Team:KU Leuven/Project/Glucosemodel/EBF

From 2013.igem.org

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β-farnesene is a terpenoid that is converted from farnesyl pyrophosphate (FPP) by the enzyme β-farnesene synthase (EC 4.2.3.47). <br/>
β-farnesene is a terpenoid that is converted from farnesyl pyrophosphate (FPP) by the enzyme β-farnesene synthase (EC 4.2.3.47). <br/>
FPP is the precursor of β-farnesene, that is produced by the building blocks, the molecules isopentenyl pyrophosphate (IPP) and its isomer dimethylallylpyrophosphate (DMAPP).<br/>
FPP is the precursor of β-farnesene, that is produced by the building blocks, the molecules isopentenyl pyrophosphate (IPP) and its isomer dimethylallylpyrophosphate (DMAPP).<br/>
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These precursors of farnesyl pyrophosphate can be produced by several metabolic pathways. Eukaryotes, other than plants, exclusively use the mevalonate pathway, producing IPP starting from acetyl-CoA. Most prokaryotes however use the non-mevalonate or DXP pathway, producing IPP starting from glyceraldehyde-3-phosphate and pyruvate. Plants use both pathways.</p>
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These precursors of farnesyl pyrophosphate can be produced by several metabolic pathways. Most prokaryotes use the non-mevalonate or DXP pathway, producing IPP starting from glyceraldehyde-3-phosphate and pyruvate. Eukaryotes, except for plants, exclusively use the mevalonate pathway, producing IPP starting from acetyl-CoA. Plants use both pathways.</p>
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     <p align="justify">On the left you can see the non-mevalonate pathway or DXP pathway, showing the conversion of pyruvate and glyceraldehyde-3-phosphate to general terpenoid precursor IPP and its isomer DMAPP.<br/>
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     <p align="justify">On the left you can see the non-mevalonate pathway or DXP pathway, showing the conversion of pyruvate and glyceraldehyde-3-phosphate to the terpenoid precursor IPP and its isomer DMAPP.<br/>
Pyr = pyruvate, G3P = glyceraldehyde-3-phosphate, DXP = 1-deoxy-D-xylulose 5-phosphate, MEP = 2-C-methylerythritol 4-phosphate, CDP-ME = 4-phosphocytidyl-2-C-methylerythritol, CDP-MEP = 4-phosphocytidyl-2-C-methyl-D-erythritol 2-phosphate, MEcPP = 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate, HMB-PP = (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate, DXS = DXP synthase, DXR = DXP reductase, CMS = CDP-ME synthase, CMK = CDP-ME kinase, MCS = MEcPP synthase, HDS = HMB-PP synthase, HDR = HMB-PP reductase</p>
Pyr = pyruvate, G3P = glyceraldehyde-3-phosphate, DXP = 1-deoxy-D-xylulose 5-phosphate, MEP = 2-C-methylerythritol 4-phosphate, CDP-ME = 4-phosphocytidyl-2-C-methylerythritol, CDP-MEP = 4-phosphocytidyl-2-C-methyl-D-erythritol 2-phosphate, MEcPP = 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate, HMB-PP = (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate, DXS = DXP synthase, DXR = DXP reductase, CMS = CDP-ME synthase, CMK = CDP-ME kinase, MCS = MEcPP synthase, HDS = HMB-PP synthase, HDR = HMB-PP reductase</p>
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     <p align="justify">Since FPP is such an important precursor, used for the biosynthesis of lots and lots of compounds, it might turn out that once we insert a plasmid containing the β-farnesene synthase gene, we obtain only a very small amount of β-farnesene, since there isn’t enough FPP available for the required amount of β-farnesene we wish to produce.<br/>
+
     <p align="justify">Since FPP is such an important precursor, used for the biosynthesis of lots and lots of compounds, it might turn out that once we insert a plasmid containing the β-farnesene synthase gene, we obtain only a very small amount of β-farnesene, since the precursor amount wasn't increased and there simply isn’t enough FPP available to produce the amount of β-farnesene to satisfy the EBF synthase enzyme we brought in.<br/>
