Difference between revisions of "Team:Technion Israel/Proof"

 
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<img src="https://static.igem.org/mediawiki/2016/d/db/T--Technion_Israel--icon_intro.png" class="img-responsive img-center cont_tabs" width="75" height="75">
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<img src="https://static.igem.org/mediawiki/2016/7/78/T--Technion_Israel--narXicon_%282%29.png" class="img-responsive img-center cont_tabs" width="75" height="75">
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<br><h4 class="text-center"><b>PctA-Tar</b></h4>
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<br><h4 class="text-center">PctA-Tar</h4>
 
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<img src="https://static.igem.org/mediawiki/2016/4/49/T--Technion_Israel--icon_lab.png" class="img-responsive img-center cont_tabs" width="75" height="75">
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<img src="https://static.igem.org/mediawiki/2016/9/9c/T--Technion_Israel--histiminicon.png" class="img-responsive img-center cont_tabs" width="75" height="75">
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<br><h4 class="text-center"><b>Histamine-Tar</b></h4>
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<br><h4 class="text-center">Histamine-Tar</h4>
 
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<p class="text-justify">
 
<p class="text-justify">
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One of S.Tars sub projects focused on altering and changing the LBD of the Tar  
+
One of S.Tars sub-projects focused on altering the LBD of Tar chemoreceptor in order to design new hybrid chimeras. That was accomplished by replacing the LBD of the original Tar chemoreceptor with a new one, from a different source, without modifying Tar signaling region. As a proof of concept for the newly designed Tar chimeras and the S.Tar project, we focused on testing the PctA-Tar hybrid.
−
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.
+
 
</p>
 
</p>
 
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<div class="col-md-12 col-sm-12">
 
<p class="text-justify">
 
<p class="text-justify">
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PctA is a chemoreceptor found in the <i> Pseudomonas Aeruginosa </i> bacterium, it mediates  
+
PctA is a chemoreceptor found in the <i> Pseudomonas Aeruginosa </i>.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>.
 
<br>To construct this chimera, the LBD sequence of the PctA was obtained from the <a href="http://www.pseudomonas.com/"target="_blank"><i> Pseudomonas </i> genome database</a>,  
 
<br>To construct this chimera, the LBD sequence of the PctA was obtained from the <a href="http://www.pseudomonas.com/"target="_blank"><i> Pseudomonas </i> genome database</a>,  
 
while the signaling region of Tar was obtained from the iGEM parts catalog  
 
while the signaling region of Tar was obtained from the iGEM parts catalog  
−
<a href="http://parts.igem.org/Part:BBa_K777000" target="_blank">(K777000)</a>. Using these two sequences, we built a Biobrick device <a href="http://parts.igem.org/Part:BBa_K1992007" target="_blank">(K1992007)</a>  
+
<a href="http://parts.igem.org/Part:BBa_K777000" target="_blank">(K777000)</a>. Using these two sequences, we built a Biobrick part <a href="http://parts.igem.org/Part:BBa_K1992007" target="_blank">(K1992007)</a>  
−
which was then transformed to bacteria that lacks chemoreceptors - <a data-toggle="popover" data-trigger="click" data-original-title="Info:" data-html="true"  
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which was tested by transforming the device to bacteria that lacks chemoreceptors - <a data-toggle="popover" data-trigger="click" data-original-title="Info:" data-html="true"  
 
data-content="An E.coli derivative, which lacks chemoreceptors genes, means this strain does not obtain chemotaxis ability (Parkinson J S, University of Utah).">
 
data-content="An E.coli derivative, which lacks chemoreceptors genes, means this strain does not obtain chemotaxis ability (Parkinson J S, University of Utah).">
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UU1250<i class="entypo-check"></i></button></a>  
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UU1250<i class="entypo-check"></i></button></a>. It is important  
−
, to be extensively tested. It is important  
+
 
to note that this chimera has been constructed before in the literature <b>(1)</b>.
 
to note that this chimera has been constructed before in the literature <b>(1)</b>.
 
