Difference between revisions of "Team:Bordeaux/Template:OverviewOurSolution"

 
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             <h3> Our Solution </h3>
 
             <h3> Our Solution </h3>
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            <h5> What is Curdlan? </h5>
  
<h5> What is Curdlan? </h5>
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            <p align="justify" style="text-indent: 3vw;"> To start with, let's talk about glucans. Glucan molecules are polysaccharides of D-glucose monomers linked by glycosidic bonds. One of them is called Curdlan, a (1→3)-β-D-glucan. This molecule is a linear homopolymer which may have as many as 12,000 glucose units. It is naturally produced by <i> Agrobacterium sp.</i> ATCC31749 which uses it like an Extracellular PolySaccharides (EPS) in it's capsule. The capsule formation is correlated with cell aggregation (floc formation) and it is suggested that the capsule and floc formation together function as protective structures in cases of Nitrogen-starvation of the post-stationary phase. The protective effects are due to the fact that Curdlan forms a capsule that completely surrounds the outer cell surface of bacteria. </p>
  
<p align="justify"> This year, the team is working on an environmental project, trying to remedy problems associated with the use of copper sulfate by bringing new solutions thanks to synthetic biology. To do that, all the work will be done using non-pathogenic micro-organisms which can easily be grown in our lab: Escherichia coli and Saccharomyces cerevisiae. Therefore our research tries to uncover ways to increase the production of this natural product that may decrease the cost in its industrial production for example. <p>
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        <p align="justify"> <i> <FONT color="#8b008b"> <b> « Ok and how will Curdlan be useful to you? » </b> </FONT> </i> </p>
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        <br>
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        <p align="justify"> <i> <b> <FONT color="#00843c"> « Let me explain our purpose. » </b> </FONT> </i> </p>
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<p align="justify"> Our project this year is to produce curdlan, a beta 1,3 glucan. Some (1→3)-β-D-glucans are encountered in some important soil-dwelling, plant-associated or human pathogenic bacteria. (CURDLAN + BACTERIA + IMMUNE S) One of the (1→3)-β-D-glucans is call Curdlan, it is produced as a capsule on Agrobacterium sp. ATTC 31749. the capsule formation is correlated with cell aggregation (floc formation). Capsule formation occurs when the N source in minimal medium is depleted, suggesting that the capsule and floc formation together function as protective structures in nutritional stress. Curdlan is typical of a secondary metabolite in that its biosynthesis occurs in the post-stationary growth phase during conditions of N-starvation. The optimisation of curdlan yield thus depends on the formation of a cell mass in the pre-stationary phase and on the biosynthetic capability of cells in the post-stationary phase. and is used as an Extracellular PolySaccharides (EPS). </p>
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<p align="justify"> Curdlan is a linear homopolymer of the monosaccharide D-glucose molecules and may have as many as 12,000 glucose units. It is a neutral polymer produced by Alcaligenes faecalis var. myxogenes 10C3 strain. Subsequent research on curdlan production focused on selection of bacterial strains and optimization of the culture media. But we would like to produce Curdlan in another bacteria, E.coli, because we are SWAG (Secretly we adore Glucan) <3 </p>
 
  
<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Curdlan_colored.svg/512px-Curdlan_colored.svg.png">
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<p align="justify"> Curdlan belongs to the class of biological response modifiers that enhance or restore normal immune defenses including antitumor, anti-infective, anti-inflammatory, and anticoagulant activities. As a matter of fact, this β1,3 glucan can stimulate the plant's immune system. </p>
 +
 
