Difference between revisions of "Team:Uppsala/Reporter System"

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                 <h1 id="first-title">UnaG Troubleshooting</h1>
 
                 <h1 id="first-title">UnaG Troubleshooting</h1>
  
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                 <p>One of the biobrick parts submitted by the 2016 Uppsala team was <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2003011"><b>UnaG combined with a histidine tag and a flexible linker</b></a> for extraction in affinity chromatography.  We decided to use this part as our reporter system when we read about it.  Mammalian intestines naturally have small amounts of bilirubin in them and also have a limited amount of oxygen present[3] (which is necessary for chromoprotein maturation [4]). we thought this could be a useful reporter.  It also came with a flexible linker, which could be used to potentially connect this reporter system with another output molecule that might be usable to act as a secondary reporter to help detect our target nematodes.   
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                 <p>One of the biobrick parts submitted by the 2016 Uppsala team was <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2003011"><b>UnaG combined with a histidine tag and a flexible linker</b></a> for extraction in affinity chromatography.  We decided to use this part as our reporter system when we read about it.  Mammalian intestines naturally have small amounts of bilirubin in them and also have a limited amount of oxygen present [1] (which is necessary for chromoprotein maturation [2]). we thought this could be a useful reporter.  It also came with a flexible linker, which could be used to potentially connect this reporter system with another output molecule that might be usable to act as a secondary reporter to help detect our target nematodes.   
 
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While observing this part's sequence however, we found that there was an error and no histidine tag would be expressed due to the start codon being placed after the histidine tag.  In addition, this part would also express less or no UnaG at all due to the RBS now having a significant amount of space between it and the start codon.  We decided to incorporate this biobrick part into a custom composite part by moving the start codon to its proper location and then proving that the histidine tag works by extracting and purifying the protein via affinity chromatography.  In addition, we conducted a fluorescent bilirubin test and used a plate reader to determine if our new part expressed more UnaG than the 2016 part.  </p>
 
While observing this part's sequence however, we found that there was an error and no histidine tag would be expressed due to the start codon being placed after the histidine tag.  In addition, this part would also express less or no UnaG at all due to the RBS now having a significant amount of space between it and the start codon.  We decided to incorporate this biobrick part into a custom composite part by moving the start codon to its proper location and then proving that the histidine tag works by extracting and purifying the protein via affinity chromatography.  In addition, we conducted a fluorescent bilirubin test and used a plate reader to determine if our new part expressed more UnaG than the 2016 part.  </p>
 
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                 <P>However extraction of this protein poses some difficulty.  UnaG, many other chromoproteins, is a membrane protein [1] and therefore needs special conditions to purify.  The following report will show how we successfully extracted and purified UnaG from BL21 E. coli cells expressing our custom made plasmid.   
+
                 <P>However extraction of this protein poses some difficulty.  UnaG, many other chromoproteins, is a membrane protein [3] and therefore needs special conditions to purify.  The following report will show how we successfully extracted and purified UnaG from BL21 E. coli cells expressing our custom made plasmid.   
 
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<h1>Refereces</h1>
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<p><strong>[1]</strong> Bowen R. Microbial Life in the Digestive Tract. online: http://www.vivo.colostate.edu/hbooks/pathphys/digestion/basics/gi_bugs.html. Accessed October 12, 2018.<br><br>
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<strong>[2]</strong> Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology | Journal of Biological Engineering | Full Text. online: https://jbioleng.biomedcentral.com/articles/10.1186/s13036-018-0100-0. Accessed October 12, 2018. <br><br>
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<strong>[3]</strong> Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. 2013. A Bilirubin-Inducible Fluorescent Protein from Eel Muscle. Cell 153: 1602–1611.</p>
  
  
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Revision as of 11:22, 14 October 2018

UnaG Troubleshooting

One of the biobrick parts submitted by the 2016 Uppsala team was UnaG combined with a histidine tag and a flexible linker for extraction in affinity chromatography. We decided to use this part as our reporter system when we read about it. Mammalian intestines naturally have small amounts of bilirubin in them and also have a limited amount of oxygen present [1] (which is necessary for chromoprotein maturation [2]). we thought this could be a useful reporter. It also came with a flexible linker, which could be used to potentially connect this reporter system with another output molecule that might be usable to act as a secondary reporter to help detect our target nematodes.

While observing this part's sequence however, we found that there was an error and no histidine tag would be expressed due to the start codon being placed after the histidine tag. In addition, this part would also express less or no UnaG at all due to the RBS now having a significant amount of space between it and the start codon. We decided to incorporate this biobrick part into a custom composite part by moving the start codon to its proper location and then proving that the histidine tag works by extracting and purifying the protein via affinity chromatography. In addition, we conducted a fluorescent bilirubin test and used a plate reader to determine if our new part expressed more UnaG than the 2016 part.


However extraction of this protein poses some difficulty. UnaG, many other chromoproteins, is a membrane protein [3] and therefore needs special conditions to purify. The following report will show how we successfully extracted and purified UnaG from BL21 E. coli cells expressing our custom made plasmid.







Refereces

[1] Bowen R. Microbial Life in the Digestive Tract. online: http://www.vivo.colostate.edu/hbooks/pathphys/digestion/basics/gi_bugs.html. Accessed October 12, 2018.

[2] Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology | Journal of Biological Engineering | Full Text. online: https://jbioleng.biomedcentral.com/articles/10.1186/s13036-018-0100-0. Accessed October 12, 2018.

[3] Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. 2013. A Bilirubin-Inducible Fluorescent Protein from Eel Muscle. Cell 153: 1602–1611.





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