</p>
 
</p>
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<p class="text-justify">
 
<p class="text-justify">
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Following the transformation, a swarming plate assay was performed in order to  
+
Following transformation, a swarming plate assay was performed in order to  
 
confirm the functionality of the hybrid receptor. A scheme of the assay is  
 
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  
+
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 5, and compared to the negative control, it is  
+
results seen in figure 5, it is  
−
clear that the chimera functions and controls the chemotactic ability of  
+
clear that the chimera functions and controls the chemotactic ability of  
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the bacteria and can lead to swarming response.
+
the bacteria leading to swarming response.  
 +
This is compared to the control, UU1250 strain, that did not show any chemotactic ability as expected and no chemotactic rings were formed.
 +
 
 
</p>
 
</p>
 
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<p class="text-justify">
 
<p class="text-justify">
 
<b>Fig. 5:</b> Swarming assay for attractant response of the PctA-Tar chimera.  
 
<b>Fig. 5:</b> Swarming assay for attractant response of the PctA-Tar chimera.  
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<b>a.</b> PctA chimera, <b>b.</b> Negative control- UU1250 strain w/o the Tar expression plasmid, <b>c. </b> positive control - ΔZ strain expressing all chemoreceptors.
+
<b>a.</b> PctA chimera, <b>b.</b> Negative control- UU1250 strain w/o the Tar expression plasmid, <b>c. </b> positive control - ΔZras strain expressing all chemoreceptors.
 
<br><br><br>
 
<br><br><br>
 
</p>
 
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<p class="text-justify">
 
<p class="text-justify">
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Next, to prove the correct localization of the chimera on both poles of the bacteria, GFP was fused  
+
Next, to prove that the chimera is localized in the membrane, GFP was fused  
−
to its C-terminus with a short linker sequence <a href="http://parts.igem.org/Part:BBa_K1992010" target="_blank">(K1992010)</a>, figure 6. The results of these tests
+
to its C-terminus with a short linker sequence <a href="http://parts.igem.org/Part:BBa_K1992010" target="_blank">(K1992010)</a>,  
−
as seen in figure 7, prove our assumption of correct localizations.  
+
figure 6. The results seen in figure 7, show that indeed the chimera is localized to the membrane (poles).  
 
</p>
 
</p>
 
</div>
 
</div>
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<img src="https://static.igem.org/mediawiki/2016/thumb/6/6a/T--Technion_Israel--Tar_pctA_flourecent.png/800px-T--Technion_Israel--Tar_pctA_flourecent.png" class="img-responsive img-center img-cont" width="700" style="cursor: pointer;">
 
<img src="https://static.igem.org/mediawiki/2016/thumb/6/6a/T--Technion_Israel--Tar_pctA_flourecent.png/800px-T--Technion_Israel--Tar_pctA_flourecent.png" class="img-responsive img-center img-cont" width="700" style="cursor: pointer;">
 
</a>
 
</a>
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<p><b>Fig. 7:</b> Results of GFP fusion. <b>(A)</b> Positive control- <i>E.Coli</i> strain expressing GFP protein,<b>(B)</b> Negative control- UU1250 strain expressing Tar chemoreceptor, <b>(C)</b>  UU1250 strain expressing Tar-GFP chemoreceptor, <b>(D)</b> UU1250 strain expressing PctA-Tar-GFP Chimera, Flourcense (490nm excitation).
+
<p><b>Fig. 7:</b> Results of GFP fusion. <b>(A)</b> Positive control- <i>E.Coli</i> strain expressing GFP protein,<b>(B)</b>  
 +
Negative control- UU1250 strain expressing Tar chemoreceptor, <b>(C)</b>  UU1250 strain expressing Tar-GFP chemoreceptor, <b>(D)</b>  
 +
UU1250 strain expressing PctA-Tar-GFP Chimera, fluorescence (490nm excitation).
 