 +
<p align="justify"> More precisely, applied to grapevine plants, <b> sulfated Curdlan </b> induces the <b> accumulation of phytoalexins </b> (organic antimicrobial substances) and the <b> expression of a set of Pathogenesis-Related proteins </b>. </p>
 +
<p align="justify"> However, non-sulfated Curdlan doesn't trigger the hypersensitive response characterized by the rapid death of cells in the local region surrounding an infection, avoiding a complete contamination of the plant. This response has been studied in Arabidopsis thaliana through a <b> mutant gene: pmr4 </b>. This mutant is resistant to mildew infections but is <b> unable to induce Pathogenesis-Related proteins expression </b>. </p>
 +
<p align="justify"> Also, activation of a Pathogenesis-Related protein called PR1 in grapevine is regulated by the <b> salicylic acid signaling pathway </b> .
 +
The lack of PR1 expression in non-sulfated Curdlan-treated grapevine could be explained by a negative feedback of glucan. This is demonstrated by the study of a double mutant of pmr4 which restore the susceptibility to mildew. It suggests that linear β-1,3 glucan negatively regulates the salicylic acid pathway.
 +
So, sulfation of the glucan would counteract the negative feedback effect. </p>
 +
<p align="justify"> To conclude, activation of the innate immune system before the invasion of pathogens is a way to improve the resistance of plant against infection and to reduce the use of chemicals products.  </p>
  
<p align="justify"> Before starting the project, we took a few weeks to decide which host organism we would use and how they coule be useful. To begin with we looked at three different organisms: Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae. We rapidly eliminated bacillus subtilis from our possible hosts due to it's lack of enzymes involved in the metabolic pathway of beta 1,3 glucans. However, we found that yeast naturally produces curdlan and that E. coli is only missing one enzyme to synthethize curdlan. We therefore concluded that we could keep these two organisms: one where we would overexpress the beta 1,3 glucan prodution using a constititive promoter and one where we would insert the ability to create curdlan by adding the enzyme that is needed. </p>
 
 
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<h6> ENZYMES + METABOLIC PATHWAY </h6>
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<p align="justify"> <i> <FONT color="#8b008b"> <b> « Ok i understand the value of producing Curdlan. How will you proceed? » </b> </FONT> </i> </p>
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<p align="justify"> <i> <FONT color="#00843c"> <b> « This is a good question i'll answer. » </b> </FONT> </i> </p>
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<p align="justify"> Before starting the project, we took a few weeks to decide which host organism we would use and how they could be useful. To begin with we looked at three different organisms: <i> Escherichia coli </i>, <i> Bacillus subtilis </i> and <i> Saccharomyces cerevisiae </i> and compared their glucan metabolic pathways. We rapidly eliminated <i> Bacillus subtilis </i> from our possible hosts due to it's lack of enzymes involved in the metabolic pathway of beta 1,3 glucans. However, we found that yeast naturally produces Curdlan in it's cell wall, like <i>Agrobacterium</i> . Furthermore, <i> Escherichia coli </i> is only missing one enzyme to synthethize Curdlan. We therefore concluded that we could keep these two organisms: one where we would overexpress the beta 1,3 glucan prodution using a constititive promoter and one where we would insert the ability to create curdlan by adding the enzyme that is needed. </p>
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<p align="justify"> In <i> Agrobacterium </i>, three genes (crdA, crdS and crdC) are required for Curdlan production.
 +
The putative operon crdASC contains crdS, encoding β-(1,3)-glucan synthase catalytic subunit, flanked by two additional genes : crdA and crdC. The first assists translocation of the nascent polymer across  the cytoplasmic membrane and the second assists the passage of the nascent polymer across the periplasm. However, all Curdlan biosynthesis is dependent of nitrogen starvation and various parameters. We want to simplify all of this. </p>
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<h5> Using Bacteria: E. coli </h5>
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<h5> Using Bacteria: <i> Escherichia coli </i> </h5>
 
   
 
   
<p align="justify"> In bacteria, three genes are totally required for curdlan production. These have been identified in Agrobacterium sp. ATCC31749, which produces curdlan in large amounts. This putative operon contains crdS, encoding β-(1,3)-glucan synthase catalytic subunit, flanked by two additional genes : crdA and crdC. The first assists translocation of nascent polymer across cytoplasmic membrane and the second assists passage of nascent polymer across the periplasm. The protective effects are due to the fact that Curdlan forms a capsule that completely surrounds the outer cell surface of bacteria. </p>
+
<p align="justify"> Firstly, we decided to produce curdlan with <i> Escherichia coli </i>, because <i> Agrobacterium </i> and it are Gram negative bacteria and have a lot of membrane similarity.  
 +
Moreover <i> Escherichia coli </i> is a little pretty good bacteria, it can be grown and cultured easily and inexpensively in a laboratory setting unlike <i> Agrobacterium </i>. </p>
  
