Team:Hong Kong CUHK/pah

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   <h2>PAH Degradation</h2>
   <h2>PAH Degradation</h2>
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  <p2> <h3>T7-RBS-QsrR (Device <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092001">BBa_K1092001</a>)</h3>
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  <p align="center"><img src="https://static.igem.org/mediawiki/2013/0/0a/20011.png"><img src="https://static.igem.org/mediawiki/2013/a/ac/20012.JPG" height="300"></p>
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  <p2> <h1>T7-RBS-QsrR (Device <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092001">BBa_K1092001</a>)</h1>
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   <p>Quinone  sensing and response repressor (QsrR) is a novel kind of thiol-stress-sensing  regulator YodB family transcriptional regulator found in the notorious pathogen <em>Staphylococcus aureus</em>. [2] It specifically  binds to a palindromic DNA sequence, blocking RNA polymerase and thus  repressing transcription. [2] However, with the presence of quinone, it  reshapes to bind with quinone molecules and leaves the target DNA, which allows  the transcription process to start. [2] Since laccase is used at first to  degrade PAHs into quinones for the proposed pathway, the quinone-like compounds  produced as intermediates can function as signaling molecules that induce the  expression of other enzymes responsible for subsequent degradations. This  method can save energy for the cell that expresses those PAH-degrading enzymes.  The protein sequence of QsrR is readily available at GenBank, with the  reference code 4HQE_A for side chain A, and 4HQE_B for side chain B.</p>
   <p>Quinone  sensing and response repressor (QsrR) is a novel kind of thiol-stress-sensing  regulator YodB family transcriptional regulator found in the notorious pathogen <em>Staphylococcus aureus</em>. [2] It specifically  binds to a palindromic DNA sequence, blocking RNA polymerase and thus  repressing transcription. [2] However, with the presence of quinone, it  reshapes to bind with quinone molecules and leaves the target DNA, which allows  the transcription process to start. [2] Since laccase is used at first to  degrade PAHs into quinones for the proposed pathway, the quinone-like compounds  produced as intermediates can function as signaling molecules that induce the  expression of other enzymes responsible for subsequent degradations. This  method can save energy for the cell that expresses those PAH-degrading enzymes.  The protein sequence of QsrR is readily available at GenBank, with the  reference code 4HQE_A for side chain A, and 4HQE_B for side chain B.</p>
   <p>QsrR  Binding region:<br />
   <p>QsrR  Binding region:<br />
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     [1] CHI, B.K.,  ALBRECHT, D., GRONAU, K., BECHER, D., HECKER, M. and ANTELMANN, H., 2010. The  redox-sensing regulator YodB senses quinones and diamide via a thiol-disulfide  switch in Bacillus subtilis. Proteomics, 10(17), pp. 3155-3164.<br />
     [1] CHI, B.K.,  ALBRECHT, D., GRONAU, K., BECHER, D., HECKER, M. and ANTELMANN, H., 2010. The  redox-sensing regulator YodB senses quinones and diamide via a thiol-disulfide  switch in Bacillus subtilis. Proteomics, 10(17), pp. 3155-3164.<br />
     [2] JI, Q.,  ZHANG, L., JONES, M.B., SUN, F., DENG, X., LIANG, H., CHO, H., BRUGAROLAS, P.,  GAO, Y.N., PETERSON, S.N., LAN, L., BAE, T. and HE, C., 2013. Molecular  mechanism of quinone signaling mediated through S-quinonization of a YodB  family repressor QsrR. Proceedings of the National Academy of Sciences,  110(13), pp. 5010-5015.</p>
     [2] JI, Q.,  ZHANG, L., JONES, M.B., SUN, F., DENG, X., LIANG, H., CHO, H., BRUGAROLAS, P.,  GAO, Y.N., PETERSON, S.N., LAN, L., BAE, T. and HE, C., 2013. Molecular  mechanism of quinone signaling mediated through S-quinonization of a YodB  family repressor QsrR. Proceedings of the National Academy of Sciences,  110(13), pp. 5010-5015.</p>
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<p>&nbsp;</p>
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   <h1>T7-RBS-Laccase (Device <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092005">BBa_K1092005</a>)</h1>
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    <h3>T7 - RBS – Dioxygenase (Device <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092003">BBa_K1092003</a>)</h3>
