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 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 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]]).   
 
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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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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<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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===Experimental Data/Experience ===
 
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===Applications of BBa_K2669000===
 
 
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<html>
  
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<h1>iGEM Uppsala 2018 Experience</h1>
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<h1>iGEM Uppsala 2018 Experience + Experimental Data</h1>
 
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>
 
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 src="https://static.igem.org/mediawiki/2018/thumb/6/68/T--Uppsala--UnaG_Comparison_PreLysis.png/800px-T--Uppsala--UnaG_Comparison_PreLysis.png" width="50%" height="20%" alt="UnaG Comparison">
 
  
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<p><b><Figure 1:</b> Bilirubin test of cells before lysis. 
 
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<ul>
 
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                                <li> Lb + bilirubin/chloroform solution</li>
 
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                                <li> Lb culture of cells transformed with [[Part:BBa K2669000]] + bilirubin/chloroform solution</li>
 
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                                <li> LB culture of cells transformed with [[Part:BBa K2003011]] + bilirubin/chloroform solution</li>
 
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                                <li> LB culture of cells transformed with[[Part:BBa K2669000]] without bilirubin </li>
 
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                            </ul>
 
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</p>
 
  
 
<img class="content-card-img" src="https://static.igem.org/mediawiki/2018/2/20/T--Uppsala--UnaG_Comparison.png" alt="UnaG Comparison">
 
<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 2:</b> Bilirubin test before/after affinity chromatography. Going from right to left the samples are:</p>  
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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>  
 
                             <ul>  
 
                             <ul>  
 
                                 <li> Lysed sample of the “bad” part before AC</li>
 
                                 <li> Lysed sample of the “bad” part before AC</li>
 
                                 <li> Lysed sample of the “good” part before AC</li>
 
                                 <li> Lysed sample of the “good” part before AC</li>
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                                 <li> "Bad" part after AC</li>
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                                 <li> "Bad" part solution after AC</li>
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                                 <li> "Good" part after AC</li>
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                                 <li> "Good" part solution after AC</li>
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                             </ul>
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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/f/fc/T--Uppsala--UnaG_Blank_Comparison.png" >
 
  
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<p><b>Figure 3: Comparison of blank tube to successful extraction/previous iGEM part. The tubes reading from left to right are as followed:</b></p>
 
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                              <ul>
 
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                                <li> Blank tube with AC elution buffer/bilirubin</li>
 
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                                <li> Tube with bilirubin + original iGEM UnaG part</li>
 
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                                <li> Our extracted modified UnaG with a moved start codon, as can be seen in <b>Figure 1</b></li>
 
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                            </ul>
 
  
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<p>A good degree of fluorescence can be seen in the last tube compared to the other two, which clearly contain none of our protein of interest. </p>
 
  
 
<img class="content-card-img" src="https://static.igem.org/mediawiki/2018/2/25/T--Uppsala--UnaGGelPictureUpdated.png" > <!-- Placeholder image -->
 
<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 4:</b> SDS-PAGE gel after affinity chromatography</p>
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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. </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>
  
 
<img src="https://static.igem.org/mediawiki/2018/d/db/T--Uppsala--UnaG_Cell_platereader.png" width="50%" height="50%">
 
<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 5:</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. </p>
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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>
 
<br>
 
<br>
 
<img src="https://static.igem.org/mediawiki/2018/8/88/T--Uppsala--Before_After_HisTrap.png" width=50% height=50%>
 
<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 6:</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 and the right samples are the supernantant containing our UnaG-protein (2018). </p>
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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><br>
  
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               <h1>Procedure:</h1>
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                            <h2>Transforming the Plasmid:</h2>
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                            <p>When the plasmids were received from IDT they were transformed into BL21 E. coli cells graciously provided to us by the esteemed Forster Laboratory.  Same-day-made competent cells using the protocol from the “Synthetic Biology Handbook”  were used to provide maximum transformation efficiency.  </p>
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                            <br>
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                            <h2>Extraction of UnaG:</h2>
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                            <p>The protocol for the extraction of our integral membrane protein from the transformed BL21 cells proceeded as follows: Note that this was done for both iGEM 2016 cells transformed with the previous part (nicknamed “bad”) and our repositioned start codon (graced with the moniker “good”).  </p>
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                            <br>
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                            <h3>Materials/Procedure</h3>
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                            <br>
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                            <ul>
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                                <li><b>Lysis Buffer:</b> PBS solution with 1mM EDTA, 5% glycerol, and 20mM Tris, pH7.4</li>
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                                <li><b>Elution Buffer:</b> 20 mM sodium phosphate, 0.5 M NaCl, 0.5 M imidazole, pH 7.4, 5% glycerol
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                                        PBS, 1mM EDTA, 5% glycerol, 20mM Tris, pH7.4</li>
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                                <li><b>Binding/Washing Buffer:</b>0.5 M NaCl, 2 EDTA-free tablets, 10 % glycerol, 20mM sodium phosphate, 1% Triton x100, pH 7.4 (400 mL total)</li>
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                                <li><b>Binding/washing buffer</b> with 1% triton x-100 by weight</li>
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                            </ul>
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                        <br>
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                            <p>Cells were centrifuged at 4000 g 25 minutes at 4 degrees Celsius and then resuspended in Lysis buffer.  Cells were lysed using cell disruption with a french press.  The now lysed cells were then centrifuged again at  at 4000 g 25 minutes at 4 degrees Celsius.  The pellet was resuspended in 20mL binding/washing buffer with 1% triton x-100.  The solution was incubated on ice for one hour before another round of centrifugation at the same temperature and speed.  After centrifugation the supernatant should contain the protein of interest.  Bilirubin tests were conducted on both solutions of the pellet and supernatant to observe any fluorescence under a UV light.  </p>
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                            <br>
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                            <p>Affinity chromatography was then performed on both “good” and “bad” solutions using prepacked “His-Gravitrap” Columns from GE Healthcare.  The protocol for use was performed according to GE healthcare’s specifications, with modified binding/washing/elution buffers.  After affinity chromatography, the resulting elutants were tested for fluorescence with a bilirubin test.  </p>
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</html>
 
</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>
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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.