Difference between revisions of "Team:Bordeaux/Description"
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<h5 align="left"> What is Curdlan? </h5> | <h5 align="left"> What is Curdlan? </h5> | ||
− | <p align="justify" style="text-indent: 3vw;"> | + | <p align="justify" style="text-indent: 3vw;"> Glucan molecules are <b>polysaccharides of D-glucose monomers linked by glycosidic bonds</b> and one of them is called <b>Curdlan </b>, a (1→3)-β-D-glucan. This molecule is a linear homopolymer which may have as many as 12,000 glucose units. It is <b>naturally produced by <i> Agrobacterium</b> sp. ATCC31749</i> which uses it as an Extracellular PolySaccharides (EPS) in it's capsule [1]. 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 for the bacteria are due to the fact that Curdlan forms a capsule that completely surrounds the outer cell surface of bacteria.</p> |
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<h6 align="justify"> <i> <FONT color="#8b008b"> « Ok and how will Curdlan be useful to you? » </FONT> </i> </h6> | <h6 align="justify"> <i> <FONT color="#8b008b"> « Ok and how will Curdlan be useful to you? » </FONT> </i> </h6> | ||
<h6 align="justify"> <i> <FONT color="#00843c"> « Let me explain our purpose. » </FONT> </i> </h6> <br> | <h6 align="justify"> <i> <FONT color="#00843c"> « Let me explain our purpose. » </FONT> </i> </h6> <br> | ||
− | <p align="justify" style="text-indent: 3vw;"> Curdlan belongs to the class of biological response modifiers that <b>enhance or restore normal natural defenses</b>. For example, it can have antitumor, anti-infective, anti-inflammatory, and anticoagulant activities (see other properties of Curdlan). In particular, this (1→3)-β-glucan can <b>stimulate | + | <p align="justify" style="text-indent: 3vw;"> Curdlan belongs to the class of biological response modifiers that <b>enhance or restore normal natural defenses</b>. For example, it can have antitumor, anti-infective, anti-inflammatory, and anticoagulant activities (see other properties of Curdlan). In particular, this (1→3)-β-glucan can <b>stimulate plant natural defenses</b>. </p> |
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<p align="justify"style="text-indent: 3vw;"> Furthermore, non-sulfated Curdlan doesn't trigger the response through a mutant gene: pmr4. This <b>mutant</b> is resistant to mildew infections but is <b> unable to induce Pathogenesis-Related proteins expression </b>. 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 (1→3)-β-glucan negatively regulates the salicylic acid pathway. So, <b>sulfation of the glucan would counteract the negative feedback effect. </b> [16]</p> | <p align="justify"style="text-indent: 3vw;"> Furthermore, non-sulfated Curdlan doesn't trigger the response through a mutant gene: pmr4. This <b>mutant</b> is resistant to mildew infections but is <b> unable to induce Pathogenesis-Related proteins expression </b>. 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 (1→3)-β-glucan negatively regulates the salicylic acid pathway. So, <b>sulfation of the glucan would counteract the negative feedback effect. </b> [16]</p> | ||
− | <p align="justify" style="text-indent: 3vw;"> To conclude, activation of natural defenses before the invasion of pathogens is a way to improve the | + | <p align="justify" style="text-indent: 3vw;"> To conclude, activation of natural defenses before the invasion of pathogens is a way to improve the plant resistance against infection and to reduce the use of chemicals products. </p> |
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− | <p align="justify" style="text-indent: 3vw;"> In <i> Agrobacterium </i>, <b>three genes (crdA, crdS and crdC) are required for Curdlan production</b>. The putative operon crdASC contains <b>crdS, encoding (1→3)-β-glucan synthase catalytic subunit</b>, flanked by two additional genes : crdA and crdC. The first assists translocation of the nascent polymer across | + | <p align="justify" style="text-indent: 3vw;"> In <i> Agrobacterium </i>, <b>three genes (crdA, crdS and crdC) are required for Curdlan production</b>. The putative operon crdASC contains <b>crdS, encoding (1→3)-β-glucan synthase catalytic subunit</b>, 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. Finally we would like to <b>sulfate</b> our Curdlan molecules chemically in order to <b>enhance its effects on the activation of the plant natural defenses</b> since it has been shown that sulfated curdlan is much more effective (see previous page [3]). <b>However</b>, all <b>Curdlan biosynthesis is dependent of nitrogen starvation</b> and various parameters. We want to <b>simplify</b> all of this. </p> |