<img src="https://static.igem.org/mediawiki/2015/2/2c/IGEM_bordeaux_gel2.jpg" >
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<p align="justify"> Secondly, we are going to put these three genes into <i> Escherichia coli </i> under an easier control as N-starvation. </p>
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<p align="justify"> Now, we are going to put these three genes into Escherichia coli through the intermediary of plasmids and then do a bacteria culture for curdlan production during its stationary phase. Then we will collect only curdlan by a purification method. Finally, curdlan will be sulfated to be in its active form. This sulfation will be made chemically. </p>
+
  
<p align="justify"> <b> What is curdlan? How is it naturally synthethised? Why is it useful for bacteria? How are we going to produce it? Can we really call it eco-friendly? What organisms are we going to use? Why? What are the advantages and disadvantages of both organisms? How did we choose the genes? Promoters? How are we going to make the biobrick? What is our biobrick? </b> </p>
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<p align="justify"> Thirdly, when we produce curdlan with <i> Escherichia coli </i>, we will sulfate Curdlan by chemical method. In fact sulfated Curdlan, it is the better form of Curdlan to activate immune plant system. </p>
  
 +
<p align="justify"> To sum up, we would like to produce Curdlan in <i> Escherichia coli </i> and then sulfate it to use it as a preventive treatment for the vine against the mildew infection and continue to produce good wine and make everyone happy. </p>
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<img style= "width:38vw; height:22vw;" src="https://static.igem.org/mediawiki/2015/1/18/Bordeaux_cell_fluo.jpg";>
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<h5> Using Yeast: S. cerevisiae </h5>
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<h5> Using Yeast: <i> Saccharomyces cerevisiae </i> </h5>
  
<p align="justify"> Yeast cell walls are made up of various layers which are represented in the following diagram. First there is a layer of proteins and mannoproteins, then a mixed layer of chitin and beta glucans and finally a mixed layer of beta 1,3 glucans and beta 1,6 glucans. Commoly, beta 1,6 glucans are extracted to <b> why> </b> using fairly simple procedures. Beta 1,3 glucan extraction is therefore not a complicated protocol. </p>
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<p align="justify"> Yeast cell walls are made up of various layers which are represented in the following diagram. First there is a layer of chitin, then a layer of beta glucans and finally a mixed layer of proteins and mannan. Commonly, the yeast cell wall is made of 5-10% of beta 1,6 glucans and 50-55% of beta 1,3 glucans and beta 1,6 glucans.</p>
  
 +
<p align="justify">  Since the layer of mannan and proteins as well as chitin is insoluble in alkali solutions, beta glucans are easily separated from the rest of the yeast cell wall. Therefore, the only alkali soluble components are a mix of beta 1,6 and beta 1,3 glucans. (aimanianda et al 2009) In order to separate the two we plan on using beta 1,6 glucanases in order to obtain a solution of beta 1,3 glucans and therefore our curdlan molecule. </p>
  
<p> SCHEMA PAROI LEVURE </p>
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<p align="justify"> We therefore decided to over-express the curdlan metabolic pathway by inserting into yeast an inducible promoter (gal1) for the glucan synthase gene (Fks1)  hoping that this would allow the cell to produce curdlan in greater quantities. This would allow us to compare our curdlan production in E. coli to the natural production in an organism and the enhanced production through the addition of a promoter.
 +
<br> To do this , we will extract the FKS1 gene yeast DNA and amplified it by PCR. We will then insert FKS1 in one hand, into plasmid pYES2 to integrate the modified plasmid in Saccharomyces cerevisiae and boost production of curdlan . On the other hand , we will integrate the plasmid FKS1 iGEM to get our famous BioBrick that we'll send to Boston. However, site-directed mutagenesis may be necessary when integrating the gene into the plasmid because there are restriction sites ( EX and SP) unwanted within the gene. </p>
  
