Team:Paris Bettencourt/ComS diffusion

From 2011.igem.org

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<h2>Introduction to the system</h2>
<h2>Introduction to the system</h2>
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<p>In case of nutriment restriction, B. Subtilis has two way of reacting. One is to <em>soprulate</em>, in order to wait for better times to come back to life again. The second is the <em>competence</em> mechanism. In this state, B. Subtilis try to catch in the medium every pieces of DNA around and make <em>homologue recombination</em> with its genome, and then devide a lot to make a chance for her new genotype to survive the hard life conditions.</p>
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<p>When it faces nutrient restriction, <i>B.subtilis</i> has two ways of reacting. One is to <em>sporulate</em> in order to wait for better times and come back to "life" again. The second is the <em>competence</em> mechanism. In this state, <i>B.subtilis</i> tries to catch in the medium every piece of DNA around and make <em>homologous recombination</em> with its genome. It then divides a lot to give a chance to its new genotype to survive the harsh conditions.</p>
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<td align="center"><u><b>Fig1:</b></u> Schematics of the MeKS system</td>
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<td align="center"><u><b>Fig1:</b></u> Schematics of the MeKS system <a href="">[1]</a></td>
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<td align="center"><u><b>Fig2:</b></u> Image of a mix between sporulated and competent <br /> state during the steady state phase.</td>
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<td align="center"><u><b>Fig2:</b></u> Image of a mix between sporulated and competent <br /> state during the steady state phase. <a href="https://2011.igem.org/Team:Paris_Bettencourt/ComS_diffusion#references">[1]</a></td>
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<br />
<br />
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<p>The choice between these two mechanism is controled by a bistable system known as <em>the MeKS system</em>. This system is usually stochastically controled by the apparition of some ComS protein in the cell, that would inhibit the MecA protease and allow the ComK protein to self amplify. But, as ComK inhibit the production of ComS, the system come back to the original state in a few hours.</p>
+
<p>The choice between these two mechanisms is controled by a bistable system known as <em>the MeKS system</em>. This system is usually stochastically controled by the apparition of ComS proteins in the cell. ComS inhibits the MecA protease and allows the ComK protein to self-amplify. But as ComK inhibits the production of ComS, the system comes back to the original state within a few hours.</p>
-
<p>A comprehensive study of this phenomenon has been done by M. Elowitz and al. and published in this paper <a href="http://www.elowitz.caltech.edu/publications/CompetenceExcitable.pdf">[1]</a> from where these figures are extracted.</p>
+
<p>A comprehensive study of this phenomenon has been conducted by M. Elowitz and al. <a href="https://2011.igem.org/Team:Paris_Bettencourt/ComS_diffusion#references">[1]</a>.</p>
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<h2>Ideas behind the design</h2>
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<h2>Idea behind the design</h2>
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<p>The ideas behind this design is to pass through the nanotube some ComS proteins. This protein is very small (40 amino-acids) and so is expected to pass very efficiently. It is also known from the M. elowitz paper <a href="http://www.elowitz.caltech.edu/publications/CompetenceExcitable.pdf">[1]</a> that very few proteins are required to trigger the switch, which makes this system a very good candidate for what we want to do.</p>
+
<p>The idea behind this design is to pass ComS proteins through the nanotube. This protein is very small (40 amino-acids) and it is expected to pass quite efficiently. We also know from the M. elowitz paper <a href="https://2011.igem.org/Team:Paris_Bettencourt/ComS_diffusion#references">[1]</a> that very few proteins are required to trigger the switch (around 200). This makes this system a very good candidate for what we want to do.</p>
-
<p>We contacted M. Elowitz, and he kindly sensed us a strain containing a chromosomally integrated reporter that monitors the level of ComK  and ComS in the cell, with the construction pComG-cfp/pComS-yfp inside. This construct could in theory directly be used as a receiver cell, but the MeKS system is known to be repressed in expodential phase. We explain later how to avoid this problem.</p>
+
<p>We contacted M. Elowitz and he kindly sent us a strain containing a chromosomally integrated reporter that monitors the level of ComK  and ComS produced by a cell (pComG-cfp/pComS-yfp). This construct could in theory directly be used as a receiver cell, but the MeKS system is known to be repressed in exponential phase. We explain later how to avoid this problem.</p>
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<p>The design can simply be summed up by the following picture:</p>
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<p>The design is summed up in the following picture:</p>
<center>
<center>
<img src="https://static.igem.org/mediawiki/2011/7/7f/ComS_summary.jpg" width=700px>
<img src="https://static.igem.org/mediawiki/2011/7/7f/ComS_summary.jpg" width=700px>
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<p><u><b>Fig3:</b></u> Schematic of the simplified general principle of the ComS design</p>
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<p><u><b>Fig3:</b></u> Schematic of the ComS design</p>
</center>
</center>
<h2>How this design works</h2>
<h2>How this design works</h2>
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<p>Here is the explanation step by step:</p>
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<p>Explanation step by step:</p>
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In standard conditions, the ComK protein, in late expodential phase, is destroyed by the protease MecA. In the emmitor cell, the system is repressed because codY is active.
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<p>In standard conditions, the ComK protein in late exponential phase is destroyed by the protease MecA. In the emitter cell, the system is repressed because codY is active.</p>
<center>
<center>
<img src="https://static.igem.org/mediawiki/2011/e/ea/ComS_principle1.jpg" width=700px>
<img src="https://static.igem.org/mediawiki/2011/e/ea/ComS_principle1.jpg" width=700px>
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<p><u><b>Fig4:</b></u> Step one, the system is repressed, and there is no ComK.</p>
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<p><u><b>Fig4:</b></u> Step one, the system is repressed and there is no ComK.</p>
</center>
</center>
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<p>Is a nanotube is etablished, some ComS will diffuse from the first cell to the second one, and block the protease by affinity inhibtion. The ComK can start amplifying, and activate the ComG promoter.</p>
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<br/>
 +
 