</p>
 
</p>
 
</div>
 
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<p class="text-justify">
 
<p class="text-justify">
−
Finally, demonstrated below is a working concept of the FlashLab project - a chip that serves  
+
Finally, in the video below is a working concept of the <a href="https://2016.igem.org/Team:Technion_Israel/Design">FlashLab project</a> - a chip that serves  
−
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. In the video, a commercial ibidi 
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ibidi chip filled with a suspension of bacteria expressing the chimera and chromoprotein (<a href="http://parts.igem.org/Part:BBa_J23100" target="_blank">J23100</a> + <a href="http://parts.igem.org/Part:BBa_K1357009" target="_blank">K1357009</a>).  
+
microfluidic chip filled with a suspension of bacteria expressing the chimera and chromoprotein  
−
A solution of Tetrachloroethylene in concentration of 10<sup>-3</sup>M, the repellent, was added to the chip  
+
(<a href="http://parts.igem.org/Part:BBa_J23100" target="_blank">J23100</a> + <a href="http://parts.igem.org/Part:BBa_K1357009" target="_blank">K1357009</a>) can been seen.
 +
A solution of repellent (10<sup>-3</sup>M Tetrachloroethylene) 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>
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<br>
 
<br>
 
<a class="pop ocenter">
 
<a class="pop ocenter">
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<img src="https://static.igem.org/mediawiki/2016/7/74/T--Technion_Israel--fig1.JPG" class="img-responsive img-center" width="700"> </a>
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<img src="https://static.igem.org/mediawiki/2016/thumb/9/95/T--Technion_Israel--FlashLab.png/800px-T--Technion_Israel--FlashLab.png" class="img-responsive img-center img-cont" style="cursor: pointer;"><br> </a>
 
<p class="text-center">
 
<p class="text-center">
−
<b>Fig. 8:</b> A steps scheme of the FlashLab concept: Add bacteria  
+
<b>Fig. 8:</b> A steps scheme of the <a href="https://2016.igem.org/Team:Technion_Israel/Design">FlashLab</a> concept: Add bacteria expressing both the chemoreceptor of your choice and a chromoprotein to a fluidic chip. Add the tested sample to the chip. If the chemoreceptor detecets the substance in the sample, a displacement of the bacteria will become visible.  
−
expressing the chemoreceptor of your choice and a chromo protein to a fluidic chip . Add the sample in question
+
.</p>
−
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.</p>
+
 
</div>
 
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<p class="text-justify">
 
<p class="text-justify">
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PISKA!
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In video 1, the displacement of the bacteria can be clearly seen in test chip compared to the control chip.
 
</p>
 
</p>
 
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</div>
 
</div>
 
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<p class="text-justify">
 
<p class="text-justify">
 
With the supporting evidence of the results presented above, it can be concluded  
 
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
+
that both concepts: LBD altering and the <a href="https://2016.igem.org/Team:Technion_Israel/Design">FlashLab</a> platform, have been proven and work under real life conditions and seem promising for detection of various substances in the near future.
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lead to the detection of various substances in the near future.
+
 
 
</p>
 
</p>
 
</div>
 
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<p class="text-justify">
 
<p class="text-justify">
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The base of the S.Tar project is the Tar chemoreceptor, one of four E. coli receptors.
+
The heart of the S.Tar project is the Tar chemoreceptor, one of four <i>E. coli</i> receptors.
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Our goal is to create a engineered bacteria which has chemotaxis receptors sensetive
+
Our goal is to create an engineered bacteria which has chemotaxis receptors sensitive
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to materials outside it’s existing receptor base.By changing Tar’s ligand binding domain  
+
to materials other than its native ligands. We show that <i>E.
−
(LBD) to that of other receptors from various sources or by mutating it we show that E.
+
coli</i> can be engineered to respond to completely new materials. By changing Tar’s ligand binding domain  
−
coli can be engineered to respond to completely new materials.
+
(LBD) to other LBDs from various sources or by mutating it.
 