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A solution may be to implement plasmids which engineer a mevalonate pathway in E. coli, thereby upregulating the production of FPP. This larger amount of FPP may then be converted to β-farnesene, creating a large enough amount of this volatile for our uses. This was demonstrated many times by J.D. Keasling in S. cerervisiae, but Martin et al. (2003) implemented this mevalonate pathway in E. coli. In the article, they described their successful efforts to create a high level production of amorphadiene by introducing the mevalonate pathway in E. coli. They found that the expression of this heterologous pathway led to such an abundance of isoprenoid precursors that cells ceased to grow or mutated to overcome the toxicity. The authors state that because IPP and DMAPP are the universal precursors to all isoprenoids, the strains reported can serve as platform hosts for the production of any terpenoid compounds for which the biosynthetic genes are available. </p>
+
A solution may be to implement plasmids which engineer a mevalonate pathway in <i>E. coli</i>, thereby upregulating the production of FPP. This larger amount of FPP may then be converted to β-farnesene, creating a large enough amount of this volatile for our uses. This was demonstrated many times by J.D. Keasling in <i>S. cerervisiae</i>, while Martin et al. (2003) implemented this mevalonate pathway in <i>E. coli</i>. In the article, they described their successful efforts to create a high level production of amorphadiene by introducing the mevalonate pathway in <i>E. coli</i>. However, expression of this heterologous pathway led to such an abundance of isoprenoid precursors that cells ceased to grow or mutated to overcome the toxicity. </p>
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     <p align="justify">Since there are eight genes responsible for the mevalonate pathway, Martin <i>et al.</i> decided to split them up into two parts. A first plasmid named pMevT, responsible for the conversion of acetyl-CoA to mevalonate, harboring the atoB, HMGS and tHMGR genes into a pBAD33 vector, and a second one named pMBIS, harboring the ERG12, ERG8, MVD1, idi and ispA genes into a pBBR1MCS-3 plasmid. Coexpression of these two operons in an ispC deficient E. coli strain produced the terpenes, even in the absence of mevalonate, indicating that the mevalonate pathway works. A combined expression of their recombinant mevalonate pathway and the synthetic gene product (ADS in their case) resulted in greatly improved yields, although data suggested that a maximum yield was not attained, indicating the possibility to further optimize this mevalonate pathway (no further literature found).</p>
+
     <p align="justify">Since there are eight genes responsible for the mevalonate pathway, Martin <i>et al.</i> decided to split them up into two parts. A first plasmid named pMevT, responsible for the conversion of acetyl-CoA to mevalonate, harboring the <i>atoB</i>, <i>HMGS</i> and <i>tHMGR</i> genes into a pBAD33 vector, and a second one named pMBIS, harboring the <i>ERG12</i>, <i>ERG8</i>, <i>MVD1</i>, <i>idi</i> and <i>ispA</i> genes into a pBBR1MCS-3 plasmid. Coexpression of these two operons in an <i>ispC</i> deficient <i>E. coli</i> strain produced the terpenes, even in the absence of mevalonate, indicating that the mevalonate pathway works. A combined expression of their recombinant mevalonate pathway and the synthetic gene product (ADS in their case) resulted in greatly improved yields.</p>
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     <p align="justify">It might be an option for other teams in the future to ask J.D. Keasling for the plasmids pMevT and pMBIS and implement them into our BanAphids along with the synthetic β-farnesene synthase gene, by which coexpression would result into high yields of β-farnesene.</p>
+
     <p align="justify">It might be an option for other teams in the future to ask J.D. Keasling for the plasmids pMevT and pMBIS and implement them into our BanAphids along with the synthetic β-farnesene synthase gene, by which coexpression could result into high yields of β-farnesene.</p>
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   We cloned and expressed the EBF synthase gene in <I>E. coli</i>, to break up (2E,6E)-farnesyl diphosphate into (E)-β-farnesene (EBF) and diphosphate (see reaction scheme below).<br/>
+
   We cloned and expressed the EBF synthase gene in <i>E. coli</i>, to break up (2E,6E)-farnesyl diphosphate into (E)-β-farnesene (EBF) and diphosphate (see reaction scheme below).<br/>