 +
<p>A nanotube is etablished, some ComS diffuses from the first cell to the second one, and blocks the protease by affinity inhibtion. The ComK can start amplifying, and activates the ComG promoter.</p>
<center>
<center>
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<p><u><b>Fig5:</b></u> The ComK protein activates the ComG promoter.</p>
<p><u><b>Fig5:</b></u> The ComK protein activates the ComG promoter.</p>
</center>
</center>
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<br/>
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<p>The ComG promoter produces CFP that report the cell has entered the competence phase.</p>
<center>
<center>
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<p><u><b>Fig6:</b></u> Schematic of the simplified general principle of the ComS design</p>
<p><u><b>Fig6:</b></u> Schematic of the simplified general principle of the ComS design</p>
</center>
</center>
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 +
<br/>
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<p>If the nanotube breaks, ComS starts to disapear. Several hours later the cell returns to its original state.</p>
 +
<h2>Problems linked to the growth phase</h2>
<h2>Problems linked to the growth phase</h2>
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<p>The MeKS system is a noise tolerent bi-stable system that regulate the competence of the cell. This system is working in the stationnary phase and is theorically repressed during the expodential phase. We investigated the issue using computer assisted sequence homology analysis, and we found 3 locuses in which we expect the protein CodY to bind, that is known to repress many genes of the steady state phase during the expodential phase.</p>  
+
<p>The MeKS system is a noise tolerent bi-stable system that regulates the competence of the cell. This system works in the stationary phase and is theoretically repressed during the exponential phase. We investigated the issue using computer assisted sequence homology analysis and found 3 locuses in which we expect protein CodY can bind. CodY is known to repress many genes of the steady state phase during the exponential phase.</p>  
-
<p>In order to avoid this problem, we have created a B. Subtilis strain ∆CodY. This will allow the MeKS system to be active during the expodential growth phase, as well as thousands of stationnary phase gene. This mutation is not lethal although it reduces the growth speed significantly.</p>
+
<p>In order to avoid this problem, we have created a <i>B.subtilis</i> strain ∆CodY. This will allow the MeKS system to be active during the exponential growth phase, as well as thousands of stationnary phase genes. This mutation is not lethal although it reduces the growth speed significantly.</p>
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<p>A CodY- strand is obtained thanks to Link Sonenshein <a href="http://www.tufts.edu/sackler//facultyIntros/sonensheinA.html">[2]</a> and this strain was crossed with the reporter strain from M. Elowitz's laboratory <a href="http://www.elowitz.caltech.edu/index.html">[2]</a> (see the paper<a href="http://www.elowitz.caltech.edu/publications/Tunability.pdf">[3]</a>) using DNA extraction and competence of the late expodential phase competence.</p>
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<p>A CodY- strain was obtained thanks to Link Sonenshein (<a href="http://www.tufts.edu/sackler//facultyIntros/sonensheinA.html">link</a>) and this strain was crossed with the reporter strain from M. Elowitz's laboratory (<a href="http://www.elowitz.caltech.edu/index.html">link</a>) (see the paper: <a href="https://2011.igem.org/Team:Paris_Bettencourt/ComS_diffusion#references">[2]</a>) using DNA extraction and competence of the late exponential phase competence.</p>
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<p>We sucessfully managed to get this strain. See the experiment page for details.</p>
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<p>We sucessfully managed to get this strain. See the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/ComS_diffusion">experiment page</a> for details.</p>
 +
<h2>Modeling and experiments</h2>
 +
<p>To know more about what we have done on this system and in the experiments, we invite you to visit the corresponding <em>modeling</em> and <em>experiment</em> pages:</p>
 +
<ul>
 +
<li><em><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion">Modelling</a></em></li>
 +
<li><em><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/ComS_diffusion">Experiments</a></em></li>
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</ul>
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<div id="citation_box">
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<p id="references">References</p>
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<ol>
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<li><i>An excitable gene regulatory circuit induces transient cellular differentiation</i>, Gürol M. Süel, Jordi Garcia-Ojalvo, Louisa M. Liberman & Michael B. Elowitz, Letter to Nature, available <a href="http://www.elowitz.caltech.edu/publications/CompetenceExcitable.pdf">here</a></li>
 +
<li><i>Tunability and Noise Dependence in Differentiation Dynamics Gürol M.</i>, Gürol M. Süel, Rajan P. Kulkarni, Jonathan Dworkin, Jordi Garcia-Ojalvo, Michael B. Elowitz, available <a href="http://www.elowitz.caltech.edu/publications/Tunability.pdf">here</a></li>
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</ol>
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</div>
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<div id="scroll_left"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs"><img src="https://static.igem.org/mediawiki/2011/0/0a/Arrow-left-big.png" style="width:100%;"></a><a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs">Go back to the designs!</a></div>
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<div id="scroll_right"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Diffusion"><img src="https://static.igem.org/mediawiki/2011/e/e0/Arrow-right-big.png" style="width:100%;"></a><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion">ComS model</a></div>
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<div id="scroll_right"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Diffusion"><img src="https://static.igem.org/mediawiki/2011/e/e0/Arrow-right-big.png" style="width:100%;"></a><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion">See the ComS model!</a></div>
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Latest revision as of 00:45, 29 October 2011