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    <p align="center"> <img src="https://static.igem.org/mediawiki/2013/e/e0/20031.png"><img src="https://static.igem.org/mediawiki/2013/e/e6/20032.png" height="300"> </p>
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<p>Catechol 1,2- dioxygenase (EC 1.13.11.1) from <em>Pseudomonas putida</em> KT2400 is an oxidative enzyme which induces  ortho-ring cleavage of catechol, a phenolic compound [1, 5]. The gene sequence  is available in GenBank (1045930).</p>
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      <p>&nbsp;</p>
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   <h3>T7-RBS-Laccase (Device <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092005">BBa_K1092005</a>)</h3>
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  <p align="center"><img src="https://static.igem.org/mediawiki/2013/f/fa/2005.png"><img src="https://static.igem.org/mediawiki/2013/d/dd/20051.png" height="300"></p>
   <p>The laccase (cotA) found in <em>Bacillus</em> sp. HR03 is a bacterial laccase  that have the potential ability to degrade a variety of aromatic compounds. [3]  Previous study showed that it can be successfully expressed in <em>Escherichia coli</em> strain BL-21(DE3), and  was correctly folded. [4] Moreover, the complete gene sequence of this laccase  was readily recorded in GenBank, with the reference code of FJ663050.1. It is  thus used as one of the two major enzymes for PAH degradation.</p>
   <p>The laccase (cotA) found in <em>Bacillus</em> sp. HR03 is a bacterial laccase  that have the potential ability to degrade a variety of aromatic compounds. [3]  Previous study showed that it can be successfully expressed in <em>Escherichia coli</em> strain BL-21(DE3), and  was correctly folded. [4] Moreover, the complete gene sequence of this laccase  was readily recorded in GenBank, with the reference code of FJ663050.1. It is  thus used as one of the two major enzymes for PAH degradation.</p>
   <p>Properties of the laccase:<br />
   <p>Properties of the laccase:<br />
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     [5]  SHARMA, P., GOEL, R. and CAPALASH, N., 2007. Bacterial laccases. World Journal  of Microbiology and Biotechnology, 23(6), pp. 823-832.<br />
     [5]  SHARMA, P., GOEL, R. and CAPALASH, N., 2007. Bacterial laccases. World Journal  of Microbiology and Biotechnology, 23(6), pp. 823-832.<br />
     [6]  ZENG, J., LIN, X., ZHANG, J., ZHU, H., CHEN, H. and WONG, M., 2013. Successive  transformation of benzo[a]pyrene by laccase of <em>Trametes versicolor</em> and pyrene-degrading <em>Mycobacterium</em> strains. Applied Microbiology and Biotechnology,  97(7), pp. 3183-3194.</p>
     [6]  ZENG, J., LIN, X., ZHANG, J., ZHU, H., CHEN, H. and WONG, M., 2013. Successive  transformation of benzo[a]pyrene by laccase of <em>Trametes versicolor</em> and pyrene-degrading <em>Mycobacterium</em> strains. Applied Microbiology and Biotechnology,  97(7), pp. 3183-3194.</p>
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   <h1>FL3-Lgt-FL3 (Protein Domain <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092103">BBa_K1092103</a>)</h1>
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   <h3>T7 - QsrR Binding Site - RBS – Dioxygenase (Device <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1092014">BBa_K1092014</a>)</h3>
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   <p>Transmembrane protein Lgt with two flexible linkers FL3
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This is a biobrick we adapted from SJTU 2012 team, BBa_K771102.
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  <p>This biobrick is similar to BBa_K1092003: T7 - RBS - Dioxygenase, with an additional QsrR binding site that allows QsrR regulation.</p>
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Prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein of E.coli. Lgt serves as transmembrane domain in our project. To link upstream and downstream domains and enzymes with Lgt, we add a flexible linker FL3 on both sides of Lgt.
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   Address: Rm. 184, Science Centre, CUHK <br/>
   Address: Rm. 184, Science Centre, CUHK <br/>
   Email: kingchan@cuhk.edu.hk  Tel: (852)-39434420  Fax: (852)-26037246
   Email: kingchan@cuhk.edu.hk  Tel: (852)-39434420  Fax: (852)-26037246
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