The enzyme prefers bivalent cations as cofactors; eg a Mg<sup>2+</sup> concentration of 5 mM should be beneficial for EBF function. The ideal pH for EBF synthase will be between 5.5-7.</p>
The enzyme prefers bivalent cations as cofactors; eg a Mg<sup>2+</sup> concentration of 5 mM should be beneficial for EBF function. The ideal pH for EBF synthase will be between 5.5-7.</p>
<center><img src="https://static.igem.org/mediawiki/2013/5/5e/Reaction.jpg" alt="reaction"/></center>
<center><img src="https://static.igem.org/mediawiki/2013/5/5e/Reaction.jpg" alt="reaction"/></center>
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The EBF construct we designed consists of constitutive promoter with a <i>lac</i> operator, the EBF synthase itself and a double terminator. EBF is not only made by aphids but also by plants and other organisms in a form of bio-mimicry. We obtained two different sources of the EBF gene. One gene originates from the soil bacterium <i>Streptomyces coelicolor</i> (Centre of Microbial and Plant Genetics of KU Leuven). we chose this because it would be a perfect chassis for the ultimate expression of EBF in a bacterial setting. The other EBF gene is from the plant <i>Artemisia annua</i> (sweet wormwood) and was a kind gift from Professor Peter Brodelius (Kalmar University, Sweden). Here we were inspired with the plant origin. The K<sub>M</sub> for the <i>Artemisia annua</i> protein 0.0021 mM, with a Kcat/K<sub>M</sub>=4.5 and a turnover number of 0.0095 s<sup>-1</sup>. For the <i>Streptomyces coelicolor</i> protein the K<sub>M</sub> is 0.0168 mM and the turnover number 0.019 s<sup>-1</sup>. <br/>
+
The EBF construct we designed consists of constitutive promoter with a <i>lac</i> operator, the EBF synthase itself and a double terminator. EBF is not only made by aphids but also by plants and other organisms in a form of bio-mimicry. We obtained two different sources of the EBF gene. One gene originates from the soil bacterium <i>Streptomyces coelicolor</i> (Centre of Microbial and Plant Genetics of KU Leuven). We chose this plant-residing bacterium because it would be a perfect chassis for the ultimate expression of EBF in our <i>E.coligy</i> system. The other EBF gene is from the plant <i>Artemisia annua</i> (sweet wormwood) and was a kind gift from Professor Peter Brodelius (Kalmar University, Sweden). Here we were inspired with the plant origin. The K<sub>M</sub> for the <i>Artemisia annua</i> protein is calculated at 0.0021 mM, with a Kcat/K<sub>M</sub>=4.5 and a turnover number of 0.0095 s<sup>-1</sup>. For the <i>Streptomyces coelicolor</i> protein the K<sub>M</sub> is 0.0168 mM and the turnover number 0.019 s<sup>-1</sup>. <br/>
Unfortunately, the EBF synthase from <i>Streptomyces coelicolor</i> is a bifunctional enzyme, not only processing β-farnesene but also containing albaflavenone synthase activity. For this reason, we chose to follow up on the  <i>Artemisia annua</i> gene and product.  
Unfortunately, the EBF synthase from <i>Streptomyces coelicolor</i> is a bifunctional enzyme, not only processing β-farnesene but also containing albaflavenone synthase activity. For this reason, we chose to follow up on the  <i>Artemisia annua</i> gene and product.  
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For our construct, our first choice was a medium strength promoter with medium RBS (BBa_K608006); we nonetheless also made the construct with a strong promoter and RBS. we used BBa_B0015 for the double terminator. The <i>lac</i> operator in front of the EBF synthase gene will play a role in switching on/off the transcription of EBF synthase gene.</p>
+
For our construct, our first choice was a medium strength promoter with medium RBS (BBa_K608006); we nonetheless also made the construct with a strong promoter and RBS. We used BBa_B0015 for the double terminator. The <i>lac</i> operator in front of the EBF synthase gene will allow us to switch on/off the transcription of EBF synthase gene.</p>
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   <h3>Gettin' the gene</h3>
   <h3>Gettin' the gene</h3>