</p>
 
</p>
 
</div><!--
 
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<img src="https://static.igem.org/mediawiki/2016/7/72/T--Technion_Israel--His_seq.png" class="img-responsive img-center img-cont" width="450">
 
<img src="https://static.igem.org/mediawiki/2016/7/72/T--Technion_Israel--His_seq.png" class="img-responsive img-center img-cont" width="450">
 
</a>
 
</a>
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<p class="text-center"><b>Fig. 1:</b> Sequencing Results. Query describes the native Tar LBD  
+
<p class="text-center"><b>Fig. 1:</b> Sequencing Results. "Query" describes the native Tar LBD  
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sequence and Sbjct describes the design mutations sequence. Each mutation regin marked with  
+
sequence and "Sbjct" describes the design mutations sequence. The mutation region is marked with color (blue or red).</p>
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another color (blue and red).</p>
+
 
</div>
 
</div>
 
</div>
 
</div>
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The bacterial world offers a relatively small selection of chemoreceptors in comparison to
 
The bacterial world offers a relatively small selection of chemoreceptors in comparison to
 
the vast number of possible ligands. These receptors evolved specifically to recognize substances  
 
the vast number of possible ligands. These receptors evolved specifically to recognize substances  
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which benefit or harm the organism in some way. On top of that the fact that the majority of known  
+
which benefit or harm the organism. On top of that the fact that the majority of known  
 
receptors today are not well characterized meant that we had very few options of creating chimeric  
 
receptors today are not well characterized meant that we had very few options of creating chimeric  
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receptors like we initially planned.<br><br>
+
receptors as we initially planned.<br><br>
 
In light of the above we had to turn to a new path – redesigning the Tar chemoreceptor to bind a  
 
In light of the above we had to turn to a new path – redesigning the Tar chemoreceptor to bind a  
 
different ligand using computational biology - The Rosetta <a href="https://2016.igem.org/Team:Technion_Israel/Software">software</a>.
 
different ligand using computational biology - The Rosetta <a href="https://2016.igem.org/Team:Technion_Israel/Software">software</a>.
−
Out of the Rosetta’s 870 suggested mutations only 11 variants were eventually cloned into the native Tar ligan-binding domain LBD.  
+
Out of the Rosetta’s 870 suggested mutations only 11 variants were eventually cloned into the native Tar ligand-binding domain (LBD).  
 
See <a href="https://2016.igem.org/Team:Technion_Israel/Modifications/Rosetta">Computational Design</a> page for more information regarding the design process.
 
See <a href="https://2016.igem.org/Team:Technion_Israel/Modifications/Rosetta">Computational Design</a> page for more information regarding the design process.
−
Out of all the tested variants only one was discovered to be attracted to histamine. Sequencing results  
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Out of all the tested variants, only one was discovered to be attracted to Histamine. Sequencing results  
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showed that the only mutations to occur in this variant were those planned by the Rosetta’s design.
+
showed that the only mutations to occur in this variant were those planned by the Rosetta’s design. The desired sequences can be seen in figure 1.  
 
</p>
 
</p>
 
</div>
 
</div>
 
</div>
 
</div>
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+
 
 +
 
 +
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<div class="col-sm-6 col-sm-offset-3">
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<a class="pop ocenter">
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<img src="https://static.igem.org/mediawiki/2016/thumb/5/5c/T--Technion_Israel--Scheme_His.png/510px-T--Technion_Israel--Scheme_His.png" class="img-responsive img-center img-cont" width="500" style="cursor: pointer;">
 +
</a>
 +
<p><b>Fig. 2:</b> Histamine-Tar filtering process scheme</p>
 +
</div> </div>
 +
 
 +
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<p class="text-justify">
 
<p class="text-justify">
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A microscopic observation was used order to test the bacteria’s response to the attractant,  
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We observed the bacteria’s response to the attractant,  
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Histamine. It is evident in figure 1b that roughly 20 minutes after the addition of the  
+
Histamine, by using a microscope. It is evident in figure 3b that roughly 20 minutes after the addition of the  
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Histamine, the concentration of bacteria in the vicinity of the Histamine is much greater  
+
Histamine, the bacteria concentration in the vicinity of the Histamine is much greater  
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than in the begining of the experiement as shown in figure 1a.
+
than in the the beginning of the experiment (figure 3a).  
 +
 
