Difference between revisions of "Team:Technion Israel/Modifications/narx"
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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"> | <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"> | ||
| − | <br><h4 class="text-center" | + | <br><h4 class="text-center">Introduction</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"> | <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"> | ||
| − | <br><h4 class="text-center" | + | <br><h4 class="text-center">Design</h4> |
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| − | <br><h4 class="text-center" | + | <br><h4 class="text-center">Results</h4> |
</a> | </a> | ||
</li> | </li> | ||
<li role="presentation" class="col-sm-3 col-xs-6"> | <li role="presentation" class="col-sm-3 col-xs-6"> | ||
| − | <a href="# | + | <a href="#Conclusion" aria-controls="Conclusion" role="tab" data-toggle="tab"> |
<img src="https://static.igem.org/mediawiki/2016/4/47/T--Technion_Israel--icon_outlook.png" class="img-responsive img-center cont_tabs" width="75" height="75"> | <img src="https://static.igem.org/mediawiki/2016/4/47/T--Technion_Israel--icon_outlook.png" class="img-responsive img-center cont_tabs" width="75" height="75"> | ||
| − | <br><h4 class="text-center"> | + | <br><h4 class="text-center">Conclusion</h4> |
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<div class="row"> | <div class="row"> | ||
<div class="col-sm-12"> | <div class="col-sm-12"> | ||
| − | + | <h2>Introduction</h2> | |
| − | + | </div> | |
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| + | <!--6 text - 6 img div--> | ||
| + | <div class="row"> | ||
| + | <div class="col-md-6 col-sm-12 vcenter"><!--6 text--> | ||
| + | <p class="text-justify"> | ||
| + | As a proof of concept of our platform, the Tar chemoreceptor LBD was replaced with the NarX LBD. | ||
| + | The NarX sensor protein of <i>E. coli</i> binds nitrite and nitrate and induces the expression | ||
| + | of proteins involved in anaerobic respiration <b>(1)</b>. We followed a protocol which was | ||
| + | previously shown to be successful <b>(1)</b>. | ||
| + | This work resulted in a NarX-Tar chimera, comprised by the NarX LBD and Tar’s cytoplasmic region. | ||
| + | According to the article the chimera was supposed to function as a repellent chemoreceptor to | ||
| + | nitrite and nitrate. | ||
| + | </p> | ||
| + | |||
| + | </p> | ||
| + | </div><!-- | ||
| + | --><div class="col-md-6 col-sm-12 vcenter"><!--6 img div--> | ||
| + | <a class="pop ocenter"> | ||
| + | <img src="https://static.igem.org/mediawiki/2016/thumb/c/c5/T--Technion_Israel--NarX.png/800px-T--Technion_Israel--NarX.png" class="img-responsive img-center img-cont" width="400" style="cursor: pointer;"> | ||
| + | </a> <br> | ||
| + | <p class="text-center"><b>Fig. 1:</b> Scheme of Tar chemoreceptor on the left, NarX-Tar chimera on the right.</p> | ||
</div> | </div> | ||
</div> | </div> | ||
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</div> | </div> | ||
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To construct this chimera, the protein sequence of both the LBD and the linker region of NarX were obtained the literature <b>(1)</b>. | To construct this chimera, the protein sequence of both the LBD and the linker region of NarX were obtained the literature <b>(1)</b>. | ||
| − | Using the DNA sequences of both frgamnets and Tar’s cytoplasmic region, we built a Biobrick device (part not submitted) <b>(2)</b>. As in the PctA, first a 3D model was generated using the | + | Using the DNA sequences of both frgamnets and Tar’s cytoplasmic region, we built a Biobrick device (part not submitted) <b>(2)</b>. As in the PctA, first a 3D model was generated using the Phyre2 Protein Fold Recognition server, to ensure the correct folding of all parts of the chimera (Figure 1, results).<br> |
<br> | <br> | ||
| − | The next step was transforming to bacteria that lacks chemoreceptors - | + | The next step was transforming 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)."> | |
