Difference between revisions of "Team:Toulouse/Modeling"

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<title>iGEM Toulouse 2015</title>
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<link rel="icon" href="https://static.igem.org/mediawiki/2015/2/2e/TLSE_ApiColi.png" type="image/png" style="width:10%;"/>
  
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<h2> Modeling</h2>
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<h4>Note</h4>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
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<div class="wrapper row0 bgded" style="background-image:url('https://static.igem.org/mediawiki/2015/0/03/TLSE_bakcground.png')">
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      <div class="title">
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    <center> <h3>Attract</h3> </center>
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    </div>
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  <center><img src=" https://static.igem.org/mediawiki/2015/5/57/TLSE_Attract_BG.png"></center>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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  <div class="title">
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      <h3>Content</h3>
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    </div>
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<center>
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    <div id="breadcrumb" class="clear" style="float: center;" >
 +
  <ul>
 +
        <li><a href="#part1">Metabolic networks</a></li>
 +
        <li><a href="#part2">Butyrate attraction test</a></li>
 +
        <li><a href="#part3">How to produce butyrate with <i>E.Coli</i></a></li>
 +
      </ul>
 +
    </div>
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<hr style="width:66%;height:1px;border:none;color:rgba(29, 5, 79, 1);background-color:rgba(29, 5, 79, 1);">
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</center>
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<p>
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    <!-- FIRST PARAGRAPH -->
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Here are a few examples from previous teams:
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<center><div class="subtitle" >  
 +
<h3>About varroasis</h3>
 +
</div></center>
 +
 
 +
    <div class="group center"> <!-- FIRST PARAGRAPH -->
 +
        <p align="justify" style="font-size:15px;">
 +
 +
As it has been presented, the aim of our project is to create a biological system able to produce <b>two molecules</b> of interest :  
 +
<b>butyric acid</b> and <b>formic acid</b>.<br>
 +
 +
To construct our biological system, we have to introduce a new balance between all metabolic ways already in our chassis.
 +
Indeed, we want to <b>optimize</b> butyrate and formate production in our bacteria with the new pathways we created for ApiColi.
 +
 
 +
Below are represented all metabolic ways and metabolites known by scientists to date in Escherichia coli K12 MG1655
 +
(most known model). It was obtained from KEGG database[1].
 +
Over a first phase, we wanted to determine metabolic ways in which our molecules of insterest are taking part, in order to
 +
well immerse ourselves in their roles and effects.
 
</p>
 
</p>
 +
      </div>
 +
 
 +
 
 +
 
 +
  <div class="group center">
 +
<br>
 +
  <img src="https://static.igem.org/mediawiki/2015/0/04/TLSE_Attract_fig1.png" />
 +
</div>
 +
<div id="part1"></div><!-- ANCHOR 1 -->
 +
<div class="group center">
 +
<br>
 +
<p>Figure 1 : <i>Varroa destructor</i> life cycle,
 +
adapted from B. Alexander</p>
 +
</div>
 +
 
 +
<div>
 +
 
 +
<div class="subtitle" >  
 +
<h3>How to attract varroa</h3>
 +
</div>
 +
 +
 +
<div class="group center">
 +
<p align="justify" style="font-size:15px;">
 +
 +
Just before capping, bee larvaes produce a wide range of molecules,
 +
those molecules warn the mite about the upcoming capping and motivate
 +
it to enter the cell [2]. 
 +
Of all these molecule, scientific studies have shown that one can
 +
significantly attract varroa:
 +
<i>butyrate</i> [3].
 +
</p>
 +
</div>
 +
 +
 +
 +
<div class="group center">
 +
      <div class="one_half first">
 +
  <p align="justify" style="font-size:15px;">
 +
  <br>
 +
      Butyrate is a volatile acid which is non-toxic for honeybees
 +
  nor the human being, because it is already present at physiologic
 +
  concentrations in the digestive tract. Moreover this molecule
 +
  is naturally
 +
  produced by some bacterial strains like <i>Clostridium</i>,
 +
  which is an asset
 +
  for this synthetic biology project [4].</p><div id="part2"></div> <!-- ANCHOR 2 --><p align="justify" style="font-size:15px;"> Therefore we decided to
 +
  modify Apicoli
 +
  so it will synthesize
 +
  butyrate in order to attract varroa.
 +
</p>  
 +
      </div>
 +
 +
      <div class="one_half">
 +
     
