Difference between revisions of "Team:Toulouse/Description/Attract"
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produced by some bacterial strains, | produced by some bacterial strains, | ||
which is an asset | which is an asset | ||
| − | for identifying key enzymatic activities for this synthetic biology project [3].</p><div id="part2"></div> <!-- ANCHOR 2 --><p align="justify" style="font-size:15px;"> Therefore, based on the patent US 8647615, we decided to | + | for identifying key enzymatic activities for this synthetic biology project [3].</p><div id="part2"></div> <!-- ANCHOR 2 --><p align="justify" style="font-size:15px;"> Therefore, based on the patent US 8647615 (Figure 1), we decided to |
modify <i>E. coli</i> | modify <i>E. coli</i> | ||
so it will synthesize | so it will synthesize | ||
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<div class="one_half"> | <div class="one_half"> | ||
<p align="justify" style="font-size:15px;"> | <p align="justify" style="font-size:15px;"> | ||
| − | To | + | To confirm this previous finding and make sure we can handle such experiment, a new protocol using a custom-made glass T-tube has been developed (Figure 2). |
| − | + | ||
In the first branch, there is a cotton soaked with 50 µL of water, | 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 | in the second a cotton with 50 µL of butyrate at 4%, and finally the | ||
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In this project, an <i>Escherichia coli</i> strain is used for its known | In this project, an <i>Escherichia coli</i> strain is used for its known | ||
simplicity of genetic manipulation and its adequacy with butyrate | simplicity of genetic manipulation and its adequacy with butyrate | ||
| − | synthesis. Indeed, among the five enzymes | + | synthesis [5]. Indeed, among the five enzymes we selected to produce butyrate from acetyl-CoA, |
two enzymes are naturally produced by the bacteria. The following | two enzymes are naturally produced by the bacteria. The following | ||
engineered butyrate pathway has been designed: | engineered butyrate pathway has been designed: | ||
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<br> | <br> | ||
The initial substrate is glucose which is decomposed into | The initial substrate is glucose which is decomposed into | ||
| − | acetyl-CoA during glycolysis. | + | acetyl-CoA during glycolysis. Butyrate pathway |
| − | + | begins with acetyl-CoA: five genes are required with two | |
homologous and three heterologous genes. | homologous and three heterologous genes. | ||
</p> | </p> | ||
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<div style="font-size:15px;"> | <div style="font-size:15px;"> | ||
<ul> | <ul> | ||
| − | <li><b><i>atoB</i></b> present in <i>E.coli</i>, coding for acetyl-CoA | + | <li><b><i>atoB</i></b> present in <i>E.coli</i> (Accession Number: <a href ="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11672"target="_blank">EG11672</a>), coding for acetyl-CoA |
acetyltransferase, an acetyltransferase catalyzing the combination | acetyltransferase, an acetyltransferase catalyzing the combination | ||
of two acetyl-CoA. | of two acetyl-CoA. | ||
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</li> | </li> | ||
| − | <li><b><i>hbd</i></b> present in <i>Clostridium acetobutylicum</i> coding for | + | <li><b><i>hbd</i></b> present in <i>Clostridium acetobutylicum</i> (Accession Number: <a href ="http://www.biocyc.org/CACE272562/NEW-IMAGE?type=GENE&object=GJIH-2684"target="_blank">GJIH-2684</a>) coding for |
3-hydroxybutyryl-CoA dehydrogenase, an oxidoreductase catalyzing | 3-hydroxybutyryl-CoA dehydrogenase, an oxidoreductase catalyzing | ||
the formation of an alcohol function. | the formation of an alcohol function. | ||
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</li> | </li> | ||
| − | <li><b><i>crt</i></b> present in <i>C.acetobutylicum</i> | + | <li><b><i>crt</i></b> present in <i>C.acetobutylicum</i> (Accession Number: <a href ="http://www.biocyc.org/CACE272562/NEW-IMAGE?type=GENE&object=GJIH-2688"target="_blank">GJIH-2688</a>) |
coding for 3-hydroxybutyryl-CoA dehydratase, | coding for 3-hydroxybutyryl-CoA dehydratase, | ||
a lyase cleaving carbon-oxygen bond. | a lyase cleaving carbon-oxygen bond. | ||
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<li><b><i>ccr</i></b> present in | <li><b><i>ccr</i></b> present in | ||
| − | <i>Streptomyces collinus</i> coding | + | <i>Streptomyces collinus</i> (Accession Number: <a href ="http://www.uniprot.org/uniprot/Q53865"target="_blank">Q53865-1</a>) coding |
for crotonyl-CoA reductase, | for crotonyl-CoA reductase, | ||
an oxidoreductase acting on | an oxidoreductase acting on | ||
| − | CH=CH double bond | + | CH=CH double bond and successfully used in <i>E. coli</i> [6]. |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
<br> | <br> | ||
<div class="group center"> | <div class="group center"> | ||
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</li> | </li> | ||
| − | <li><b><i>tesB</i></b> present in <i>E.coli</i> | + | <li><b><i>tesB</i></b> present in <i>E.coli</i> (Accession Number: <a href ="http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10995"target="_blank">EG10995</a>) |
coding for acyl-CoA transferase 2, | coding for acyl-CoA transferase 2, | ||
a thiolase which enables coenzyme A transfer. | a thiolase which enables coenzyme A transfer. | ||
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</div> | </div> | ||
<div class="group center"> | <div class="group center"> | ||
| − | <p align="justify" style="font-size:15px;">Concerning heterologous genes (hbd, crt and ccr), | + | <p align="justify" style="font-size:15px;">Concerning heterologous genes (<i>hbd</i>, <i>crt</i> and <i>ccr</i>), codon optimizations have been performed in order to enable a correct expression of these genes in <i>E. coli</i>. |
| − | The genetic construction is then done by assembling the five genes presented earlier, which are placed under the control of P(Bla) constitutive promoter (BBa_I14018). | + | The genetic construction is then done by assembling the five genes presented earlier, which are placed under the control of the P(Bla) constitutive promoter (BBa_I14018). Ribosome binding sites (RBS ; BBa_B0030) are added before the coding sequences to ensure protein expression. A strong terminator (BBa_B1006) is used to end this construction. The final biobrick was cloned into a pSB1C3 vector (<a href="https://static.igem.org/mediawiki/2015/9/9e/PSB1C3_ccr_butyrate.xdna.png"target="_blank">here</a>).</p> |
</div> | </div> | ||
| − | <center><img src="https://static.igem.org/mediawiki/2015/ | + | <center><img src="https://static.igem.org/mediawiki/2015/6/6f/TLSE_Parts_image4.PNG" style="width:65%;"/></center> |
Latest revision as of 01:46, 19 September 2015
Attract
Content
How to attract Varroa destructor?