| − | <br>Since the NarX-Tar chimera is supposed to serve as a repellent chemoreceptor, the conventional assay is a chemical in plug assay, in which the repellent is added to a motility buffer and the movement of the bacteria is detected (See <a href="https://2016.igem.org/Team:Technion_Israel/Experiments">chemical in plug assay</a>). Here sodium nitrate was used as a repellent for the NarX-Tar strain. | + | UU1250<i class="entypo-check"></i></button></a>, |
| − | <br> | + | and to test the chemotactic ability of the cloned strain the following chemotaxis assays were performed<br> |
| − | <br>In | + | <br>Since the NarX-Tar chimera is supposed to serve as a repellent chemoreceptor, the conventional assay is a chemical in plug assay, in which the repellent is added to a motility buffer and the movement of the bacteria is detected (See <a href="https://2016.igem.org/Team:Technion_Israel/Experiments">chemical in plug assay</a>). Here sodium nitrate was used as a repellent for the NarX-Tar strain.<br> |
| + | <br>Following, a <a href="https://static.igem.org/mediawiki/2016/f/f3/T--Technion_Israel--Chemotaxis_assays.pdf" target="_blank">drop assay</a> was conducted. A suspension of bacteria in motility buffer was placed on a microscope slide and a drop of repellent was added in the concentrations of 10<sup>-2</sup>M and 10<sup>-6</sup>M. The slide was monitored throughout the entire procedure in order to examine the response of bacteria. | ||
| + | <br> | ||
| + | <br>In addition, GFP was fused to the NarX-Tar chimera's C-terminus, in order to validate the location of the expressed chemoreceptor on both poles of the bacterial membrane. Flow cytometry analysis was conducted in order to verify the expression of the NarX-Tar chimera. We generated the NarX-Tar-GFP fusion gene that we planned to use for the localization assay. To verify the successful cloning of GFP to the NarX-Tar chimera, we screened 20 clones with flow cytometry. | ||
| + | |||
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<img src="https://static.igem.org/mediawiki/2016/a/a1/T--Technion_Israel--narXcircute.png" class="img-responsive img-center" width="450" style="cursor: pointer;"> | <img src="https://static.igem.org/mediawiki/2016/a/a1/T--Technion_Israel--narXcircute.png" class="img-responsive img-center" width="450" style="cursor: pointer;"> | ||
</a> | </a> | ||
| − | <p class="text-center"><b>Fig. | + | <p class="text-center"><b>Fig. 1:</b> Biobrick device of the NarX-Tar chimera.</p> |
</div> | </div> | ||
</div> | </div> | ||
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<div class="row"><!-- #1 row --> | <div class="row"><!-- #1 row --> | ||
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 --> | <div class="col-sm-8 col-sm-offset-2"><!-- 8/12 --> | ||
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<div class="col-md-12 col-sm-12"> | <div class="col-md-12 col-sm-12"> | ||
| − | + | <h2 class="">Results</h2> | |
| + | </div> | ||
| + | </div> | ||
| + | <div class="row"> | ||
| + | <div class="col-md-12 col-sm-12"> | ||
<p class="text-justify"> | <p class="text-justify"> | ||
| − | The results of the 3D structure were not promising, as the folding was not achieved in the | + | The results of the 3D structure were not promising, as the folding was not |
| + | achieved in the correct manner, as can be seen in figure 1a. The 3D structure | ||
| + | of the native Tar is presented in figure 1b. | ||
| + | </p> | ||
| + | </div> | ||
| + | </div> | ||
| − | + | <br> | |
| + | <div class="row"> | ||
| + | <div class="col-sm-12"><!-- 8/12 --> | ||
| + | <div class="col-md-6 col-sm-12"> | ||
| + | <p class="text-justify">a.</p> | ||
| + | <a class="pop"> | ||
| + | <img src="https://static.igem.org/mediawiki/2016/7/7d/T--Technion_Israel--narx-tar.PNG" class="img-responsive img-center img-cont" style="cursor: pointer;"><br> | ||
| + | </a> | ||
| + | </div> | ||
| + | <div class="col-md-6 col-sm-12"> | ||
| + | <p class="text-justify">b.</p> | ||
| + | <a class="pop"> | ||