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To get the two sources of the target gene, we exploited different methods. In the case of EBF synthase gene from <i>Streptomyces coelicolor</i>, we got this gene with the help of colony PCR. In the story of EBF synthase gene from <i>Artemisia annua</i>, we received the gene in the pET28 vector from the research group in university of Kalmar. In this gene an additional <i>EcoRI</i> restriction site is present, which will conflict with the standard iGEM cloning work. Therefore we performed site specific mutation to get rid of this restriction site after transferring the gene into pSB1C3 backbone.  
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In the case of EBF synthase gene from <i>Streptomyces coelicolor</i>, we amplified this gene with the a colony PCR. The EBF synthase gene from <i>Artemisia annua</i> was received in the pET28 vector from professor Brodelius (Kalmar University, Sweden). In this gene an additional <i>EcoRI</i> restriction site is present, which will conflict with the standard iGEM cloning work. Therefore we removed this site via site directed mutagenesis after transferring the gene into the iGEM pSB1C3 backbone.  
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   <h3>Cutting and pasting</h3>
   <h3>Cutting and pasting</h3>
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After obtaining the target gene in the standard pSB1C3 backbone, we started our cloning work. The general concept we adapted is cutting the vector of promoter or terminator open, in which case the promoter or terminator is at the end of the linearised vector followed by ligating the insert into this vector. The reason why we undertake this strategy is because the size of promoter and terminator is so small, the possibility of false positives will be high if we use the 3A assembly method. In the situation of ligating the insert in front of the double terminator, we cut the vector of double terminator with <i>EcoRI</i> and <i>XbaI</i> restriction sites, cut the insert with <i>EcoRI</i> and <i>SpeI</i> restriction site. On the other hand, the promoter vector is cut with <i>SpeI</i> and <i>PstI</i> restriction sites, and the insert is cut with <i>XbaI</i> and <i>PstI</i> restriction sites. <br/>
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Once we obtained the target gene (EBF) in the standard pSB1C3 backbone, we started our cloning work. We used a pSB1C3 with promoter or terminator as chassis, cut this open and inserted the gene / ... . the 3A assembly method was too difficult mostlikely because the size of promoter and terminator are so different compared to the gene insert. When ligating the insert in front of the double terminator, we cut the vector with <i>EcoRI</i> and <i>XbaI</i>, and the insert with <i>EcoRI</i> and <i>SpeI</i>. The promotor vector on the other hand is cut with <i>SpeI</i> and <i>PstI</i> restriction sites, and the insert is cut with <i>XbaI</i> and <i>PstI</i> restriction sites. This works because <i>SpeI</i> and <i>XbaI</i> are isoschizomers.<br/>
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The ligations were performed in two ways in parallel. In one setup we ligated for 20 minutes at 16 ℃, and in comparison, the second ligation of the same products is conducted at 16 ℃ overnight.<br/>
+
Ligations were performed in parallel in two different ways. In one setup we ligated for 20 minutes at 16 ℃, and in comparison, the second ligation of the same products was conducted at 16 ℃ overnight.<br/>
For transformation, we used both chemically competent cells and electrocompetent cells. Electroporation had a higher efficiency when compared to heat shock transformation. </p>
For transformation, we used both chemically competent cells and electrocompetent cells. Electroporation had a higher efficiency when compared to heat shock transformation. </p>
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   <h3>Confirmation</h3>
   <h3>Confirmation</h3>
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As soon as we observed colonies after transformation, we needed to confirm the products. The first step we did was usually a colony PCR to check if the insert is in the vector; however the colony PCR did not work every time. If it works, we will select the good ones to inoculate, otherwise randomly select some colonies to do the inoculation. The plasmid extraction was done on the overnight inoculated culture, and then we could confirm the size by digestion the plasmid. Only if the sample preceded these two confirmations, we will send the good ones to sequence, which will be the final confirmation.