 
</p>
 
</p>
 
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<p class="text-center"><b>Fig. 1:</b>  microscope results of chemotaxis activity for variant His_9 with 10mM of Histamine.<b> a.</b> Tar-Histamine after 0 minutes (when the Histamine added).<b> b.</b> Tar-Histamine after 20 minutes.<b> c.</b> Control after 0 minutes (when the Histamine added).<b> d.</b> Control after 20 minutes.
+
<p class="text-center"><b>Fig. 3:</b>  Microscope results of chemotaxis activity for variant His_9 with 10mM Histamine. (a) Tar-Histamine: before adding Histamine. (b) Tar-Histamine: 20 minutes after adding Histamine. (c) Tar-Histamine: before adding the Motility buffer (control solution). (d)  Tar-Histamine: 20 minutes after adding the Motility buffer.  
 
</p>
 
</p>
 
</div>
 
</div>
 
</div>
 
</div>
  
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</div>
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</div>
 +
</div>
  
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<br>
 
 
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<br>
 
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<p class="text-justify">
 
<p class="text-justify">
−
To prove the correct localization of the LBD on both poles of the bacteria, GFP was fused to its C-terminus with a short linker sequence <a href="http://parts.igem.org/Part:BBa_E0040" target="_blank">(E0040)</a> . The results of these tests as seen in figure 2, prove our assumption of correct localizations.
+
To prove the correct localization of the Tar-Histamine, GFP was fused to its C-terminus with a short linker sequence <a href="http://parts.igem.org/Part:BBa_E0040" target="_blank">(E0040)</a> . The results seen in figure 4 show that indeed the chimera is localized to the membrane (poles).
  
  
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<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
 
<a class="pop ocenter">
 
<a class="pop ocenter">
 
<img src="https://static.igem.org/mediawiki/2016/thumb/e/e3/T--Technion_Israel--His-GFP.png/800px-T--Technion_Israel--His-GFP.png" class="img-responsive img-center img-cont" width="600" style="cursor: pointer;">
 
<img src="https://static.igem.org/mediawiki/2016/thumb/e/e3/T--Technion_Israel--His-GFP.png/800px-T--Technion_Israel--His-GFP.png" class="img-responsive img-center img-cont" width="600" style="cursor: pointer;">
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<br>
 
<br>
 
<p class="text-center">
 
<p class="text-center">
−
<b>Fig. 2:</b>  Results of GFP fusion.<b> a.</b> White light of Tar-Histamine-GFP <b>b.</b> Flourcense (490nm excitation) of Tar-Histamine-GFP <b>c.</b> White light of normal Tar <b>d.</b> Flourcense (490nm excitation) of normal Tar
+
<b>Fig. 4:</b>  Results of GFP fusion. (A) Positive control- E.Coli strain expressing GFP protein, (B) Negative control- UU1250 strain expressing Tar chemoreceptor, (C) UU1250 strain expressing Tar-GFP chemoreceptor, (D) UU1250 strain expressing Histamine-Tar-GFP Chimera, fluorescence (490nm excitation).
 +
 
 +
 
 
</p>
 
</p>
 
</div>
 
</div>
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<div class="col-md-6 col-sm-12 vcenter"><!--6 text-->
 
