Difference between revisions of "Team:Technion Israel/Tar improvements"
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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"> | ||
| − | As Tar is the template chemoreceptor of our project we need first to characterize it in | + | As Tar is the template chemoreceptor of our project, we need first to characterize it in |
| − | terms of response, movement and location in vivo. In order to do so, plasmid expressing | + | terms of response, movement and location <i> in vivo </i>. In order to do so, plasmid expressing |
| − | Tar was cloned to chemoreceptors free <I>E.coli</I> | + | Tar was cloned to chemoreceptors free <I>E.coli</I> strain |
<a data-toggle="popover" data-trigger="click" data-original-title="Info:" data-html="true" | <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"> | + | data-content="an <i> E.coli </i> derivative, which lacks chemoreceptors genes, means this strain does not obtain chemotaxis ability"> |
UU1250<i class="entypo-check"></i></button></a>. | UU1250<i class="entypo-check"></i></button></a>. | ||
A proper characterization of the bacteria will serve as good comparison for our newly | A proper characterization of the bacteria will serve as good comparison for our newly | ||
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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"> | ||
| − | Expression of a sole chemoreceptor in bacteria and high expression of it increases the sensitivity | + | Expression of a sole chemoreceptor in bacteria and high expression of it, increases the sensitivity |
to the chemoreceptors ligands <b>(1)</b>. Due to these properties we constructed a high expression | to the chemoreceptors ligands <b>(1)</b>. Due to these properties we constructed a high expression | ||
system using the strongest Anderson promoter (<a href="http://parts.igem.org/Part:BBa_J23100" target="_blank">J23100</a>) | system using the strongest Anderson promoter (<a href="http://parts.igem.org/Part:BBa_J23100" target="_blank">J23100</a>) | ||
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<a href="http://parts.igem.org/Part:BBa_J23100" target="_blank">J23100 </a> promoter, | <a href="http://parts.igem.org/Part:BBa_J23100" target="_blank">J23100 </a> promoter, | ||
<a href="http://parts.igem.org/Part:BBa_B0034" target="_blank">B0034 </a> RBS, | <a href="http://parts.igem.org/Part:BBa_B0034" target="_blank">B0034 </a> RBS, | ||
| − | <a href="http://parts.igem.org/Part:BBa_K777000" target="_blank">K777000 </a> Tar chemoreceptor and | + | <a href="http://parts.igem.org/Part:BBa_K777000" target="_blank">K777000 </a> Tar chemoreceptor and |
<a href="http://parts.igem.org/Part:BBa_B0015" target="_blank">terminator</a>. | <a href="http://parts.igem.org/Part:BBa_B0015" target="_blank">terminator</a>. | ||
</p> | </p> | ||
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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"> | ||
| − | E.coli native chemoreceptors cluster in the cell poles. This property is critical for signal | + | <i> E.coli </i> native chemoreceptors cluster in the cell poles. This property is critical for signal |
amplification and adaptation of the cell. Although little is known about the mechanism of | amplification and adaptation of the cell. Although little is known about the mechanism of | ||
| − | localization, it is important that this property will preserve in order to keep a functional | + | localization, it is important that this property will preserve, in order to keep a functional |
and sensitive chemotaxis response <b>(2)</b>.<br> | and sensitive chemotaxis response <b>(2)</b>.<br> | ||
<br> | <br> | ||
| − | GFP labeling is a very common way to examine the migration and | + | GFP labeling is a very common way to examine the migration and localization of certain proteins <i> in vivo </i>. |
Fusion of GFP (<a href="http://parts.igem.org/Part:BBa_E0040" target="_blank">E0040</a>) to Tar | Fusion of GFP (<a href="http://parts.igem.org/Part:BBa_E0040" target="_blank">E0040</a>) to Tar | ||
| − | chemoreceptor enables us to track the migration and | + | chemoreceptor enables us to track the migration and localization of the protein to the cell poles as |
expected. The fusion conducted using flexible linker (<a href="http://parts.igem.org/Part:BBa_J18921" target="_blank">J18921</a>) | expected. The fusion conducted using flexible linker (<a href="http://parts.igem.org/Part:BBa_J18921" target="_blank">J18921</a>) | ||
in order to keep the domain structures of the proteins. The Tar-GFP (<a href="http://parts.igem.org/Part:BBa_K1992003" target="_blank">K1992003</a>) | in order to keep the domain structures of the proteins. The Tar-GFP (<a href="http://parts.igem.org/Part:BBa_K1992003" target="_blank">K1992003</a>) | ||