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After we observed observed colonies the next day, we needed to confirm the products. The first step we did was usually a colony PCR to check if the insert Only plasmids which succeeded in both controls were send for sequencing, the final confirmation.
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   <h3>gBlocks</h3>
   <h3>gBlocks</h3>
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Meanwhile, we also built the construct with <i>lac</i> operator in between the promoter and gene with gBlocks. We designed the gBlocks and assembled them together, followed by ligating the insert into pSB1C3 backbone. The positive colonies also needed to go through three confirmation steps mentioned above before we conclude we made them.  
+
Meanwhile, we also built the EBF construct with a <i>lac</i> operator between the promoter and gene, using the gBlock principle. We designed the gBlocks, assembled them and ligated the insert into pSB1C3 backbone. The colonies obtained also went through the three confirmation steps mentioned above before we were satisfied.  
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Of course we met a lot of difficulties during the cloning work, but we kept trying different ways to overcome the obstacles, and finally we made the following bricks.<ol>
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At the end of a trying summer, we finally made the following bricks.<ol>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060001">BBa_K1060001</a> This is a coding biobrick with the insert length of 1386bp, it is EBF synthase gene from Streptomyces coelicolor in pSB1C3 backbone.</li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060001">BBa_K1060001</a> This is a coding biobrick with the EBF synthase gene from Streptomyces coelicolor in pSB1C3 backbone and an insert length of 1386bp.</li>
 +
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060002">BBa_K1060002</a> This is another coding biobrick with EBF synthase gene from Artemisia annua in pSB1C3 backbone and an insert length of 1725bp.</li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060002">BBa_K1060002</a> This is another coding biobrick with the insert length of 1725bp, it is EBF synthase gene from Artemisia annua in pSB1C3 backbone.</li>
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K106000">BBa_K1060008</a> This is an intermediate biobrick with EBF of Artemisia annua in front of a double terminator. </li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K106000">BBa_K1060008</a> This is an intermediate biobrick with EBF of Artemisia annua in front of double terminator. </li>
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060009">BBa_K1060009</a> This is a generator biobrick with a medium constitutive expression of EBF synthase from Artemisia annua in the pSB1C3 backbonethe and an insert length of 1924bp.</li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060009">BBa_K1060009</a> This is a generator biobrick with the insert length of 1924bp, it is medium constitutive expression of EBF synthase from Artemisia annua, in the pSB1C3 backbone.</li>
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060014">BBa_K1060014</a> This is another generator biobrick with a strong constitutive expression of EBF synthase from <i>Artemisia annua</i> in the pSB1C3 backbone and an insert length of 1923bp.</li>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060014">BBa_K1060014</a> This is another generator biobrick with the insert length of 1923bp, it is strong constitutive expression of EBF synthase from <i>Artemisia annua</i>, in the pSB1C3 backbone.</li>
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060011">BBa_K1060011</a> This is a generator biobrick with a medium constitutive expression of EBF synthase from <i>Artemisia annua</i> AND a lac operator after the promoter and an insert length of 1965bp.</li></ol></p>
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+
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1060011">BBa_K1060011</a> This is a generator biobrick with the insert length of 1965bp, it is medium constitutive expression of EBF synthase from <i>Artemisia annua</i> with lac operator after the promoter.</li></ol></p>
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Revision as of 06:20, 4 October 2013