 +
<img src="https://static.igem.org/mediawiki/2015/e/e6/TLSE_Attract_fig2.png">
 +
<p>Figure 2: Results of butyrate attraction
 +
test with quadrants method
 +
</p>
 +
 +
          </div>
 +
  </div>
 +
 +
<div class="subtitle" >  
 +
<h3>Butyrate attraction test</h3>
 +
</div>
 +
 +
 +
    <div class="group center"> <!-- FIRST PARAGRAPH -->
 +
     
 +
  <div class="one_half first">
 +
 
 +
<img src="https://static.igem.org/mediawiki/2015/b/b8/TLSE_Attract_fig3.png">
 +
<p>Figure 3: Butyrate attraction test using
 +
T tube, with varroa mite in the middle
 +
 +
</p>
 +
  </div>
 +
 
 +
  <div class="one_half">
 +
  <p align="justify" style="font-size:15px;">
 +
To check adequacy and relevance of this study (Figure 2),
 +
an experiment using a T-tube has been developed (Figure 3).
 +
In the first branch, there is a cotton soaked with 50 µL of water,
 +
in the second a cotton with  50 µL of butyrate at 4%, and finally the
 +
last one contains the varroa.</p> <div id="part3"> <!-- ANCHOR 3 --> </div> <p align="justify" style="font-size:15px;">The butyrate being very volatile, our
 +
system
 +
used a pump to renew air, producing a concentration gradient.
 +
</p>
 +
      </div>
 +
 
 +
</div>
 +
 +
<div class="subtitle" >  
 +
<h3>How to produce butyrate with <i>E.coli</i>?</h3>
 +
</div>
 +
 +
<div class="group center">
 +
     
 +
  <p align="justify" style="font-size:15px;">
 +
    In this project, an <i>Escherichia coli</i> strain is used for its known
 +
simplicity of genetic manipulation and its adequacy with butyrate
 +
synthesis. Indeed, among the five enzymes of the butyrate pathway,
 +
two enzymes are naturally produced by the bacteria. The following
 +
engineered butyrate pathway has been designed:
 +
</p>   <br>
 +
      </div>
 +
 +
 
 +
  <div class="group center"> <!-- CENTERED FIGURE -->
 +
  <img src="https://static.igem.org/mediawiki/2015/0/02/TLSE_Attract_fig4.png" />
 +
</div>
 +
  <div class="group center">
 +
<figcaption>Figure 4: Engineered butyrate pathway</figcaption>
 +
 
 +
</div>
 +
 
 +
<div class="group center">
 +
     
 +
  <p align="justify" style="font-size:15px;">
 +
  <br>
 +
    The initial substrate is glucose which is decomposed into
 +
acetyl-CoA during glycolysis. Finally, butyrate pathway
 +
begin with acetyl-CoA: five genes are required with two
 +
homologous and three heterologous genes.
 +
</p>  
 +
 +
</div>
 +
<br>
 +
 +
 +
<div style="font-size:15px;">
 +
<ul>
 +
  <li><b><i>atoB</i></b> present in <i>E.coli</i>, coding for acetyl-CoA
 +
  acetyltransferase, an acetyltransferase catalyzing the combination
 +
  of two acetyl-CoA.
 +
<br>
 +
<div class="group center">
 +
<br>
 +
  <img src="https://static.igem.org/mediawiki/2015/c/c5/TLSE_Attract_fig5.png" />
 +
</div>
 +
  <div class="group center">
 +
<br>
 +
<p class="legend">Figure 5: Reaction catalyzed by acetyl-CoA
 +
acetyltransferase </p>
 +
</div>
 +
 
 +
  </li>
 +
 
 +
  <li><b><i>hbd</i></b> present in <i>Clostridium acetobutylicum</i> coding for
 +
  3-hydroxybutyryl-CoA dehydrogenase, an oxidoreductase catalyzing
 +
  the formation of an alcohol function.
 +
  <br>
 +
    <div class="group center">
 +
<br>
 +
  <img src="https://static.igem.org/mediawiki/2015/d/d6/TLSE_Attract_fig6.png" />
 +
</div>
 +
  <div class="group center">
 +
<br>
 +
<p class="legend">Figure 6: Reaction catalyzed by
 +
3-hydroxybutyryl-CoA dehydrogenase
 +
</p>
 +
</div>
 +
  </li>
 +
 