expressed using the two expression systems (<a href="http://parts.igem.org/Part:BBa_K1992008" target="_blank">K1992008</a> and | expressed using the two expression systems (<a href="http://parts.igem.org/Part:BBa_K1992008" target="_blank">K1992008</a> and | ||
<a href="http://parts.igem.org/Part:BBa_K1992009" target="_blank">K1992009</a>) and obtained using fluorescence microscope | <a href="http://parts.igem.org/Part:BBa_K1992009" target="_blank">K1992009</a>) and obtained using fluorescence microscope | ||
| − | (fig. 3 and fig. 4). In both cases high concentration of fluorescence can be seen in the cell poles indicating a proper | + | (fig. 3 and fig. 4). In both cases, high concentration of fluorescence can be seen in the cell poles indicating a proper |
migration and functionality of the Tar receptor. Comparison between the two expression systems (strong RBS and native RBS) | migration and functionality of the Tar receptor. Comparison between the two expression systems (strong RBS and native RBS) | ||
| − | + | did not show any significant difference. | |
</p> | </p> | ||
</div> | </div> | ||
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<a href="https://2016.igem.org/Team:Technion_Israel/Experiments" target="_blank">Swarming assay</a> conducted | <a href="https://2016.igem.org/Team:Technion_Israel/Experiments" target="_blank">Swarming assay</a> conducted | ||
to both RBS and native RBS (fig. 5 and fig. 6). Both exhibit chemotaxis response and movement compared to the | to both RBS and native RBS (fig. 5 and fig. 6). Both exhibit chemotaxis response and movement compared to the | ||
| − | negative | + | negative and positive control. Moreover, these results show a difference in radius size between the RBS |
| − | and the native RBS ( | + | and the native RBS (fig 7). The larger radius of the native RBS suggested higher a sensitivity of the chemotaxis |
| − | system that caused by a higher expression of Tar <b>(1)</b>. | + | system, that caused by a higher expression of Tar <b>(1)</b>. |
</p> | </p> | ||
</div> | </div> | ||
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<a href="https://2016.igem.org/Team:Technion_Israel/Experiments" target="_blank">chip microscope assay</a>. | <a href="https://2016.igem.org/Team:Technion_Israel/Experiments" target="_blank">chip microscope assay</a>. | ||
The bacteria express Tar moving toward high concentration of aspartate. As can be seen (fig 8) after | The bacteria express Tar moving toward high concentration of aspartate. As can be seen (fig 8) after | ||
| − | 15 minutes the number of the bacteria in the frame rises that compared to the control (fig 9) that | + | 15 minutes, the number of the bacteria in the frame rises that compared to the control (fig 9) that |
remains approximately the same. | remains approximately the same. | ||
</p> | </p> | ||
| Line 470: | Line 470: | ||
Repellent response of Tar receptor tested using | Repellent response of Tar receptor tested using | ||
<a href="https://2016.igem.org/Team:Technion_Israel/Experiments" target="_blank">chip color assay</a>. | <a href="https://2016.igem.org/Team:Technion_Israel/Experiments" target="_blank">chip color assay</a>. | ||
| − | The bacteria express Tar moving away from the high concentration of Co+2. As can | + | The bacteria express Tar moving away from the high concentration of Co<sup>+2</sup>. As can |
| − | be seen (fig 10) after 15 minutes the colored bacteria formed a cluster visible to | + | be seen (fig 10) after 15 minutes, the colored bacteria formed a cluster visible to |
| − | the naked eye, that compared to the control ( | + | the naked eye, that compared to the control (fig 11) which did not form cluster. <b> missimg results </b> |
</p> | </p> | ||
</div> | </div> | ||
Revision as of 22:00, 16 October 2016
Introduction
As Tar is the template chemoreceptor of our project, we need first to characterize it in terms of response, movement and location in vivo . In order to do so, plasmid expressing Tar was cloned to chemoreceptors free E.coli strain UU1250. A proper characterization of the bacteria will serve as good comparison for our newly designed chemoreceptors, allowing us to examine if they have the right properties indicating functional chemoreceptors.
Expression
Expression of a sole chemoreceptor in bacteria and high expression of it, increases the sensitivity
to the chemoreceptors ligands (1). Due to these properties we constructed a high expression
system using the strongest Anderson promoter (J23100)
and the strongest RBS (B0034)
according to Warsaw 2010's measurement.
This plasmid, K1992004,
then cloned to UU1250 strain for high expression of single chemoreceptor (fig. 1).