| + | <img src="https://static.igem.org/mediawiki/2016/b/b4/T--Technion_Israel--Tar_fig2b.PNG" class="img-responsive img-center img-cont" style="cursor: pointer;"><br> | ||
| + | </a> | ||
| + | </div> | ||
| + | <div class="col-md-12 col-sm-12"> | ||
| + | <p class="text-center"> | ||
| + | <b>Fig. 1:</b> <b>(a)</b>NarX-Tar chimera 3D structure. The Tar signaling regions is in gray, the NarX LBD is in red. <b>(b)</b>Native Tar 3D structure.</p> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
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| − | <br> | + | |
| + | <div class="row"> | ||
| + | <div class="col-md-12 col-sm-12"> | ||
| + | <p class="text-justify"> | ||
| + | When tested on the chemical in plug assay no movement was detected, indicating that | ||
| + | the NarX-Tar strain is not responsive to sodium nitrate. (figure 2) | ||
| + | </p> | ||
| + | </div> | ||
| + | </div> | ||
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| + | <!-- 12 img div --> | ||
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| + | <div class="col-md-12 col-sm-12"> | ||
| + | <a class="pop ocenter"> | ||
| + | <img src="https://static.igem.org/mediawiki/2016/b/be/T--Technion_Israel--NarX_in_plug_assay.png" class="img-responsive img-center img-cont" width="700"" style="cursor: pointer;"> | ||
| + | </a> | ||
| + | <p class="text-center"><b>Fig. 2:</b> Chemical in plug assay results: on the left, | ||
| + | positive control- ΔZ in the presence of the attractant aspartic acid. On | ||
| + | the rightNarX-Tar strain with repellent sodium nitrate.</p> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | <br> | ||
| − | < | + | <div class="row"> |
| − | + | <div class="col-md-12 col-sm-12"> | |
| − | + | <p class="text-justify"> | |
| − | <div class="col-md-12 col-sm-12"> | + | The expected results of the drop assay were a rapid tumbling response of the bacteria. |
| − | + | Nevertheless, the strain showed no response to different concentrations of sodium | |
| − | + | nitrate and unfortunately a sufficient documentation hasn't been obtained.<br> | |
| − | the NarX-Tar | + | <br> |
| + | Lastly, the testing of the clone carrying the GFP gene fused to the chimera with flow | ||
| + | cytometry showed no indication to fluorescence. In figure 3, we plotted each clone as | ||
| + | a single histogram (light green histograms) and compared them with the histograms of a | ||
| + | positive control (Pct-Tar-GFP; dark green) and a negative control (NarX-Tar only, black). | ||
| + | As comparison between the single histograms is tedious, we plotted all histograms in | ||
| + | one figure for easier comparison. As can be seen in figure 4, the fluorescence of | ||
| + | NarX-Tar-GFP is comparable with the fluorescence of the negative strain indicating that | ||
| + | all colonies could not been cloned successfully. Note that the negative control showed | ||
| + | two peaks, one peak which was defined as negative, and the second, albeit smaller peak | ||
| + | overlapped with the fluorescence of PctA-Tar (positive control). This is probably due | ||
| + | to a very high concentration of bacteria (event rate: 21000 events/sec). As a result, | ||
| + | the samples were diluted in the ratio of 1:4 in order to avoid false positive results. | ||
| + | </p> | ||
| + | </div> | ||
| + | </div> | ||
| − | + | <br> | |
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| − | <br> | + | |
| − | < | + | |
| − | <div class="col-md-12 col-sm-12"> | + | <div class="row"> |
| + | <div class="col-md-12 col-sm-12"> | ||
<a class="pop ocenter"> | <a class="pop ocenter"> | ||
| − | <img src="https://static.igem.org/mediawiki/2016/ | + | <img src="https://static.igem.org/mediawiki/2016/c/cd/T--Technion_Israel--iGEM_NarX_layout1.png" class="img-responsive img-center img-cont" width="700"" style="cursor: pointer;"> |
</a> | </a> | ||
| − | + | <p class="text-center"><b>Fig. 3:</b> Flow cytometry results.</p> | |
| − | + | ||
| − | + | ||
| − | <p class="text-center"><b>Fig. | + | |
| − | + | ||
</div> | </div> | ||
| − | </div> | + | </div> |
| + | |||
| + | <br> | ||
| + | <br> | ||
