. It is not as effective as PpDyP for most compounds, but very efficient in degrading ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid)).

The BioBrick will be constructed via PCR.



Pseudomonas putida MET94 dye-decolorizing peroxidase (PpDyP) (BBa_K1336004)


This enzyme is found in P. putida. Although it is relatively novel, and has not yet been studied in detail, it seem to be an extremely versatile and powerful biocatalyst; it oxidises a wide variety of substrates very efficiently. This will broaden the spectrum of action of our decolourising device, and thus being able to degrade other toxic compounds typically found in industrial wastewaters.

This BioBrick will be constructed via PCR.


Octaprenyl Diphosphate Synthase (ispB) (BBa_K1336005)


Octaprenyl diphosphate synthase is a crucial enzyme in the E. coli metabolism, being responsible for the synthesis of the side chains of isoprene quinones.

In order to knock down this gene, an anti-sense RNA sequence was designed in BioBick format via PCR. This would allow us to, in the future, develop through bio-directed evolution an E. coli strain completely dependent on certain synthetic compounds, such as azo-dyes.



Extracellular Nuclease (nucB) (BBa_K729004)


This part, submitted by the 2012 UCL iGEM team, was tested in the presence of azo-dye contaminants as a safety approach involving the degradation of extracellular DNA, and thus inhibiting DNA transfer between our synthetic organism and other bacterial species present in the environment.


More information on the characterisation of this part can be found in the results page.


SpyGFP (BBa_K239009)


This part, developed by the 2012 UCL iGEM team, was designed to function as a stress-sensor, producing GFP when exposed to shear stress.

We aimed to re-purpose this sensor, testing whether the presence of the azo-dyes in the medium was detected by the cells as "stress", with a subsequent production of GFP.


Contact Us

University College London
Gower Street - London
WC1E 6BT
Biochemical Engineering Department
Phone: +44 (0)20 7679 2000
Email: ucligem2014@gmail.com

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