Fig. 1: K1992004 - High expression biological circuit ; J23100 promoter, B0034 RBS, K777000 Tar chemoreceptor and terminator.
In order to optimize the sensitivity of our system we also decided to examine the effect of the Tar native RBS on the expression level. The strong RBS was replaced by the native RBS of Tar as found in the E.coli genome. The new expression system K1992005 differs only by the RBS, allowing the comparison between the expression levels of the two RBS's.
Fig. 2: K1992005 - High expression circuit using the Tar native RBS.
Location
E.coli native chemoreceptors cluster in the cell poles. This property is critical for signal
amplification and adaptation of the cell. Although little is known about the mechanism of
localization, it is important that this property will preserve, in order to keep a functional
and sensitive chemotaxis response (2).
GFP labeling is a very common way to examine the migration and localization of certain proteins in vivo .
Fusion of GFP (E0040) to Tar
chemoreceptor enables us to track the migration and localization of the protein to the cell poles as
expected. The fusion conducted using flexible linker (J18921)
in order to keep the domain structures of the proteins. The Tar-GFP (K1992003)
expressed using the two expression systems (K1992008 and
K1992009) and obtained using fluorescence microscope
(fig. 3 and fig. 4). In both cases, high concentration of fluorescence can be seen in the cell poles indicating a proper
migration and functionality of the Tar receptor. Comparison between the two expression systems (strong RBS and native RBS)
did not show any significant difference.
a.
b.
Fig. 3: Tar-GFP expressed using B0034 RBS. (a) The cells under white light (b) the cells under 488nm wavelength.
a.
b.
Fig. 4: Tar-GFP expressed using the native RBS. (a) The cells under white light (b) the cells under 488nm wavelength
Response and movement
Tar exhibits attraction response toward aspartate and a repellent response away from
Ni+2 and Co+2 concentrations (3). Various chemotaxis assays performed,
using those substances, to show the bacteria desired response and movement. In turn these results
will be used as reference in order to test the bacteria behavior with our designed chemoreceptors.
Swarming assay conducted
to both RBS and native RBS (fig. 5 and fig. 6). Both exhibit chemotaxis response and movement compared to the
negative and positive control. Moreover, these results show a difference in radius size between the RBS
and the native RBS (fig 7). The larger radius of the native RBS suggested higher a sensitivity of the chemotaxis
system, that caused by a higher expression of Tar (1).
Fig. 5: (a) Tar expression in UU1250 strain, resulting a halo indicating a functional chemotaxis response. (b) Negative control- UU1250 strain w/o the Tar expression plasmid. (c) positive control - ΔZ strain expressing all chemoreceptors.
Fig. 6: (a) Tar expression using the native RBS in UU1250 strain, resulting a halo indicating a functional chemotaxis response. (b) Negative control- UU1250 strain w/o the Tar expression plasmid. (c) positive control - ΔZ strain expressing all chemoreceptors.
Fig. 7: (a) Tar expression in UU1250 strain cloned with K1992004 expretion system - strong RBS. (b) Tar expression in UU1250 strain cloned with K1992004 expretion system - Tar native RBS
Attractant response of the Tar receptor tested using chip microscope assay. The bacteria express Tar moving toward high concentration of aspartate. As can be seen (fig 8) after 15 minutes, the number of the bacteria in the frame rises that compared to the control (fig 9) that remains approximately the same.
a.
b.
Fig. 8: (a) cells expressing Tar w aspartate t=0 (b) cells expressing Tar w aspartate t=15 min
a.
b.
Fig. 9: (a) cells expressing Tar w motility buffer t=0 (b) cells expressing Tar w motility buffer t=15 min
Repellent response of Tar receptor tested using chip color assay. The bacteria express Tar moving away from the high concentration of Co+2. As can be seen (fig 10) after 15 minutes, the colored bacteria formed a cluster visible to the naked eye, that compared to the control (fig 11) which did not form cluster. missimg results
1. SOURJIK, Victor; BERG, Howard C. Functional interactions between receptors in bacterial chemotaxis. Nature, 2004, 428.6981: 437-441.
2. SHIOMI, Daisuke, et al. Helical distribution of the bacterial chemoreceptor via colocalization with the Sec protein translocation machinery. Molecular microbiology, 2006, 60.4: 894-906.
3. BI, Shuangyu; LAI, Luhua. Bacterial chemoreceptors and chemoeffectors.Cellular and Molecular Life Sciences, 2015, 72.4: 691-708.