<p align="justify"> We therefore decided to overexpress this metabolic pathway by inserting into yeast a contitutive promoter for the glucan synthase hoping that this would allow the cell to prouce curdlan in greater quantities. This would allow us to compare our curdlan production in E. coli to the natural production in an organism and the enhanced production through the addition of a promoter. </p>
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<img style= "width:38vw; height:15vw;" src="https://static.igem.org/mediawiki/2015/thumb/8/86/Bordeaux_cell_wall.png/800px-Bordeaux_cell_wall.png" >
  
<p align="justify"> in order to do so the promoter used is ... </p>
 
  
<p> SCHEMA PROMOTEUR et SCHEMA BILAN </p>
 
  
 
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<h6> Effect on the plant </h6>
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        <p align="justify"> <i> <FONT color="#8b008b"> <b> « It's very clear now. It looks like cool. But, i have a last question: why did you choose this subject? » </b> </FONT> </i> </p>
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        <p align="justify"> <i> <FONT color="#32cd32"> <b> « Because, as explained above, downy mildew is a real problem for the Aquitaine region. That is why we wanted to bring an ecological solution to this problem. And also, we are SWAG (Secretly We Adore Glucan) » </b> </FONT> </i> </p>
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</section>
  
<p align="justify"> Curdlan is a linear beta-1,3-glucan. This molecule is a polymer composed of many units of glucose, a commonly used sugar. It is produced by bacteria such as Agrobacterium, even by yeast. <p>
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<section id="statistic" class="parallax" style="background-image: url(https://static.igem.org/mediawiki/2015/thumb/d/d4/Bordeaux_Photos1_boites.001.png/800px-Bordeaux_Photos1_boites.001.png)";>
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        <p align="justify"> </p>
<h6> Now, why choose curdlan to replace copper sulfate? </h6>
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</section>
  
<p> In fact, this β1,3 glucan stimulates the plant's immune system. Activation of the innate immune system before the invasion of pathogens is a way to improve the resistance of plant against infection and reduce the use of chemicals products. </p>
 
  
<p> Blabla how work curdlan on plant immune system + Schema </p>
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        <h5> Other useful properties of Curdlan </h5>
  
<p align="justify"> Activation of signaling pathways in grapevine by sulfated glucans could be deduced from the recent analysis of the pmr4 Arabidopsis mutant. PMR4 is considered to be the main b(1,3) glucan synthase responsible for curdlan deposition upon biotic and abiotic stresses. This pmr4 mutant is resistant to powdery mildew infection and is unable to produce a pathogen-induced curdlan response. The susceptibility to powdery mildew was restored in the pmr4 nahg double mutant, suggesting that linear β-1,3 glucan negatively regulates the SA pathway. Because PR1 activation in grapevine is regulated by the SA signaling pathway, the lack of PR1 expression in curdlan-treated grapevine could be explained by a negative feedback of the glucan. Consequently, sulfation of the glucan would counteract the negative feedback effect. </p>
+
        <p align="justify"> Curdlan belongs to the class of biological response modifiers that enhance or restore normal immune defenses, including antitumor, anti-infective, anti-inflammatory, and anticoagulant activities. CrdS is an integral inner membrane protein with seven transmembrane (TM) helices, one non-membrane-spanning amphipathic helix and a Nout–Cin disposition </p>
  
 +
        <p align="justify"> Sulfation of Curdlan. Acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus (HIV) is a severe disease that can destroy the body’s immune system, so the discovery of methods to prevent AIDS infection is of great importance. All the other curdlan clinical applications in cancer, diabetes, hypertension, hypertriglyceridemia etc. are listed <a href ="https://static.igem.org/mediawiki/2015/f/fb/Bordeaux_Clinical_Applications.pdf"> here</a>.
  
