Difference between revisions of "Team:Technion Israel/Proof"
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<img src="https://static.igem.org/mediawiki/2016/thumb/4/43/T--Technion_Israel--Proof_fig1.png/800px-T--Technion_Israel--Proof_fig1.png" class="img-responsive img-center" width="100%"> </a> | <img src="https://static.igem.org/mediawiki/2016/thumb/4/43/T--Technion_Israel--Proof_fig1.png/800px-T--Technion_Israel--Proof_fig1.png" class="img-responsive img-center" width="100%"> </a> | ||
| − | <p class="text-center"><b>Fig. 1:</b> Tar chemoreceptor on the left, PctA-Tar chimera on the right.</p> | + | <p class="text-center"><b>Fig. 1:</b> Scheme of Tar chemoreceptor on the left, PctA-Tar chimera on the right.</p> |
</div> | </div> | ||
</div> | </div> | ||
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<div class="col-md-12 col-sm-12"> | <div class="col-md-12 col-sm-12"> | ||
<p class="text-justify"> | <p class="text-justify"> | ||
| − | PctA is a chemoreceptor found in the Pseudomonas Aeruginosa bacterium, it mediates | + | PctA is a chemoreceptor found in the <i> Pseudomonas Aeruginosa </i> bacterium, it mediates |
chemotaxis towards amino acids and away from organic compounds. It can sense all | chemotaxis towards amino acids and away from organic compounds. It can sense all | ||
| − | amino acids except for Aspartate <b>(1)</b> | + | amino acids except for Aspartate <b>(1)</b>. |
| − | To construct this chimera, the LBD sequence of the PctA was obtained from the Pseudomonas | + | To construct this chimera, the LBD sequence of the PctA was obtained from the <i> Pseudomonas </i> |
genome database while the signaling region of Tar was obtained from the iGEM parts catalog | genome database while the signaling region of Tar was obtained from the iGEM parts catalog | ||
<b>(part number)</b>. Using these two sequences, we built a Biobrick device <b>(part number)</b> | <b>(part number)</b>. Using these two sequences, we built a Biobrick device <b>(part number)</b> | ||
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<br> | <br> | ||
<p class="text-justify"> | <p class="text-justify"> | ||
| − | As an initial step, we generated a 3D model of the PctA-Tar chimera, figure | + | As an initial step, we generated a 3D model of the PctA-Tar chimera, figure 3, using the |
Phyre2 Protein Fold Recognition server to assure the correct folding of both the LBD and the signaling regions. | Phyre2 Protein Fold Recognition server to assure the correct folding of both the LBD and the signaling regions. | ||
</p> | </p> | ||
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<img src="https://static.igem.org/mediawiki/2016/6/62/T--Technion_Israel--Proof_fig3.png" class="img-responsive img-center img-cont" width="700"" style="cursor: pointer;"> | <img src="https://static.igem.org/mediawiki/2016/6/62/T--Technion_Israel--Proof_fig3.png" class="img-responsive img-center img-cont" width="700"" style="cursor: pointer;"> | ||
</a> | </a> | ||
| − | <p class="text-center"><b>Fig. 3<b> PctA-Tar chimera 3D structure. The Tar signaling regions is in gray, the PctA LBD is in red.</p> | + | <p class="text-center"><b>Fig. 3</b> PctA-Tar chimera 3D structure. The Tar signaling regions is in gray, the PctA LBD is in red.</p> |
</div> | </div> | ||
</div> | </div> | ||
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presented below, figure 4. It is important to mention that this assay was | presented below, figure 4. It is important to mention that this assay was | ||
performed on BA medium as the original assay on TB medium failed. From the | performed on BA medium as the original assay on TB medium failed. From the | ||
| − | results seen below, figure | + | results seen below, figure 5, and compared to the negative control, it is |
clear that the chimera functions and controls the chemotactic ability of | clear that the chimera functions and controls the chemotactic ability of | ||
the bacteria and can lead to swarming response. | the bacteria and can lead to swarming response. | ||
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<div class="col-md-12 col-sm-12"> | <div class="col-md-12 col-sm-12"> | ||
<p class="text-justify"> | <p class="text-justify"> | ||
| − | <b>Figure 7:</b> Results of GFP fusion. (a)White light of PctA-Tar-GFP Chimera (b) Flourcense (490nm excitation) | + | <b>Figure 7:</b> Results of GFP fusion. (a) White light of PctA-Tar-GFP Chimera (b) Flourcense (490nm excitation) |
of PctA-Tar-GFP Chimera (c)White light of normal Tar (b) Flourcense (490nm excitation) of normal Tar. | of PctA-Tar-GFP Chimera (c)White light of normal Tar (b) Flourcense (490nm excitation) of normal Tar. | ||
</p> | </p> | ||
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as a detection tool based on the chemotaxis system of <I>E. coli</I> bacteria - by using a commercial | as a detection tool based on the chemotaxis system of <I>E. coli</I> bacteria - by using a commercial | ||
ibidi chip filled with a suspension of bacteria expressing the chimera and chromoprotein <b>(part number)</b>. | ibidi chip filled with a suspension of bacteria expressing the chimera and chromoprotein <b>(part number)</b>. | ||
| − | A solution of Tetrachloroethylene in concentration of 9×10<sup>- | + | A solution of Tetrachloroethylene in concentration of 9×10<sup>-5</sup>M, the repellent, was added to the chip |
and the displacement of the bacteria was monitored and recorded. | and the displacement of the bacteria was monitored and recorded. | ||
</p> | </p> | ||
Revision as of 19:09, 16 October 2016
One of S.Tars sub projects focused on altering and changing the LBD of the Tar chemoreceptor in order to design new hybrid chimeras. These changes were made by replacing the LBD of the original Tar chemoreceptor with a new one, from a different source, while keeping the signaling region of Tar untouched. As a proof of concept for the newly designed Tar chimeras and the S.Tar project, we focused on testing the PctA-Tar hybrid.
