Team:ITB Indonesia/Parts

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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:ITB_Indonesia/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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<a href="https://2014.igem.org/Team:ITB_Indonesia"style="color:#000000">Home </a> </td>
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<a href="https://2014.igem.org/Team:ITB_Indonesia/Team"style="color:#000000"> Team </a> </td>
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<a href="https://2014.igem.org/Team:ITB_Indonesia/Parts"style="color:#000000"> Parts</a></td>
 
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<ul>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia">HOME</a></li>
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<li>TEAM
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<ul>
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<li><a href="https://igem.org/Team.cgi?id=1387" >OFFICIAL TEAM PROFILE</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Team">TEAM MEMBER</a></li>
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</ul>
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</li>
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<li>PROJECT
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<ul>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Project">OVERVIEW</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/DegMod">DEGRADATION MODULE</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/ConMod">CONVERTION MODULE</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/RepMod">REPORTER MODULE</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/SelfMod">SELF REGULATORY MODULE</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/FutureSystem">FUTURE SYSTEM</a></li>
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    </ul>
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</li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Modeling">MODELING</a></li>
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<li>WETLAB
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<ul>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/protocol">PROTOCOL</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Parts">PARTS</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Attributions">ATTRIBUTIONS</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Safety">SAFETY</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Data">DATA</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/ProteinModel">PROTEIN MODEL</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Achievement">ACHIEVEMENT</a></li>
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</ul>
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</li>
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<li>NOTEBOOK
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<ul>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/nb-wetlab">WETLAB</a></li>
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</ul>
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</li>
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<li>HUMAN PRACTICE
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<ul>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Unpas">INTRO SYNBIO TO UNPAS</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/SynBio">SYNBIO CLASS</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/SynbiGreen">SYNBIGREEN SURVEY</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Medsos">SOCIAL MEDIA</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/OnMedia">MEDIA</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Biosafety">BIOSAFETY SEMINAR</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/MeetUp">INDONESIA TEAMS MEET UP</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/Kids">FUN WITH KIDS</a></li>
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<li><a href="https://2014.igem.org/Team:ITB_Indonesia/UPI">SHARING SYNBIO IN UPI</a></li>
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</ul>
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</li>
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</ul>
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</div>
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<!--Parts Submitted to the Registry  -->
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<br>
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<tr><td > <h3> Parts Submitted to the Registry </h3></td>
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<h1>PARTS</h1>
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<td ></td >
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<br>
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<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
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<img src="https://static.igem.org/mediawiki/2014/d/db/Parts1.JPG">
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<br>
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<h1>PARTS DESCRIPTION</h1>
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<p>
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<br>
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An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox.
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<ol type="A">
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<li>Reporter Module</li>
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<p>
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<img src="https://static.igem.org/mediawiki/2014/8/8c/RepMod.JPG">
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<strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.  
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<p align="justify">The construction of reporter module is consist of inducible promoter PibpAB <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K339010">(BBa_K339010)</a>, RBS <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0034">(BBa_B0034)</a>, amilCP <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K592025">(BBa_K592025) </a>, and double terminator <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0015"> (Bba_B0015) </a>. BBa_K1387000 consist of RBS (Bba_B0034), amilCP (BBa_K592025) and double terminator  (BBa_B0015), while the complete module was contained in <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K1387001">(Bba_K1387001)</a>. The reporter module will have a blue chromoprotein when the inclusion body is formed in the cell. This mechanism then acts as an indicator of cytoplasmic stress, in this situation is caused by inclussion body.</p>
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</p>
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<br><li>Degradation Module</li>
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<img src="https://static.igem.org/mediawiki/2014/6/69/DegMod.JPG">
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<p>
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<p align="justify">The casette of degradation module <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K1387006">(BBa_K1387006) </a> is comprised of constitutive promoter, tet operator, RBS, outer membrane protein A (ompA) fused with LC Cutinase, and double terminator. By using constitutive promoter, we expect the recombinant protein, in this case ompA-LC Cutinase, will be synthesized indefinitely. OmpA is outer membrane protein, it comprises of β–strand B3-B7. Rather than using full sequence of ompA, we use ompA (46-159) fused with lipoprotein signal sequence, thus exposing it on the cell surface of bacteria1. We fuse lpp-ompA with LC Cutinase, an enzyme that exhibit esterase activity. LC-Cutinase esterase activity will cleave the ester bond on PET and releasing terephthalic acid and ethylene glycol as a product. Fusion strategy of lpp-ompA on LC Cutinase gene is one of our way to create a whole cell biocatalyst which will be an effective molecular machinery to degrade PET on the environment. Due to constitutive expression of the recombinant protein in E.coli, there is a possibility of formation of insoluble protein inside the cell (inclusion body), because of that, we put tet operator upstream of RBS for further regulation (Georgiou et al, 1996).</p>
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Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.
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<br><li>Self-Regulatory Module</li>
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</p>
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<img src="https://static.igem.org/mediawiki/2014/b/b4/Sr1.JPG">
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<p align="justify">pIBPAB is a hybrid promoter that induced by inclusion body from unfunctional protein. This promoter followed by strong RBS <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0034">(BBa_B0034)</a>, make a new part called  <a style="color:#342D7E" href="http://parts.igem.org/Part:Bba_K1387005"> Bba_K1387005 </a> </p>
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<img src="https://static.igem.org/mediawiki/2014/d/de/Sr2.JPG">
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<p align="justify">This casette <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0034">(BBa_K1387002)</a> consist of TetR <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_C0040">(BBa_C0040)</a> and Double Terminator <a style="color:#342D7E"href="http://parts.igem.org/Part:BBa_B0015"> (Bba_B0015) </a>. TetR is tetracycline repressor that bind to operator region and repressing the expression of downstream gene. In our system, the degradation module consist of TetO (Tet Operator) which is region of TetR (Tet Repressor) placed.</p>
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<h3>When should you put parts into the Registry?</h3>
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<br><img src="https://static.igem.org/mediawiki/2014/f/f2/Sr3.JPG">
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<p>The construction of reporter module is consist of inducible promoter PibpAB <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K339010">(BBa_K339010)</a>RBS <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0034">(BBa_B0034)</a>, amilCP <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K592025">(BBa_K592025) </a>, and double terminator <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0015"> (Bba_B0015) </a>. <a style="color:#342D7E"href="hhttp://parts.igem.org/Part:BBa_K1387000"> BBa_K1387000 </a> consist of RBS <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0034">(BBa_B0034)</a>, amilCP <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K592025">(BBa_K592025) </a> and double terminator <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_B0015"> (Bba_B0015) </a>, while the complete module was contained in <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K1387001">BBa_K1387001 </a>. The reporter module will have a blue chromoprotein when the inclusion body is formed in the cell. This mechanism then acts as an indicator of cytoplasmic stress, in this situation is caused by inclussion body.</p>
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<p>
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<br><li>Convertion Module</li>
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As soon as possible! We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.  
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<img src="https://static.igem.org/mediawiki/2014/7/7a/ConMod.JPG">
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</p>
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<p align="justify">Improvisation the part submitted by UC Davis team <a style="color:#342D7E" href="http://parts.igem.org/Part:BBa_K936024">BBa_K936024</a> by combining the construct with terminator, so we can characterize the expression of the enzymes and performe the assay for ethylene glycol utilization better than before. We name this BioBrick as convertion module.</p>
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The information needed to initially create a part on the Registry is:
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<li>Part Name</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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<br><li>References</li>
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<p align="justify">Georgiou,G., Stephens,L., Stathopoulos,C., Poetschke,L., Mendenhall,J.,  and Earhart,F. 1996. Display of β-Lactamase on Eschericia coli Surface : Outer Membrane Phenotypes Conferred by Lpp’-ompA’- β-Lactamase Fusions. <i> Protein Engineering, 9, 239-247</i>.</p>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part.
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You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry"> Add a Part to the Registry</a> link.
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<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
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<groupparts>iGEM013 ITB_Indonesia</groupparts>
 

