Difference between revisions of "Part:BBa K2669000"

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<partinfo>BBa_K2669000 short</partinfo>
 
<partinfo>BBa_K2669000 short</partinfo>
  
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WORK IN PROGRESS
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K2669000 SequenceAndFeatures</partinfo>
  
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UnaG is a unique chromoprotein since it expresses a fluorescent signal when in contact with bilirubin. This means (unlike most other chromoproteins) it can be used as a reporter in anaerobic environments or even potentially in environments where bilirubin is naturally present, such as the intestines. While researching the previous work from the iGEM Uppsala 2016 team, we noticed that their part ([[Part:BBa_K2003011]]) had an error in it (a misplaced start codon) which would lead to not only reduced UnaG expression but also not include the histidine tag their part should be expressing according to the igem registry!
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UnaG is a unique chromoprotein since it expresses fluorescent signal when in contact with bilirubin. This means (unlike most other chromoproteins) it can be used as a reporter in anaerobic environments or even potentially in environments where bilirubin is naturally present, such as the intestines. While researching the previous work from the iGEM Uppsala 2016 team, we noticed that their part ([[Part:BBa_K2003011]]) had an error in it (a misplaced start codon) which would lead to not only reduced UnaG expression but also not include the histidine tag their part should be expressing according to the igem registry!
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We decided that we would rectify this issue by engineering a composite part with the start codon in the correct position and compare it to the previous part ([[Part:BBa_K2003011]]).  We designed this composite part by combining a strong promoter ([[Part:BBa_J23119]]), a strong RBS ([[Part:BBa_J34801]]), and a double terminator ([[Part:BBa_B0014]]) around the modified UnaG part ([[Part:BBa_K2669001]]).   
 
We decided that we would rectify this issue by engineering a composite part with the start codon in the correct position and compare it to the previous part ([[Part:BBa_K2003011]]).  We designed this composite part by combining a strong promoter ([[Part:BBa_J23119]]), a strong RBS ([[Part:BBa_J34801]]), and a double terminator ([[Part:BBa_B0014]]) around the modified UnaG part ([[Part:BBa_K2669001]]).   
  
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<b>Warning:</b>This part also contains a <b>GSG linker</b> that has a stop codon directly after it.  If you would like to use [[Part:BBa_K2669001]] as a linker protein, you must delete or move this stop codon. 
  
 
===Source===
 
===Source===
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As mentioned above, this part contains a strong promoter (BBa_J23119), a strong RBS (BBa_J34801), and a double terminator (BBa_B0014).  In addition, it contains the sequence from BBa_K2003011, only with a change to the start codon location, resulting in [[Part:BBa_K2669001]].  The original source of UnaG is from the paper “A Bilirubin-Inducible Fluorescent Protein from Eel Muscle” by Kumagai A et. al, which characterized the UnaG protein from the muscle of a species of Japanese eel.   
 
As mentioned above, this part contains a strong promoter (BBa_J23119), a strong RBS (BBa_J34801), and a double terminator (BBa_B0014).  In addition, it contains the sequence from BBa_K2003011, only with a change to the start codon location, resulting in [[Part:BBa_K2669001]].  The original source of UnaG is from the paper “A Bilirubin-Inducible Fluorescent Protein from Eel Muscle” by Kumagai A et. al, which characterized the UnaG protein from the muscle of a species of Japanese eel.   
  
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===How we made it===
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<html>
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<b>Please note:</b> The exact procedure can be found at the end of  <a href="http://2018.igem.org/wiki/index.php?title=Team:Uppsala/UnaG"><b>our UnaG wiki page</b></a>.
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</html>
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<html>
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<h1>iGEM Uppsala 2018 Experience + Experimental Data</h1>
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After transforming our cells with a low copy amplicilin plasmid containing this composite part, cell lysis and affinity chromotography were used to extract UnaG from our cells.  <b>Please note:</b> The exact procedure can be found at the end of  <a href="http://2018.igem.org/wiki/index.php?title=Team:Uppsala/UnaG"><b>our UnaG wiki page</b></a>.  Conducting "bilirubin tests" (the addition of a small amount of bilirubin dissolved in chloroform to samples) allowed us to see if UnaG was present in our samples, since as mentioned earlier UnaG fluoresces in the presence of bilirubin.  </p>
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<img class="content-card-img" src="https://static.igem.org/mediawiki/2018/2/20/T--Uppsala--UnaG_Comparison.png" alt="UnaG Comparison">
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<p><b>Figure 1:</b> Bilirubin test before/after affinity chromatography(AC). The samples where analyzed under a UV lamp at wavelength 312 nm. Going from left to right the samples are:</p>
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                            <ul>
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                                <li> Lysed sample of the “bad” part before AC</li>
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                                <li> Lysed sample of the “good” part before AC</li>
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                                <li> "Bad" part solution after AC</li>
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                                <li> "Good" part solution after AC</li>
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                            </ul> <br>
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<p> It can be observed from figure 1 that UnaG fluorescence can be seen in all tubes except the third one. This supports our claim that our new part functions and provides a histidine tag to the protein, whereas the old part did not have a histidine tag and therefore it should not bind in the IMAC column. </p>
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<img class="content-card-img" src="https://static.igem.org/mediawiki/2018/2/25/T--Uppsala--UnaGGelPictureUpdated.png" > <!-- Placeholder image -->
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                            <p><b>Figure 2:</b> SDS-PAGE gel after affinity chromatography</p>
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                            <p>UnaG is approximately 15.6 kDa, showing that it is indeed in the extracted sample.  Other proteins are shown, and this is likely because we used no imidazole in the initial running buffer, leading to unspecific binding.  We did this to ensure that we obtained as much UnaG as possible in our sample so that we could conduct fluorescence tests visible by the naked eye.  The samples are (1)the 2018 biobrick and (2) the 2016 biobrick.</p>
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<img src="https://static.igem.org/mediawiki/2018/d/db/T--Uppsala--UnaG_Cell_platereader.png" width="50%" height="50%">
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<p><b>Figure 3:</b> Fluorescence measurement of unlysed cells. From left to right: Bacterial strain BL21 transformed with a plasmid containing <a href="https://parts.igem.org/Part:BBa_K2669000">Part:BBa_K2669000</a> from 2018, Bl21 transfected with <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K2003011">Part:BBa_K2003011</a> from 2016 and normal BL21 cells, all at the same OD600 value. Excitation wavelengths of 448 nm and emission wavelength 527 nm were used. </p>
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<br>
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<img src="https://static.igem.org/mediawiki/2018/8/88/T--Uppsala--Before_After_HisTrap.png" width=50% height=50%>
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<p><b>Figure 4:</b> The supernantant of lysed cells before and after affinity chromotography.  Because of our lysis method UnaG was suspended in the supernatant of the cell cultures.  The left samples are supernantant containing the UnaG-protein from 2016 (<a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K2003011">Part:BBa_K2003011</a>) and the right samples are the supernantant containing our UnaG-protein (2018). </p>
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<br>
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<h2>Conclusion</h2>
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<p> The histidine tag seems to function as intended.  In addition,  the amount of UnaG produced seems to be sufficient to both extract the protein of interest and to observe its florescence both when cells are lysed and when they are intact.  </p>
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<br><br>
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</html>
  