iGem

Secret garden

Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!


  • A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
  • For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
  • We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?

Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!

tree ladybugcartoon

In this part, we will give some more information about the E-β-farnesene (aka EBF) part of the project. EBF is an alarm pheromone, released by almost all of the 4000 aphid species known thus far in response to the presence of predators (eg the ladybug) or other disturbances. In response to the produced EBF, aphids change their metabolism and turn into a winged form, allowing them to "flee the scene" and thus increase their survival rate. Apart from the short term repelling effect, EBF can also cause long term effects : changes in aphid’s development, fecundity, survival when introduced to different growth stages, etc. Moreover, natural aphid predators such as the ladybugs are attracted by EBF.
Hence, having our BanAphids produce EBF should help to repel aphids from our plant of choice. In the following sections, we will take you on a tour through the pathways that result in EBF, a general background of EBF synthase, the model and the genes, the wetlab work, and the biobricks we built for the EBF part.

β-farnesene is a terpenoid that is converted from farnesyl pyrophosphate (FPP) by the enzyme β-farnesene synthase (EC 4.2.3.47).
FPP is the precursor of β-farnesene, that is produced by the building blocks, the molecules isopentenyl pyrophosphate (IPP) and its isomer dimethylallylpyrophosphate (DMAPP).
These precursors of farnesyl pyrophosphate can be produced by several metabolic pathways. Most prokaryotes use the non-mevalonate or DXP pathway, producing IPP starting from glyceraldehyde-3-phosphate and pyruvate. Eukaryotes, except for plants, exclusively use the mevalonate pathway, producing IPP starting from acetyl-CoA. Plants use both pathways.

Mevalonate Pathway

Mevalonate pathway, showing the conversion of acetyl-CoA to general terpenoid precursor IPP and its isomer DMAPP.

Non-Mevalonate Pathway

On the left you can see the non-mevalonate pathway or DXP pathway, showing the conversion of pyruvate and glyceraldehyde-3-phosphate to the terpenoid precursor IPP and its isomer DMAPP.
Pyr = pyruvate, G3P = glyceraldehyde-3-phosphate, DXP = 1-deoxy-D-xylulose 5-phosphate, MEP = 2-C-methylerythritol 4-phosphate, CDP-ME = 4-phosphocytidyl-2-C-methylerythritol, CDP-MEP = 4-phosphocytidyl-2-C-methyl-D-erythritol 2-phosphate, MEcPP = 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate, HMB-PP = (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate, DXS = DXP synthase, DXR = DXP reductase, CMS = CDP-ME synthase, CMK = CDP-ME kinase, MCS = MEcPP synthase, HDS = HMB-PP synthase, HDR = HMB-PP reductase

Since FPP is such an important precursor, used for the biosynthesis of lots and lots of compounds, it might turn out that once we insert a plasmid containing the β-farnesene synthase gene, we obtain only a very small amount of β-farnesene, since the precursor amount wasn't increased and there simply isn’t enough FPP available to produce the amount of β-farnesene to satisfy the EBF synthase enzyme we brought in.
A solution may be to implement plasmids which engineer a mevalonate pathway in E. coli, thereby upregulating the production of FPP. This larger amount of FPP may then be converted to β-farnesene, creating a large enough amount of this volatile for our uses. This was demonstrated many times by J.D. Keasling in S. cerervisiae, while Martin et al. (2003) implemented this mevalonate pathway in E. coli. In the article, they described their successful efforts to create a high level production of amorphadiene by introducing the mevalonate pathway in E. coli. However, expression of this heterologous pathway led to such an abundance of isoprenoid precursors that cells ceased to grow or mutated to overcome the toxicity.

#

Since there are eight genes responsible for the mevalonate pathway, Martin et al. decided to split them up into two parts. A first plasmid named pMevT, responsible for the conversion of acetyl-CoA to mevalonate, harboring the atoB, HMGS and tHMGR genes into a pBAD33 vector, and a second one named pMBIS, harboring the ERG12, ERG8, MVD1, idi and ispA genes into a pBBR1MCS-3 plasmid. Coexpression of these two operons in an ispC deficient E. coli strain produced the terpenes, even in the absence of mevalonate, indicating that the mevalonate pathway works. A combined expression of their recombinant mevalonate pathway and the synthetic gene product (ADS in their case) resulted in greatly improved yields.

It might be an option for other teams in the future to ask J.D. Keasling for the plasmids pMevT and pMBIS and implement them into our BanAphids along with the synthetic β-farnesene synthase gene, by which coexpression could result into high yields of β-farnesene.

We cloned and expressed the EBF synthase gene in E. coli, to break up (2E,6E)-farnesyl diphosphate into (E)-β-farnesene (EBF) and diphosphate (see reaction scheme below).
The enzyme prefers bivalent cations as cofactors; eg a Mg2+ concentration of 5 mM should be beneficial for EBF function. The ideal pH for EBF synthase will be between 5.5-7.

