Difference between revisions of "Team:Austin UTexas/Parts"

 
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{{Austin_UTexas}}
 
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<h2>Registry Parts</h2>
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<p> We submitted three parts to the registry.  These parts are described below.  The link to each page is shown in bold text.</p>
  
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<h3>pH Sensors</h3>
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<h2><center>Parts</center></h2>
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<h4>CpxA-CpxR</h4>
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<h2>pH Sensors</h2>
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<p>CpxA-CpxR is a two-component mechanism that is activated at pH 7.4 and repressed at pH 6.0. CpxA is an intermembrane protein that autophosphorylates at a certain external pH, CpxR (a kinase) then gets phosphorylated by CpxA and acts as a transcription factor. This system originally is a transcription factor for the virF gene, but virF was replaced with a reporter. The original sequence was found in <i>Shigella sonnei</i>, but E. coli has a homolog of these proteins so all that is required on the construct is the appropriate prefix/suffix and CpxR binding site. <b>The BioBrick can be found on the iGEM registry as: <a href="http://parts.igem.org/Part:BBa_K2097000">K2097000</a></b>, as well as on our results page <a href="https://2016.igem.org/Team:Austin_UTexas/Results#section6">here</a>.</p>
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Possessing the ability to monitor the brewing process of kombucha without disturbing the microenvironment and using a very visible color reporter would allow for greater insights as to how the populations of organisms and pH may change due to competition amongst other bacteria and yeast in the beverage and SCOBY of the kombucha. The byproducts produced by the kombucha as it brews causes the tea to become more acidic, leading to our team searching for pH sensitive promoters, and for ways to implement these into kombucha.
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Though an acidic sensor was what was required for our kombucha analysis, the identification of sensors in other areas of the pH spectrum were explored as well. Three sequences were identified, the CadC operon for the acidic range, CpxA-CpxR complex for the neutral range, and the P-atp2 promoter from the BioBrick Registry (<a href="http://parts.igem.org/Part:BBa_K1675021">BBa_K1675021</a>) for the basic range. Each sequence was paired with a unique corresponding reporter sequence so that if each pH sensitive plasmid were in the same environment, the specific pH of the system could be seen. The reporters used were, <a href="http://parts.igem.org/Part:BBa_E1010">BBa_E1010</a> for the CadC construct, <a href="http://parts.igem.org/Part:BBa_K1033916">BBa_K1033916</a> for the CpxA-CpxR complex, and <a href="http://partsregistry.org/Part:BBa_K592009">BBa_K592009</a> for the P-atp2 promoter.
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<u>CadC</u>
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The CadC operon is a native pathway in <i>E. coli</i>, involved in the cadaverine synthesis pathway. The protein CadC protein on the operon is produced and activates segments downstream of the operon on the CadBA receptors. The CadC protein is pH sensitive to an external pH 5.5 and below, as well as lysine dependent. A point mutation on codon 265, in which argenine is converted to cystine, causes the CadC protein to become lysine independent (Dell, Neely, Olson, 1994).
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Unfortunately, we have been unable to grow the modified CadC operon in <i>E. coli</i> suggesting some form of cell toxicity. Due to this apparent toxicity, no data regarding this mutant CadC could be collected. Alternative candidates are being explored for other pH sensors that sense in the acidic range.
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<u>CpxA-CpxR</u>
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CpxA-CpxR is a two-component mechanism that is activated at pH 7.4 and repressed at pH 6.0. CpxA is an intermembrane protein that autophosphorylates at a certain external pH, CpxR (a kinase) then gets phosphorylated by CpxA and acts as a transcription factor. This system originally is a transcription factor for the virF gene, but we replaced virF with the Reporter. The original sequence was found in Shigella sonnei, but E. coli has a homolog of these proteins so all that is required on the construct is the appropriate prefix/suffix and CpxR binding site.
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[[File:T--Austin_UTexas--Cpx_pH_Culture_Tubes_2.png|thumb|left|600px| Insert caption here.]]
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The order from left to right is Control pH 6-9 and then Experimental pH 6-9. These are showing the gradient change in expression accordingly with the change of pH due to a pH-dependent promotor compared to consistent expression accordingly with a promoter that is always "on". The main point is that the Control at pH 6 has more expression of the Yellow-Green Chromoprotein than the Experimental at pH 6. The pH-Dependent promoter of the Experimental group is down-regulated at pH 6 whereas the control is not. Also, there is an increase in YGCP expression between the Experiment pH 7 and pH 8 that is not seen in the Control between pH 7 and pH 8. The normalized data is below shows the relative expression of YGCP. The construct can be found on the iGEM registry as: Bba_K2097000.
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[[File:T--Austin_UTexas--pH_Dependent_Promoter.jpeg|thumb|left|600px| Insert caption here.]]
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<u>P-atp2</u>
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The P-atp2 promoter, native to the bacterium <i>Corynebacterium glutamicum</i> is reportedly induced at pH 7, to pH 9 (<a href="https://2015.igem.org/Team:BIT-China/Parts">BIT-China-2015</a> and <a href="http://parts.igem.org/Part:BBa_K1675021">BBa_K1675021</a>). Utilizing the blue chromoprotein (<a href="http://partsregistry.org/Part:BBa_K592009">BBa_K592009</a>), a test was designed in which a plasmid containing the P-atp2 promoter with the blue chromoprotein was grown alongside an <i>E. coli</i> line that contained a plasmid with just the blue chromoprotein. We expected to see constant blue chromoprotein production in the control series (those that lacked P-atp2) and a visual increase in blue chromoprotein as the pH was raised from 6 to 9 in the cells that contained the P-atp2 construct.
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<u>Next Steps and the GOX Sequences as Putative Promoters</u>
 