Fig. 1: Scheme of Tar chemoreceptor on the left, PctA-Tar chimera on the right.
PctA is a chemoreceptor found in the Pseudomonas Aeruginosa bacterium, it mediates chemotaxis towards amino acids and away from organic compounds. It can sense all amino acids except for Aspartate (1). To construct this chimera, the LBD sequence of the PctA was obtained from the Pseudomonas genome database while the signaling region of Tar was obtained from the iGEM parts catalog (part number). Using these two sequences, we built a Biobrick device (part number) which was then transformed to bacteria that lacks chemoreceptors - UU1250 (Parkinson J S, University of Utah) to be extensively tested. It is important to note that this chimera has been constructed before in the literature (1)
Fig. 2: Biobrick device of the PctA-Tar chimera.
Test and results:
As an initial step, we generated a 3D model of the PctA-Tar chimera, figure 3, using the Phyre2 Protein Fold Recognition server to assure the correct folding of both the LBD and the signaling regions.
Fig. 3 PctA-Tar chimera 3D structure. The Tar signaling regions is in gray, the PctA LBD is in red.
Following the transformation, a swarming plate assay was performed in order to
confirm the functionality of the hybrid receptor. A scheme of the assay is
presented below, figure 4. It is important to mention that this assay was
performed on BA medium as the original assay on TB medium failed. From the
results seen below, figure 5, and compared to the negative control, it is
clear that the chimera functions and controls the chemotactic ability of
the bacteria and can lead to swarming response.
Fig. 4 a scheme for the swarming plate assay. In brief: Using a low percentage agar media plate, add a drop of bacteria to the middle of the plate. Incubate at 30 degrees for several hours. A halo or “chemotactic ring” should be formed in the agar plate.
a.
b.
c.
Fig. 5: Swarming assay for attractant response of the PctA-Tar chimera.
a. PctA chimera, b. UU1250, c.∆Z.
Next, to prove the correct localization of the chimera on both poles of the bacteria, GFP was fused to its C-terminus with a short linker sequence (part number), figure 6. The results of these tests as seen in figure 7, prove our assumption of correct localizations.
Fig. 6: Biobrick device of the PctA-Tar chimera fused to GFP.
a.
b.
c.
d.
Figure 7: Results of GFP fusion. (a) White light of PctA-Tar-GFP Chimera (b) Flourcense (490nm excitation) of PctA-Tar-GFP Chimera (c)White light of normal Tar (b) Flourcense (490nm excitation) of normal Tar.
Finally, demonstrated below is a working concept of the FlashLab project - a chip that serves
as a detection tool based on the chemotaxis system of E. coli bacteria - by using a commercial
ibidi chip filled with a suspension of bacteria expressing the chimera and chromoprotein (part number).
A solution of Tetrachloroethylene in concentration of 9×10-5M, the repellent, was added to the chip
and the displacement of the bacteria was monitored and recorded.
Fig. 8: A steps scheme of the FlashLab concept: Add bacteria expressing the chemoreceptor of your choice and a chromo protein to a fluidic chip . Add the sample in question to said chip. If the sample contains the substance that is recognized by the chemoreceptor, a displacement of the bacteria will become visible. If not, then the no displacement will be seen.
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With the supporting evidence of the results presented above, it can be concluded that both concepts have been proved and work under real life conditions and might lead to the detection of various substances in the near future.
1. Reyes-Darias, J.A., Yang, Y., Sourjik, V., and Krell, T. (2015). Correlation between signal input and output in PctA and PctB amino acid chemoreceptor of Pseudomonas aeruginosa. Mol. Microbiol. 96, 513–525.