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===Usage and Biology===
 
  
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<span class='h3bb'>Sequence and Features</span>
 
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<partinfo>BBa_K2669000 SequenceAndFeatures</partinfo>
 
  
  

Latest revision as of 18:45, 17 October 2018


Strongly constitutive His-tagged+flexible linker UnaG

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

UnaG is a unique chromoprotein since it expresses a fluorescent signal when in contact with bilirubin. This means (unlike most other chromoproteins) it can be used as a reporter in anaerobic environments or even potentially in environments where bilirubin is naturally present, such as the intestines. While researching the previous work from the iGEM Uppsala 2016 team, we noticed that their part (Part:BBa_K2003011) had an error in it (a misplaced start codon) which would lead to not only reduced UnaG expression but also not include the histidine tag their part should be expressing according to the igem registry!

We decided that we would rectify this issue by engineering a composite part with the start codon in the correct position and compare it to the previous part (Part:BBa_K2003011). We designed this composite part by combining a strong promoter (Part:BBa_J23119), a strong RBS (Part:BBa_J34801), and a double terminator (Part:BBa_B0014) around the modified UnaG part (Part:BBa_K2669001).

Warning:This part also contains a GSG linker that has a stop codon directly after it. If you would like to use Part:BBa_K2669001 as a linker protein, you must delete or move this stop codon.

Source

As mentioned above, this part contains a strong promoter (BBa_J23119), a strong RBS (BBa_J34801), and a double terminator (BBa_B0014). In addition, it contains the sequence from BBa_K2003011, only with a change to the start codon location, resulting in Part:BBa_K2669001. The original source of UnaG is from the paper “A Bilirubin-Inducible Fluorescent Protein from Eel Muscle” by Kumagai A et. al, which characterized the UnaG protein from the muscle of a species of Japanese eel.

How we made it

Please note: The exact procedure can be found at the end of our UnaG wiki page.

iGEM Uppsala 2018 Experience + Experimental Data

After transforming our cells with a low copy amplicilin plasmid containing this composite part, cell lysis and affinity chromotography were used to extract UnaG from our cells. Please note: The exact procedure can be found at the end of our UnaG wiki page. Conducting "bilirubin tests" (the addition of a small amount of bilirubin dissolved in chloroform to samples) allowed us to see if UnaG was present in our samples, since as mentioned earlier UnaG fluoresces in the presence of bilirubin.

UnaG Comparison

Figure 1: Bilirubin test before/after affinity chromatography(AC). The samples where analyzed under a UV lamp at wavelength 312 nm. Going from left to right the samples are:

  • Lysed sample of the “bad” part before AC
  • Lysed sample of the “good” part before AC
  • "Bad" part solution after AC
  • "Good" part solution after AC

It can be observed from figure 1 that UnaG fluorescence can be seen in all tubes except the third one. This supports our claim that our new part functions and provides a histidine tag to the protein, whereas the old part did not have a histidine tag and therefore it should not bind in the IMAC column.

Figure 2: SDS-PAGE gel after affinity chromatography

UnaG is approximately 15.6 kDa, showing that it is indeed in the extracted sample. Other proteins are shown, and this is likely because we used no imidazole in the initial running buffer, leading to unspecific binding. We did this to ensure that we obtained as much UnaG as possible in our sample so that we could conduct fluorescence tests visible by the naked eye. The samples are (1)the 2018 biobrick and (2) the 2016 biobrick.

Figure 3: Fluorescence measurement of unlysed cells. From left to right: Bacterial strain BL21 transformed with a plasmid containing Part:BBa_K2669000 from 2018, Bl21 transfected with Part:BBa_K2003011 from 2016 and normal BL21 cells, all at the same OD600 value. Excitation wavelengths of 448 nm and emission wavelength 527 nm were used.


Figure 4: The supernantant of lysed cells before and after affinity chromotography. Because of our lysis method UnaG was suspended in the supernatant of the cell cultures. The left samples are supernantant containing the UnaG-protein from 2016 (Part:BBa_K2003011) and the right samples are the supernantant containing our UnaG-protein (2018).


Conclusion

The histidine tag seems to function as intended. In addition, the amount of UnaG produced seems to be sufficient to both extract the protein of interest and to observe its florescence both when cells are lysed and when they are intact.