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<a href="http://parts.igem.org/Part:BBa_K2097001">Blue chromoprotein with strong promoter and RBS</a>
 
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<a href="http://parts.igem.org/Part:BBa_K2097002">Yellow-green chromoprotein with medium promoter and RBS</a>
 
  
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<h3>Composite Parts</h3>
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<h4>Blue Chromoprotein</h4>
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<p>This is a composite part made up of <a href="http://partsregistry.org/Part:BBa_K592009">BBa_K592009</a> (blue chromoprotein) and <a href="http://partsregistry.org/Part:BBa_K608002"> BBa_K608002  </a> (a strong RBS and promoter). The protein exhibits a strong blue/purple color when expressed. <a href="http://partsregistry.org/Part:BBa_K608002"> BBa_K608002 </a> is made up of a promoter, <a href="http://partsregistry.org/Part:BBa_J23104"> BBa_J23104</a>, and an RBS, <a href="http://partsregistry.org/Part:BBa_K608002"> BBa_B0034</a>. <b>The BioBrick can be found on the iGEM registry as: <a href="http://parts.igem.org/Part:BBa_K2097001">K2097001</a></b>, as well as on our results page <a href="https://2016.igem.org/Team:Austin_UTexas/Results">here</a>.</p>
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<h4>Yellow-Green Chromoprotein</h4>
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<p>This is a composite part made up of <a href="http://parts.igem.org/Part:BBa_K1033916">BBa_K1033916</a> (amajLime, a yellow-green chromoprotein) and <a href="http://parts.igem.org/Part:BBa_K608006"> BBa_K608006</a> (a medium promoter and RBS). It is made up of a medium promoter, <a href="http://parts.igem.org/Part:BBa_J23110"> BBa_J23110</a>, and a medium RBS, <a href="http://parts.igem.org/Part:BBa_B0032"> BBa_B0032</a>. <b>The BioBrick can be found on the iGEM registry as: <a href="http://parts.igem.org/Part:BBa_K2097002">K2097002</a></b>, as well as on our results page <a href="https://2016.igem.org/Team:Austin_UTexas/Results">here</a></p>
 
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
 
<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
 
<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing 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.</p>
 
<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing 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.</p>
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<p>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 you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
 
<p>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 you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
 
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Latest revision as of 00:03, 20 October 2016

Registry Parts


We submitted three parts to the registry. These parts are described below. The link to each page is shown in bold text.

pH Sensors


CpxA-CpxR

CpxA-CpxR is a two-component mechanism that is activated at pH 7.4 and repressed at pH 6.0. CpxA is an intermembrane protein that autophosphorylates at a certain external pH, CpxR (a kinase) then gets phosphorylated by CpxA and acts as a transcription factor. This system originally is a transcription factor for the virF gene, but virF was replaced with a reporter. The original sequence was found in Shigella sonnei, but E. coli has a homolog of these proteins so all that is required on the construct is the appropriate prefix/suffix and CpxR binding site. The BioBrick can be found on the iGEM registry as: K2097000, as well as on our results page here.

Composite Parts


Blue Chromoprotein

This is a composite part made up of BBa_K592009 (blue chromoprotein) and BBa_K608002 (a strong RBS and promoter). The protein exhibits a strong blue/purple color when expressed. BBa_K608002 is made up of a promoter, BBa_J23104, and an RBS, BBa_B0034. The BioBrick can be found on the iGEM registry as: K2097001, as well as on our results page here.


Yellow-Green Chromoprotein

This is a composite part made up of BBa_K1033916 (amajLime, a yellow-green chromoprotein) and BBa_K608006 (a medium promoter and RBS). It is made up of a medium promoter, BBa_J23110, and a medium RBS, BBa_B0032. The BioBrick can be found on the iGEM registry as: K2097002, as well as on our results page here