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<br> Curdlan is also neutral and insoluble in water. If it is heated in aqueous suspension , it adopts simple helical conformations ( 55-80 ° C) or triple helical connected ( 80-130 ° C). It then acts as a gelling and form two types of gels (low-set gel or high-set gel) . This property is widely used in the food industry since Indeed, curdlan is a food additive ( E424 ).</p>
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<br> <b> Reference :</b> <a href ="http://link.springer.com/chapter/10.1007%2F978-1-4615-2486-1_14#page-1"> www.link.springer.com</a>
  
 
<h5> Other useful properties of Curdlan </h5>
 
 
<p align="justify"> Curdlan belongs to the class of biological response modifiers that enhance or restore normal immune defenses, including antitumor, anti-infective, anti-inflammatory, and anticoagulant activities. CrdS is an integral inner membrane protein with seven transmembrane (TM) helices, one non-membrane-spanning amphipathic helix and a Nout–Cin disposition </p>
 
 
 
<p align="justify"> Sulfation of Curdlan. Acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus (HIV) is a severe disease that can destroy the body’s immune system, so the discovery of methods to prevent AIDS infection is of great importance. </p>
 
  
  

Latest revision as of 09:05, 28 July 2015

Our Solution

What is Curdlan?

To start with, let's talk about glucans. Glucan molecules are polysaccharides of D-glucose monomers linked by glycosidic bonds. One of them is called Curdlan, a (1→3)-β-D-glucan. This molecule is a linear homopolymer which may have as many as 12,000 glucose units. It is naturally produced by Agrobacterium sp. ATCC31749 which uses it like an Extracellular PolySaccharides (EPS) in it's capsule. The capsule formation is correlated with cell aggregation (floc formation) and it is suggested that the capsule and floc formation together function as protective structures in cases of Nitrogen-starvation of the post-stationary phase. The protective effects are due to the fact that Curdlan forms a capsule that completely surrounds the outer cell surface of bacteria.




« Ok and how will Curdlan be useful to you? »


« Let me explain our purpose. »




Curdlan belongs to the class of biological response modifiers that enhance or restore normal immune defenses including antitumor, anti-infective, anti-inflammatory, and anticoagulant activities. As a matter of fact, this β1,3 glucan can stimulate the plant's immune system.

More precisely, applied to grapevine plants, sulfated Curdlan induces the accumulation of phytoalexins (organic antimicrobial substances) and the expression of a set of Pathogenesis-Related proteins .

However, non-sulfated Curdlan doesn't trigger the hypersensitive response characterized by the rapid death of cells in the local region surrounding an infection, avoiding a complete contamination of the plant. This response has been studied in Arabidopsis thaliana through a mutant gene: pmr4 . This mutant is resistant to mildew infections but is unable to induce Pathogenesis-Related proteins expression .

Also, activation of a Pathogenesis-Related protein called PR1 in grapevine is regulated by the salicylic acid signaling pathway . The lack of PR1 expression in non-sulfated Curdlan-treated grapevine could be explained by a negative feedback of glucan. This is demonstrated by the study of a double mutant of pmr4 which restore the susceptibility to mildew. It suggests that linear β-1,3 glucan negatively regulates the salicylic acid pathway. So, sulfation of the glucan would counteract the negative feedback effect.

To conclude, activation of the innate immune system before the invasion of pathogens is a way to improve the resistance of plant against infection and to reduce the use of chemicals products.


« Ok i understand the value of producing Curdlan. How will you proceed? »


« This is a good question i'll answer. »


Before starting the project, we took a few weeks to decide which host organism we would use and how they could be useful. To begin with we looked at three different organisms: Escherichia coli , Bacillus subtilis and Saccharomyces cerevisiae and compared their glucan metabolic pathways. We rapidly eliminated Bacillus subtilis from our possible hosts due to it's lack of enzymes involved in the metabolic pathway of beta 1,3 glucans. However, we found that yeast naturally produces Curdlan in it's cell wall, like Agrobacterium . Furthermore, Escherichia coli is only missing one enzyme to synthethize Curdlan. We therefore concluded that we could keep these two organisms: one where we would overexpress the beta 1,3 glucan prodution using a constititive promoter and one where we would insert the ability to create curdlan by adding the enzyme that is needed.