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 [1]. Of all these molecules, scientific studies have shown that one can significantly attract varroa: butyrate [2].
Butyrate is a volatile acid which is non-toxic for honeybees
nor for the human being, because it is already present at physiologic
concentrations in their digestive tract. Moreover this molecule
is naturally
produced by some bacterial strains,
which is an asset
for identifying key enzymatic activities for this synthetic biology project [3].
Therefore, based on the patent US 8647615 (Figure 1), we decided to modify E. coli so it will synthesize butyrate in order to attract varroa [4].
Figure 1: Results of butyrate attraction test with quadrants method, US 8647615 B1 [4].
Butyrate attraction test
Figure 2: Butyrate attraction test using T tube, with varroa mite in the middle
To confirm this previous finding and make sure we can handle such experiment, a new protocol using a custom-made glass T-tube has been developed (Figure 2). 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.
Butyrate being very volatile, our system used a pump to renew air, producing a concentration gradient as seen here.
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 [5]. Indeed, among the five enzymes we selected to produce butyrate from acetyl-CoA, two enzymes are naturally produced by the bacteria. The following engineered butyrate pathway has been designed:
The initial substrate is glucose which is decomposed into
acetyl-CoA during glycolysis. Butyrate pathway
begins with acetyl-CoA: five genes are required with two
homologous and three heterologous genes.
- atoB present in E.coli (Accession Number: EG11672), coding for acetyl-CoA
acetyltransferase, an acetyltransferase catalyzing the combination
of two acetyl-CoA.
Figure 4: Reaction catalyzed by acetyl-CoA acetyltransferase
- hbd present in Clostridium acetobutylicum (Accession Number: GJIH-2684) coding for
3-hydroxybutyryl-CoA dehydrogenase, an oxidoreductase catalyzing
the formation of an alcohol function.
Figure 5: Reaction catalyzed by 3-hydroxybutyryl-CoA dehydrogenase
- crt present in C.acetobutylicum (Accession Number: GJIH-2688)
coding for 3-hydroxybutyryl-CoA dehydratase,
a lyase cleaving carbon-oxygen bond.
Figure 6: Reaction catalyzed by 3-hydroxybutyryl-CoA deshydratase
- ccr present in
Streptomyces collinus (Accession Number: Q53865-1) coding
for crotonyl-CoA reductase,
an oxidoreductase acting on
CH=CH double bond and successfully used in E. coli [6].
Figure 7: Reaction catalyzed by crotonyl-CoA reductase
- tesB present in E.coli (Accession Number: EG10995)
coding for acyl-CoA transferase 2,
a thiolase which enables coenzyme A transfer.
Figure 8: Reaction catalyzed by acyl-CoA transferase 2
Concerning heterologous genes (hbd, crt and ccr), codon optimizations have been performed in order to enable a correct expression of these genes in E. coli. The genetic construction is then done by assembling the five genes presented earlier, which are placed under the control of the P(Bla) constitutive promoter (BBa_I14018). Ribosome binding sites (RBS ; BBa_B0030) are added before the coding sequences to ensure protein expression. A strong terminator (BBa_B1006) is used to end this construction. The final biobrick was cloned into a pSB1C3 vector (here).
READ MORE
References
-
[1] 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
- [2] Peter EA Teal, Adrian J. Duehl, Mark J. Carroll. The United States Of America, As Represented By The Secretary Of Agriculture. 2014. Methods for attracting honey bee parasitic mites, US 8647615 B1.
- [3] 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
- [4] Peter EA Teal, Adrian J. Duehl, Mark J. Carroll. The United States Of America, As Represented By The Secretary Of Agriculture. 2014. Methods for attracting honey bee parasitic mites, US 8647615 B1. [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 ZY, 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. Eur. J. Biochem. 233: 954–962