 +
  <li><b><i>crt</i></b> present in <i>C.acetobutylicum</i>
 +
  coding for 3-hydroxybutyryl-CoA dehydratase,
 +
  a lyase cleaving carbon-oxygen bond.
 +
<br>
 +
  <div class="group center">
 +
<br>
 +
  <img src="https://static.igem.org/mediawiki/2015/6/67/TLSE_Attract_fig7.png" />
 +
</div>
 +
    <div class="group center">
 +
<br>
 +
<p class="legend">Figure 7:
 +
Reaction catalyzed by 3-hydroxybutyryl-CoA deshydratase
 +
 +
</p>
 +
</div>
 +
  </li>
 +
 
 +
  <li><b><i>ccr</i></b> present in
 +
  <i>Streptomyces collinus</i> coding
 +
  for crotonyl-CoA reductase,
 +
  an oxidoreductase acting on
 +
  CH=CH double bond. This enzyme
 +
  is also in <i>C.acetobutylicum</i> with
 +
  <b>bcd</b> gene coding for butyryl-CoA dehydrogenase,
 +
  with the disadvantage
 +
  to run with Electron Transfer
 +
  Flavoprotein (ETF) which complicates the reaction [6].
 +
<br>
 +
  <div class="group center">
 +
<br>
 +
  <img src="https://static.igem.org/mediawiki/2015/5/57/TLSE_Attract_fig8.png" />
 +
</div>
 +
  <br>
 +
  <div class="group center">
 +
<br>
 +
<p class="legend">Figure 8: Reaction
 +
catalyzed by crotonyl-CoA reductase
 +
</p>
 +
</div>
 +
 
 +
  </li>
 +
 
 +
    <li><b><i>tesB</i></b> present in <i>E.coli</i>
 +
coding for acyl-CoA transferase 2,
 +
a thiolase which enables coenzyme A transfer.
 +
  <br>
 +
  <div class="group center">
 +
<br>
 +
  <img src="https://static.igem.org/mediawiki/2015/3/34/TLSE_Attract_fig9.png" />
 +
</div>
 +
<div class="group center">
 +
<br>
 +
<p class="legend">Figure 9: Reaction
 +
catalyzed by acyl-CoA transferase 2
 +
</p>
 +
</div>
 +
 
 +
  </li>
 +
 
 +
</ul>
 +
 
 +
</div>
 +
 +
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<div class="wrapper row4">
 +
 +
<div class="container clear" style="padding-top:30px;">
 +
<center><p class="maintitle">  
 +
References
 +
</p></center>
 +
<br>
 +
<div class="clear">
 
<ul>
 
<ul>
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
<li><a href="http://www.kegg.jp/kegg-bin/highlight_pathway?scale=0.5&map=eco01100&keyword=">
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
+
[1] KEGG Metabolic pathways - Escherichia coli K-12 MG1655</a></li>
−
</ul>
+
  
 +
<li>
 +
[2] Le Conte Y, Arnold G, Trouiller J, Masson C, Chappe B, Ourisson G. 1989. Attraction of the parasitic mite varroa to the drone larvae of honey bees by simple aliphatic esters. Science 245:638–639.</li>
  
 +
<li>
 +
[3] Methods for attracting honey bee parasitic mites. [accessed 2015 Jul 24].
 +
</li>
 +
 +
<li>
 +
[4] Louis P, Flint HJ. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294:1–8.
 +
</li>
 +
[5] Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC. 2008. Metabolic engineering of Escherichia coli for 1-butanol production. Metabolic Engineering 10:305–311.
 +
<li>
 +
[6] Wallace KK, Bao Z-Y, Dai H, Digate R, Schuler G, Speedie MK, Reynolds KA. 1995. Purification of Crotonyl-CoA Reductase from Streptomyces collinus and Cloning, Sequencing and Expression of the Corresponding Gene in Escherichia coli. European Journal of Biochemistry 233:954–962.
 +
</li>
 +
</ul>
 
</div>
 
</div>
 +
<br>
 +
</div>
 +
</div>
 +
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<!-- #######################        FOOTER        ######################################################################### -->
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 +
</html>{{Toulouse/footer}}<html>
 +
 +
  
 +
</body>
 
</html>
 
</html>

Revision as of 14:44, 28 August 2015

iGEM Toulouse 2015

Attract


Content

About varroasis

As it has been presented, the aim of our project is to create a biological system able to produce two molecules of interest : butyric acid and formic acid.
To construct our biological system, we have to introduce a new balance between all metabolic ways already in our chassis. Indeed, we want to optimize butyrate and formate production in our bacteria with the new pathways we created for ApiColi. Below are represented all metabolic ways and metabolites known by scientists to date in Escherichia coli K12 MG1655 (most known model). It was obtained from KEGG database[1]. Over a first phase, we wanted to determine metabolic ways in which our molecules of insterest are taking part, in order to well immerse ourselves in their roles and effects.