In Agrobacterium , three genes (crdA, crdS and crdC) are required for Curdlan production. The putative operon crdASC contains crdS, encoding β-(1,3)-glucan synthase catalytic subunit, flanked by two additional genes : crdA and crdC. The first assists translocation of the nascent polymer across the cytoplasmic membrane and the second assists the passage of the nascent polymer across the periplasm. However, all Curdlan biosynthesis is dependent of nitrogen starvation and various parameters. We want to simplify all of this.


Using Bacteria: Escherichia coli

Firstly, we decided to produce curdlan with Escherichia coli , because Agrobacterium and it are Gram negative bacteria and have a lot of membrane similarity. Moreover Escherichia coli is a little pretty good bacteria, it can be grown and cultured easily and inexpensively in a laboratory setting unlike Agrobacterium .

Secondly, we are going to put these three genes into Escherichia coli under an easier control as N-starvation.

Thirdly, when we produce curdlan with Escherichia coli , we will sulfate Curdlan by chemical method. In fact sulfated Curdlan, it is the better form of Curdlan to activate immune plant system.

To sum up, we would like to produce Curdlan in Escherichia coli and then sulfate it to use it as a preventive treatment for the vine against the mildew infection and continue to produce good wine and make everyone happy.

Using Yeast: Saccharomyces cerevisiae

Yeast cell walls are made up of various layers which are represented in the following diagram. First there is a layer of chitin, then a layer of beta glucans and finally a mixed layer of proteins and mannan. Commonly, the yeast cell wall is made of 5-10% of beta 1,6 glucans and 50-55% of beta 1,3 glucans and beta 1,6 glucans.

Since the layer of mannan and proteins as well as chitin is insoluble in alkali solutions, beta glucans are easily separated from the rest of the yeast cell wall. Therefore, the only alkali soluble components are a mix of beta 1,6 and beta 1,3 glucans. (aimanianda et al 2009) In order to separate the two we plan on using beta 1,6 glucanases in order to obtain a solution of beta 1,3 glucans and therefore our curdlan molecule.

We therefore decided to over-express the curdlan metabolic pathway by inserting into yeast an inducible promoter (gal1) for the glucan synthase gene (Fks1) hoping that this would allow the cell to produce curdlan in greater quantities. This would allow us to compare our curdlan production in E. coli to the natural production in an organism and the enhanced production through the addition of a promoter.
To do this , we will extract the FKS1 gene yeast DNA and amplified it by PCR. We will then insert FKS1 in one hand, into plasmid pYES2 to integrate the modified plasmid in Saccharomyces cerevisiae and boost production of curdlan . On the other hand , we will integrate the plasmid FKS1 iGEM to get our famous BioBrick that we'll send to Boston. However, site-directed mutagenesis may be necessary when integrating the gene into the plasmid because there are restriction sites ( EX and SP) unwanted within the gene.



« It's very clear now. It looks like cool. But, i have a last question: why did you choose this subject? »


« Because, as explained above, downy mildew is a real problem for the Aquitaine region. That is why we wanted to bring an ecological solution to this problem. And also, we are SWAG (Secretly We Adore Glucan) »


Other useful properties of Curdlan

Curdlan belongs to the class of biological response modifiers that enhance or restore normal immune defenses, including antitumor, anti-infective, anti-inflammatory, and anticoagulant activities. CrdS is an integral inner membrane protein with seven transmembrane (TM) helices, one non-membrane-spanning amphipathic helix and a Nout–Cin disposition

Sulfation of Curdlan. Acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus (HIV) is a severe disease that can destroy the body’s immune system, so the discovery of methods to prevent AIDS infection is of great importance. All the other curdlan clinical applications in cancer, diabetes, hypertension, hypertriglyceridemia etc. are listed here.

Curdlan is also neutral and insoluble in water. If it is heated in aqueous suspension , it adopts simple helical conformations ( 55-80 ° C) or triple helical connected ( 80-130 ° C). It then acts as a gelling and form two types of gels (low-set gel or high-set gel) . This property is widely used in the food industry since Indeed, curdlan is a food additive ( E424 ).







Reference : www.link.springer.com