reaction

The EBF construct we designed consists of constitutive promoter with a lac operator, the EBF synthase itself and a double terminator. EBF is not only made by aphids but also by plants and other organisms in a form of bio-mimicry. We obtained two different sources of the EBF gene. One gene originates from the soil bacterium Streptomyces coelicolor (Centre of Microbial and Plant Genetics of KU Leuven). We chose this plant-residing bacterium because it would be a perfect chassis for the ultimate expression of EBF in our E.coligy system. The other EBF gene is from the plant Artemisia annua (sweet wormwood) and was a kind gift from Professor Peter Brodelius (Kalmar University, Sweden). Here we were inspired with the plant origin. The KM for the Artemisia annua protein is calculated at 0.0021 mM, with a Kcat/KM=4.5 and a turnover number of 0.0095 s-1. For the Streptomyces coelicolor protein the KM is 0.0168 mM and the turnover number 0.019 s-1.
Unfortunately, the EBF synthase from Streptomyces coelicolor is a bifunctional enzyme, not only processing β-farnesene but also containing albaflavenone synthase activity. For this reason, we chose to follow up on the Artemisia annua gene and product. For our construct, our first choice was a medium strength promoter with medium RBS (BBa_K608006); we nonetheless also made the construct with a strong promoter and RBS. We used BBa_B0015 for the double terminator. The lac operator in front of the EBF synthase gene will allow us to switch on/off the transcription of EBF synthase gene.

Gettin' the gene

In the case of EBF synthase gene from Streptomyces coelicolor, we amplified this gene with the a colony PCR. The EBF synthase gene from Artemisia annua was received in the pET28 vector from professor Brodelius (Kalmar University, Sweden). In this gene an additional EcoRI restriction site is present, which will conflict with the standard iGEM cloning work. Therefore we removed this site via site directed mutagenesis after transferring the gene into the iGEM pSB1C3 backbone.

Cutting and pasting

Once we obtained the target gene (EBF) in the standard pSB1C3 backbone, we started our cloning work. We used a pSB1C3 with promoter or terminator as chassis, cut this open and inserted the gene / ... . the 3A assembly method was too difficult mostlikely because the size of promoter and terminator are so different compared to the gene insert. When ligating the insert in front of the double terminator, we cut the vector with EcoRI and XbaI, and the insert with EcoRI and SpeI. The promotor vector on the other hand is cut with SpeI and PstI restriction sites, and the insert is cut with XbaI and PstI restriction sites. This works because SpeI and XbaI are isoschizomers.
Ligations were performed in parallel in two different ways. In one setup we ligated for 20 minutes at 16 ℃, and in comparison, the second ligation of the same products was conducted at 16 ℃ overnight.
For transformation, we used both chemically competent cells and electrocompetent cells. Electroporation had a higher efficiency when compared to heat shock transformation.

Confirmation

After we observed observed colonies the next day, we needed to confirm the products. The first step we did was usually a colony PCR to check if the insert Only plasmids which succeeded in both controls were send for sequencing, the final confirmation.

gBlocks

Meanwhile, we also built the EBF construct with a lac operator between the promoter and gene, using the gBlock principle. We designed the gBlocks, assembled them and ligated the insert into pSB1C3 backbone. The colonies obtained also went through the three confirmation steps mentioned above before we were satisfied.

For more details of the labwork and the wetlab difficulties as well as how we overcame them, please consult the page of our wetlab journal.

At the end of a trying summer, we finally made the following bricks.

  1. BBa_K1060001 This is a coding biobrick with the EBF synthase gene from Streptomyces coelicolor in pSB1C3 backbone and an insert length of 1386bp.
  2. BBa_K1060002 This is another coding biobrick with EBF synthase gene from Artemisia annua in pSB1C3 backbone and an insert length of 1725bp.
  3. BBa_K1060008 This is an intermediate biobrick with EBF of Artemisia annua in front of a double terminator.
  4. BBa_K1060009 This is a generator biobrick with a medium constitutive expression of EBF synthase from Artemisia annua in the pSB1C3 backbonethe and an insert length of 1924bp.
  5. BBa_K1060014 This is another generator biobrick with a strong constitutive expression of EBF synthase from Artemisia annua in the pSB1C3 backbone and an insert length of 1923bp.
  6. BBa_K1060011 This is a generator biobrick with a medium constitutive expression of EBF synthase from Artemisia annua AND a lac operator after the promoter and an insert length of 1965bp.