Team IGEM Paris 2011

The ComS diffusion system

Introduction to the system

When it faces nutrient restriction, B.subtilis has two ways of reacting. One is to sporulate in order to wait for better times and come back to "life" again. The second is the competence mechanism. In this state, B.subtilis tries to catch in the medium every piece of DNA around and make homologous recombination with its genome. It then divides a lot to give a chance to its new genotype to survive the harsh conditions.


Fig1: Schematics of the MeKS system [1] Fig2: Image of a mix between sporulated and competent
state during the steady state phase. [1]

The choice between these two mechanisms is controled by a bistable system known as the MeKS system. This system is usually stochastically controled by the apparition of ComS proteins in the cell. ComS inhibits the MecA protease and allows the ComK protein to self-amplify. But as ComK inhibits the production of ComS, the system comes back to the original state within a few hours.

A comprehensive study of this phenomenon has been conducted by M. Elowitz and al. [1].

Idea behind the design

The idea behind this design is to pass ComS proteins through the nanotube. This protein is very small (40 amino-acids) and it is expected to pass quite efficiently. We also know from the M. elowitz paper [1] that very few proteins are required to trigger the switch (around 200). This makes this system a very good candidate for what we want to do.

We contacted M. Elowitz and he kindly sent us a strain containing a chromosomally integrated reporter that monitors the level of ComK and ComS produced by a cell (pComG-cfp/pComS-yfp). This construct could in theory directly be used as a receiver cell, but the MeKS system is known to be repressed in exponential phase. We explain later how to avoid this problem.

The design is summed up in the following picture:

Fig3: Schematic of the ComS design

How this design works

Explanation step by step:

In standard conditions, the ComK protein in late exponential phase is destroyed by the protease MecA. In the emitter cell, the system is repressed because codY is active.

Fig4: Step one, the system is repressed and there is no ComK.


A nanotube is etablished, some ComS diffuses from the first cell to the second one, and blocks the protease by affinity inhibtion. The ComK can start amplifying, and activates the ComG promoter.

Fig5: The ComK protein activates the ComG promoter.


The ComG promoter produces CFP that report the cell has entered the competence phase.

Fig6: Schematic of the simplified general principle of the ComS design


If the nanotube breaks, ComS starts to disapear. Several hours later the cell returns to its original state.

Problems linked to the growth phase

The MeKS system is a noise tolerent bi-stable system that regulates the competence of the cell. This system works in the stationary phase and is theoretically repressed during the exponential phase. We investigated the issue using computer assisted sequence homology analysis and found 3 locuses in which we expect protein CodY can bind. CodY is known to repress many genes of the steady state phase during the exponential phase.

In order to avoid this problem, we have created a B.subtilis strain ∆CodY. This will allow the MeKS system to be active during the exponential growth phase, as well as thousands of stationnary phase genes. This mutation is not lethal although it reduces the growth speed significantly.

A CodY- strain was obtained thanks to Link Sonenshein (link) and this strain was crossed with the reporter strain from M. Elowitz's laboratory (link) (see the paper: [2]) using DNA extraction and competence of the late exponential phase competence.

We sucessfully managed to get this strain. See the experiment page for details.

Modeling and experiments

To know more about what we have done on this system and in the experiments, we invite you to visit the corresponding modeling and experiment pages:

References

  1. An excitable gene regulatory circuit induces transient cellular differentiation, Gürol M. Süel, Jordi Garcia-Ojalvo, Louisa M. Liberman & Michael B. Elowitz, Letter to Nature, available here
  2. Tunability and Noise Dependence in Differentiation Dynamics Gürol M., Gürol M. Süel, Rajan P. Kulkarni, Jonathan Dworkin, Jordi Garcia-Ojalvo, Michael B. Elowitz, available here