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<div class="row"> | <div class="row"> | ||
| − | + | <div class="col-md-12 col-sm-12"> | |
| − | < | + | <a class="pop ocenter"> |
| − | + | <img src="https://static.igem.org/mediawiki/2016/a/a8/T--Technion_Israel--iGEM_NarX_layout2.png" class="img-responsive img-center img-cont" width="700"" style="cursor: pointer;"> | |
| − | + | </a> | |
| − | + | <p class="text-center"><b>Fig. 4:</b> A comparison between NarX colonies (light green), positive control (dark green) and negative (black) control.</p> | |
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| + | </div> | ||
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<div class="cont_box"> | <div class="cont_box"> | ||
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<div class="row"> | <div class="row"> | ||
<div class="col-sm-12"> | <div class="col-sm-12"> | ||
| − | + | <h2 class="">Conclusion</h2> | |
| + | </div> | ||
| + | </div> | ||
| + | <div class="row"> | ||
| + | <div class="col-sm-12"> | ||
<p class="text-justify"> | <p class="text-justify"> | ||
| − | As the results showed, NarX-Tar strain failed to show any response to sodium nitrate. Moreover, as the reporter gene (GFP) showed no indication of expression, this subproject was put aside. | + | As the results showed, NarX-Tar strain failed to show any response to sodium |
| − | It is unfortunate that the NarX-Tar clone was not successful, as it could have served as an additional proof of concept the S.Tar platform, in addition to the other strains we have cloned. | + | nitrate. Moreover, as the reporter gene (GFP) showed no indication of expression, |
| − | + | this subproject was put aside.<br> | |
| + | It is unfortunate that the NarX-Tar clone was not successful, as it could have | ||
| + | served as an additional proof of concept the S.Tar platform, in addition to the | ||
| + | other strains we have cloned. | ||
</p> | </p> | ||
</div> | </div> | ||
</div> | </div> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
</div><!-- END: #1 row --> | </div><!-- END: #1 row --> | ||
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<!-- ==================== END: 4 Outlook ==================== --> | <!-- ==================== END: 4 Outlook ==================== --> | ||
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| − | + | <p class="references"> | |
| − | + | References:<br> | |
| − | + | 1. R Ward, S.M., Delgado, A., Gunsalus, R.P., and Manson, M.D. (2002). A NarX-Tar chimera mediates repellent chemotaxis to nitrate and nitrite. Mol. Microbiol. 44, 709–719.<br><br> | |
| − | + | 2. <a href="http://www.ecogene.org/sources/1"target="_blank">The complete <i>E. coli</i> genome sequence.</a><br> | |
| − | References:<br> | + | </p> |
| − | + | ||
| − | + | ||
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</div> | </div> | ||
</div> | </div> | ||
| + | </div> | ||
| − | <br> | + | <br> |
| − | <br> | + | <br> |
| − | + | ||
<a id="back-to-top" href="#" class="btn btn-lg back-to-top" role="button" title="Up" data-toggle="tooltip" data-placement="left"><img src="https://static.igem.org/mediawiki/2016/5/5a/T--Technion_Israel--up_arrow.png" alt=""></a> | <a id="back-to-top" href="#" class="btn btn-lg back-to-top" role="button" title="Up" data-toggle="tooltip" data-placement="left"><img src="https://static.igem.org/mediawiki/2016/5/5a/T--Technion_Israel--up_arrow.png" alt=""></a> | ||
Latest revision as of 23:18, 19 October 2016
Introduction
As a proof of concept of our platform, the Tar chemoreceptor LBD was replaced with the NarX LBD. The NarX sensor protein of E. coli binds nitrite and nitrate and induces the expression of proteins involved in anaerobic respiration (1). We followed a protocol which was previously shown to be successful (1). This work resulted in a NarX-Tar chimera, comprised by the NarX LBD and Tar’s cytoplasmic region. According to the article the chimera was supposed to function as a repellent chemoreceptor to nitrite and nitrate.
Fig. 1: Scheme of Tar chemoreceptor on the left, NarX-Tar chimera on the right.