<div class="col-md-6 col-sm-12 vcenter"><!--6 text-->
 
<p class="text-justify">
 
<p class="text-justify">
−
Finally, demonstrated in video 1 is a working concept of the FlashLab project -  
+
Finally, in the video below, a working concept of the <a href="https://2016.igem.org/Team:Technion_Israel/Design">FlashLab project</a> -  
−
a chip that serves as a detection tool based on the chemotaxis system of E.  
+
a chip that serves as a detection tool based on the chemotaxis system of <i>E.  
−
coli bacteria - by using a commercial ibidi chip filled with a suspension of  
+
coli</i> bacteria is presented. In the video, a commercial ibidi microfluidic chip filled with a suspension of  
−
bacteria expressing the chemoreceptor and chromoprotein
+
bacteria expressing both the chemoreceptor and chromoprotein
−
<a href="http://parts.igem.org/Part:BBa_K1357008" target="_blank">(K1357008)</a>.
+
(<a href="http://parts.igem.org/Part:BBa_K1992011" target="_blank">K1992011</a> + <a href="http://parts.igem.org/Part:BBa_K1357008" target="_blank">K1357008</a>) can been seen.
−
A solution of Histamine in concentration of 10<sup>-3</sup>M, the attractant,
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A solution of attractant (10<sup>-3</sup>M Histamine)
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was added to the chip and the displacement of the bacteria was monitored  
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was added to the chip and bacteria displacement was monitored and recorded
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and recorded.
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<p class="text-center"><b>Video 1:</b> from left to right:  
 
<p class="text-center"><b>Video 1:</b> from left to right:  
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(1) Histamine-Tar with Histamine atrractent added.
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(1) Histamine-Tar with Histamine attractant added.
 
(2) Histamine-Tar with Motility buffer added (control).<br>
 
(2) Histamine-Tar with Motility buffer added (control).<br>
 
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With the supporting evidence of the results presented above, it can be concluded
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The results presented above, mainly proves the concept of the ability to alter the LBD of a chemoreceptor using software.
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that both concepts have been proved and work under real life conditions and might  
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Moreover, these results might help with breakthroughs and lead to newly designed reporters for novel detection.
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lead to the detection of various substances in the near future.
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Latest revision as of 02:09, 20 October 2016

S.tar, by iGEM Technion 2016

S.Tar, by iGEM Technion 2016

PctA-Tar chimera Introduction



One of S.Tars sub-projects focused on altering the LBD of Tar chemoreceptor in order to design new hybrid chimeras. That was accomplished by replacing the LBD of the original Tar chemoreceptor with a new one, from a different source, without modifying Tar signaling region. 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 native Tar chemoreceptor, native PctA receptor and PctA-Tar chimera. Adapted from (1)



PctA is a chemoreceptor found in the Pseudomonas Aeruginosa .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 (K777000). Using these two sequences, we built a Biobrick part (K1992007) which was tested by transforming the device to bacteria that lacks chemoreceptors - UU1250. 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 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 in figure 5, it is clear that the chimera functions and controls the chemotactic ability of the bacteria leading to swarming response. This is compared to the control, UU1250 strain, that did not show any chemotactic ability as expected and no chemotactic rings were formed.

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. Negative control- UU1250 strain w/o the Tar expression plasmid, c. positive control - ΔZras strain expressing all chemoreceptors.


Next, to prove that the chimera is localized in the membrane, GFP was fused to its C-terminus with a short linker sequence (K1992010), figure 6. The results seen in figure 7, show that indeed the chimera is localized to the membrane (poles).

Fig. 6: Biobrick device of the PctA-Tar chimera fused to GFP.




Fig. 7: Results of GFP fusion. (A) Positive control- E.Coli strain expressing GFP protein,(B) Negative control- UU1250 strain expressing Tar chemoreceptor, (C) UU1250 strain expressing Tar-GFP chemoreceptor, (D) UU1250 strain expressing PctA-Tar-GFP Chimera, fluorescence (490nm excitation).




Finally, in the video 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. In the video, a commercial ibidi microfluidic chip filled with a suspension of bacteria expressing the chimera and chromoprotein (J23100 + K1357009) can been seen. A solution of repellent (10-3M Tetrachloroethylene) 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 both the chemoreceptor of your choice and a chromoprotein to a fluidic chip. Add the tested sample to the chip. If the chemoreceptor detecets the substance in the sample, a displacement of the bacteria will become visible. .




In video 1, the displacement of the bacteria can be clearly seen in test chip compared to the control chip.