Latest revision as of 02:11, 18 October 2014


PARTS




PARTS DESCRIPTION


  1. Reporter Module
  2. The construction of reporter module is consist of inducible promoter PibpAB (BBa_K339010), RBS (BBa_B0034), amilCP (BBa_K592025) , and double terminator (Bba_B0015) . BBa_K1387000 consist of RBS (Bba_B0034), amilCP (BBa_K592025) and double terminator (BBa_B0015), while the complete module was contained in (Bba_K1387001). The reporter module will have a blue chromoprotein when the inclusion body is formed in the cell. This mechanism then acts as an indicator of cytoplasmic stress, in this situation is caused by inclussion body.


  3. Degradation Module
  4. The casette of degradation module (BBa_K1387006) is comprised of constitutive promoter, tet operator, RBS, outer membrane protein A (ompA) fused with LC Cutinase, and double terminator. By using constitutive promoter, we expect the recombinant protein, in this case ompA-LC Cutinase, will be synthesized indefinitely. OmpA is outer membrane protein, it comprises of β–strand B3-B7. Rather than using full sequence of ompA, we use ompA (46-159) fused with lipoprotein signal sequence, thus exposing it on the cell surface of bacteria1. We fuse lpp-ompA with LC Cutinase, an enzyme that exhibit esterase activity. LC-Cutinase esterase activity will cleave the ester bond on PET and releasing terephthalic acid and ethylene glycol as a product. Fusion strategy of lpp-ompA on LC Cutinase gene is one of our way to create a whole cell biocatalyst which will be an effective molecular machinery to degrade PET on the environment. Due to constitutive expression of the recombinant protein in E.coli, there is a possibility of formation of insoluble protein inside the cell (inclusion body), because of that, we put tet operator upstream of RBS for further regulation (Georgiou et al, 1996).


  5. Self-Regulatory Module
  6. pIBPAB is a hybrid promoter that induced by inclusion body from unfunctional protein. This promoter followed by strong RBS (BBa_B0034), make a new part called Bba_K1387005

    This casette (BBa_K1387002) consist of TetR (BBa_C0040) and Double Terminator (Bba_B0015) . TetR is tetracycline repressor that bind to operator region and repressing the expression of downstream gene. In our system, the degradation module consist of TetO (Tet Operator) which is region of TetR (Tet Repressor) placed.


    The construction of reporter module is consist of inducible promoter PibpAB (BBa_K339010)RBS (BBa_B0034), amilCP (BBa_K592025) , and double terminator (Bba_B0015) . BBa_K1387000 consist of RBS (BBa_B0034), amilCP (BBa_K592025) and double terminator (Bba_B0015) , while the complete module was contained in BBa_K1387001 . The reporter module will have a blue chromoprotein when the inclusion body is formed in the cell. This mechanism then acts as an indicator of cytoplasmic stress, in this situation is caused by inclussion body.


  7. Convertion Module
  8. Improvisation the part submitted by UC Davis team BBa_K936024 by combining the construct with terminator, so we can characterize the expression of the enzymes and performe the assay for ethylene glycol utilization better than before. We name this BioBrick as convertion module.


  • References
  • Georgiou,G., Stephens,L., Stathopoulos,C., Poetschke,L., Mendenhall,J., and Earhart,F. 1996. Display of β-Lactamase on Eschericia coli Surface : Outer Membrane Phenotypes Conferred by Lpp’-ompA’- β-Lactamase Fusions. Protein Engineering, 9, 239-247.