Design and Implementation
To construct this chimera, the protein sequence of both the LBD and the linker region of NarX were obtained the literature (1).
Using the DNA sequences of both frgamnets and Tar’s cytoplasmic region, we built a Biobrick device (part not submitted) (2). As in the PctA, first a 3D model was generated using the Phyre2 Protein Fold Recognition server, to ensure the correct folding of all parts of the chimera (Figure 1, results).
The next step was transforming to bacteria that lacks chemoreceptors -
UU1250,
and to test the chemotactic ability of the cloned strain the following chemotaxis assays were performed
Since the NarX-Tar chimera is supposed to serve as a repellent chemoreceptor, the conventional assay is a chemical in plug assay, in which the repellent is added to a motility buffer and the movement of the bacteria is detected (See chemical in plug assay). Here sodium nitrate was used as a repellent for the NarX-Tar strain.
Following, a drop assay was conducted. A suspension of bacteria in motility buffer was placed on a microscope slide and a drop of repellent was added in the concentrations of 10-2M and 10-6M. The slide was monitored throughout the entire procedure in order to examine the response of bacteria.
In addition, GFP was fused to the NarX-Tar chimera's C-terminus, in order to validate the location of the expressed chemoreceptor on both poles of the bacterial membrane. Flow cytometry analysis was conducted in order to verify the expression of the NarX-Tar chimera. We generated the NarX-Tar-GFP fusion gene that we planned to use for the localization assay. To verify the successful cloning of GFP to the NarX-Tar chimera, we screened 20 clones with flow cytometry.
Fig. 1: Biobrick device of the NarX-Tar chimera.
Results
The results of the 3D structure were not promising, as the folding was not achieved in the correct manner, as can be seen in figure 1a. The 3D structure of the native Tar is presented in figure 1b.
a.
b.
Fig. 1: (a)NarX-Tar chimera 3D structure. The Tar signaling regions is in gray, the NarX LBD is in red. (b)Native Tar 3D structure.
When tested on the chemical in plug assay no movement was detected, indicating that the NarX-Tar strain is not responsive to sodium nitrate. (figure 2)
Fig. 2: Chemical in plug assay results: on the left, positive control- ΔZ in the presence of the attractant aspartic acid. On the rightNarX-Tar strain with repellent sodium nitrate.
The expected results of the drop assay were a rapid tumbling response of the bacteria.
Nevertheless, the strain showed no response to different concentrations of sodium
nitrate and unfortunately a sufficient documentation hasn't been obtained.
Lastly, the testing of the clone carrying the GFP gene fused to the chimera with flow
cytometry showed no indication to fluorescence. In figure 3, we plotted each clone as
a single histogram (light green histograms) and compared them with the histograms of a
positive control (Pct-Tar-GFP; dark green) and a negative control (NarX-Tar only, black).
As comparison between the single histograms is tedious, we plotted all histograms in
one figure for easier comparison. As can be seen in figure 4, the fluorescence of
NarX-Tar-GFP is comparable with the fluorescence of the negative strain indicating that
all colonies could not been cloned successfully. Note that the negative control showed
two peaks, one peak which was defined as negative, and the second, albeit smaller peak
overlapped with the fluorescence of PctA-Tar (positive control). This is probably due
to a very high concentration of bacteria (event rate: 21000 events/sec). As a result,
the samples were diluted in the ratio of 1:4 in order to avoid false positive results.
Fig. 3: Flow cytometry results.
Fig. 4: A comparison between NarX colonies (light green), positive control (dark green) and negative (black) control.
Conclusion
As the results showed, NarX-Tar strain failed to show any response to sodium
nitrate. Moreover, as the reporter gene (GFP) showed no indication of expression,
this subproject was put aside.
It is unfortunate that the NarX-Tar clone was not successful, as it could have
served as an additional proof of concept the S.Tar platform, in addition to the
other strains we have cloned.
References:
1. R Ward, S.M., Delgado, A., Gunsalus, R.P., and Manson, M.D. (2002). A NarX-Tar chimera mediates repellent chemotaxis to nitrate and nitrite. Mol. Microbiol. 44, 709–719.
2. The complete E. coli genome sequence.