Video 1: from left to right: (1) PctA-Tar chimera with Tetrachloroethylene repellent added. (2) PctA-Tar chimera with Motility buffer added (control).




With the supporting evidence of the results presented above, it can be concluded that both concepts: LBD altering and the FlashLab platform, have been proven and work under real life conditions and seem promising for detection of various substances in the near future.

Histamine-Tar Introduction


The heart of the S.Tar project is the Tar chemoreceptor, one of four E. coli receptors. Our goal is to create an engineered bacteria which has chemotaxis receptors sensitive to materials other than its native ligands. We show that E. coli can be engineered to respond to completely new materials. By changing Tar’s ligand binding domain (LBD) to other LBDs from various sources or by mutating it.

Fig. 1: Sequencing Results. "Query" describes the native Tar LBD sequence and "Sbjct" describes the design mutations sequence. The mutation region is marked with color (blue or red).



The bacterial world offers a relatively small selection of chemoreceptors in comparison to the vast number of possible ligands. These receptors evolved specifically to recognize substances which benefit or harm the organism. On top of that the fact that the majority of known receptors today are not well characterized meant that we had very few options of creating chimeric receptors as we initially planned.

In light of the above we had to turn to a new path – redesigning the Tar chemoreceptor to bind a different ligand using computational biology - The Rosetta software. Out of the Rosetta’s 870 suggested mutations only 11 variants were eventually cloned into the native Tar ligand-binding domain (LBD). See Computational Design page for more information regarding the design process. Out of all the tested variants, only one was discovered to be attracted to Histamine. Sequencing results showed that the only mutations to occur in this variant were those planned by the Rosetta’s design. The desired sequences can be seen in figure 1.

Fig. 2: Histamine-Tar filtering process scheme

Test and results

We observed the bacteria’s response to the attractant, Histamine, by using a microscope. It is evident in figure 3b that roughly 20 minutes after the addition of the Histamine, the bacteria concentration in the vicinity of the Histamine is much greater than in the the beginning of the experiment (figure 3a).

a.

b.

c.

d.

Fig. 3: Microscope results of chemotaxis activity for variant His_9 with 10mM Histamine. (a) Tar-Histamine: before adding Histamine. (b) Tar-Histamine: 20 minutes after adding Histamine. (c) Tar-Histamine: before adding the Motility buffer (control solution). (d)  Tar-Histamine: 20 minutes after adding the Motility buffer.



To prove the correct localization of the Tar-Histamine, GFP was fused to its C-terminus with a short linker sequence (E0040) . The results seen in figure 4 show that indeed the chimera is localized to the membrane (poles).





Fig. 4: Results of GFP fusion. (A) Positive control- E.Coli strain expressing GFP protein, (B) Negative control- UU1250 strain expressing Tar chemoreceptor, (C) UU1250 strain expressing Tar-GFP chemoreceptor, (D) UU1250 strain expressing Histamine-Tar-GFP Chimera, fluorescence (490nm excitation).




Finally, in the video below, a working concept of the FlashLab project - a chip that serves as a detection tool based on the chemotaxis system of E. coli bacteria is presented. In the video, a commercial ibidi microfluidic chip filled with a suspension of bacteria expressing both the chemoreceptor and chromoprotein (K1992011 + K1357008) can been seen. A solution of attractant (10-3M Histamine) was added to the chip and bacteria displacement was monitored and recorded


Video 1: from left to right: (1) Histamine-Tar with Histamine attractant added. (2) Histamine-Tar with Motility buffer added (control).




The results presented above, mainly proves the concept of the ability to alter the LBD of a chemoreceptor using software. Moreover, these results might help with breakthroughs and lead to newly designed reporters for novel detection.

References:
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.

2. Moretti, R., Bender, B.J., Allison, B. and Meiler, J., 2016. Rosetta and the Design of Ligand Binding Sites. Computational Design of Ligand Binding Proteins, pp.47-62.




S.tar, by iGEM Technion 2016