Figure 1 : Varroa destructor life cycle, adapted from B. Alexander

How to attract varroa

Just before capping, bee larvaes produce a wide range of molecules, those molecules warn the mite about the upcoming capping and motivate it to enter the cell [2]. Of all these molecule, scientific studies have shown that one can significantly attract varroa: butyrate [3].


Butyrate is a volatile acid which is non-toxic for honeybees nor the human being, because it is already present at physiologic concentrations in the digestive tract. Moreover this molecule is naturally produced by some bacterial strains like Clostridium, which is an asset for this synthetic biology project [4].

Therefore we decided to modify Apicoli so it will synthesize butyrate in order to attract varroa.

Figure 2: Results of butyrate attraction test with quadrants method

Butyrate attraction test

Figure 3: Butyrate attraction test using T tube, with varroa mite in the middle

To check adequacy and relevance of this study (Figure 2), an experiment using a T-tube has been developed (Figure 3). In the first branch, there is a cotton soaked with 50 µL of water, in the second a cotton with 50 µL of butyrate at 4%, and finally the last one contains the varroa.

The butyrate being very volatile, our system used a pump to renew air, producing a concentration gradient.

How to produce butyrate with E.coli?

In this project, an Escherichia coli strain is used for its known simplicity of genetic manipulation and its adequacy with butyrate synthesis. Indeed, among the five enzymes of the butyrate pathway, two enzymes are naturally produced by the bacteria. The following engineered butyrate pathway has been designed:


Figure 4: Engineered butyrate pathway


The initial substrate is glucose which is decomposed into acetyl-CoA during glycolysis. Finally, butyrate pathway begin with acetyl-CoA: five genes are required with two homologous and three heterologous genes.


  • atoB present in E.coli, coding for acetyl-CoA acetyltransferase, an acetyltransferase catalyzing the combination of two acetyl-CoA.


    Figure 5: Reaction catalyzed by acetyl-CoA acetyltransferase

  • hbd present in Clostridium acetobutylicum coding for 3-hydroxybutyryl-CoA dehydrogenase, an oxidoreductase catalyzing the formation of an alcohol function.


    Figure 6: Reaction catalyzed by 3-hydroxybutyryl-CoA dehydrogenase

  • crt present in C.acetobutylicum coding for 3-hydroxybutyryl-CoA dehydratase, a lyase cleaving carbon-oxygen bond.


    Figure 7: Reaction catalyzed by 3-hydroxybutyryl-CoA deshydratase

  • ccr present in Streptomyces collinus coding for crotonyl-CoA reductase, an oxidoreductase acting on CH=CH double bond. This enzyme is also in C.acetobutylicum with bcd gene coding for butyryl-CoA dehydrogenase, with the disadvantage to run with Electron Transfer Flavoprotein (ETF) which complicates the reaction [6].



    Figure 8: Reaction catalyzed by crotonyl-CoA reductase

  • tesB present in E.coli coding for acyl-CoA transferase 2, a thiolase which enables coenzyme A transfer.


    Figure 9: Reaction catalyzed by acyl-CoA transferase 2

References


  • [1] KEGG Metabolic pathways - Escherichia coli K-12 MG1655
  • [2] Le Conte Y, Arnold G, Trouiller J, Masson C, Chappe B, Ourisson G. 1989. Attraction of the parasitic mite varroa to the drone larvae of honey bees by simple aliphatic esters. Science 245:638–639.
  • [3] Methods for attracting honey bee parasitic mites. [accessed 2015 Jul 24].
  • [4] Louis P, Flint HJ. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294:1–8.
    • [5] Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC. 2008. Metabolic engineering of Escherichia coli for 1-butanol production. Metabolic Engineering 10:305–311.
  • [6] Wallace KK, Bao Z-Y, Dai H, Digate R, Schuler G, Speedie MK, Reynolds KA. 1995. Purification of Crotonyl-CoA Reductase from Streptomyces collinus and Cloning, Sequencing and Expression of the Corresponding Gene in Escherichia coli. European Journal of Biochemistry 233:954–962.