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− | <p align="justify" style="text-indent: 3vw;"> Before starting the project, we took a few weeks to decide <b>which host organism we would use</b> 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 β-glucan metabolic pathways. We rapidly eliminated <i> Bacillus subtilis </i> from our possible hosts due to | + | <p align="justify" style="text-indent: 3vw;"> Before starting the project, we took a few weeks to decide <b>which host organism we would use</b> 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 β-glucan metabolic pathways. We rapidly eliminated <i> Bacillus subtilis </i> from our possible hosts due to its lack of enzymes involved in the metabolic pathway of (1→3)-β-glucans (Figure 5). However, we found that <b><i>Saccharomyces cerevisiae</i> naturally produces Curdlan</b> in its cell wall, like <i>Agrobacterium</i>. Furthermore, <b><i> Escherichia coli </i> is only missing one enzyme</b> (the <b>β-Glucan synthase</b>) to synthethize Curdlan. We therefore concluded that we could keep these two organisms: one where we would overexpress the (1→3)-β-glucan synthase using a constitutive promoter and one where we would insert the ability to create Curdlan by adding the enzyme that is needed throught the crdASC putative operon.</p> |
<p class="reference" align="left"> <b>Literature Cited: </b> </p> | <p class="reference" align="left"> <b>Literature Cited: </b> </p> | ||
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<h5> Using Bacteria: <br> <i> Escherichia coli </i> </h5> | <h5> Using Bacteria: <br> <i> Escherichia coli </i> </h5> | ||
− | <p align="justify" style="text-indent: 3vw;"> | + | <p align="justify" style="text-indent: 3vw;"> First, we decided to produce Curdlan with <b><i> Escherichia coli </i></b>, because <i> Agrobacterium tumefasciens</i> because both of them are Gram negative bacteria and have a lot of <b>membrane similarity</b>. Moreover <i> Escherichia coli </i> is a simple bacteria that can be <b>grown and cultured easily and inexpensively</b> in a laboratory unlike <i> Agrobacterium </i>. Indeed, Curdlan production in <i> Agrobacterium </i> requires Nitrogen Starvation and its growth parameters need to be relatively precise. This is not the case with <i> E. coli </i> in our project. </p> |
− | <p align="justify" style="text-indent: 3vw;"> Since <i> E. coli </i> naturally produces UDP Glucose (metabolite number 3 on Figure 5), adding the (1→3)-β-glucan synthase would theoretically allow Curdlan production. We therefore inserted the three genes which code for the β-glucan synthase and metabolic transporters in <i> Agrobacterium </i> (crdASC) into <i> E. coli </i>. However, since our gene sequences for crdA, crdS, and crdC originally come from <i> Agrobacterium </i> we decided to <b>optimize our gene codons</b> for <i> E. coli </i> with IDT | + | <p align="justify" style="text-indent: 3vw;"> Since <i> E. coli </i> naturally produces UDP Glucose (metabolite number 3 on Figure 5), adding the (1→3)-β-glucan synthase would theoretically allow Curdlan production. We therefore inserted the three genes which code for the β-glucan synthase and metabolic transporters in <i> Agrobacterium </i> (crdASC) into <i> E. coli </i>. However, since our gene sequences for crdA, crdS, and crdC originally come from <i> Agrobacterium </i> we decided to <b>optimize our gene codons</b> for <i> E. coli </i> with IDT codon optimization tool in order to make sure that our gene would correctly be expressed. Furthermore, we decided to place the genes under an easier control than N-starvation by using a <b>promoter</b> which is <b>activated in stationary phase</b>. (osmY, <a href= "http://parts.igem.org/Part:BBa_J45992" style=" color: #8b008b;"> BBa_J45992 </a> characterized by MIT in 2006). This should theoretically allow maximum production in simple conditions. </p> |
<img style= "width:30vw; height:8vw; align:center;" src= "https://static.igem.org/mediawiki/2015/7/79/Bordeaux_Biobrick.jpg"> | <img style= "width:30vw; height:8vw; align:center;" src= "https://static.igem.org/mediawiki/2015/7/79/Bordeaux_Biobrick.jpg"> | ||
− | <p align="justify" style="text-indent: 3vw;"> All three genes were synthesized by IDT separately with the correct ends to allow integration in the iGEM plasmids and an easy creation of our biobricks. We planned on amplifying our fragments by PCR and creating different biobricks with different assemblies of our genes and plasmids in order to find the <b>effect of each gene on Curdlan production</b> and to <b>verify the | + | <p align="justify" style="text-indent: 3vw;"> All three genes were synthesized by IDT separately with the correct ends to allow integration in the iGEM plasmids and an easy creation of our biobricks. We planned on amplifying our fragments by PCR and creating different biobricks with different assemblies of our genes and plasmids in order to find the <b>effect of each gene on Curdlan production</b> and to <b>verify the efficiency of our promoter</b>. </p> |
<p align="justify" style="text-indent: 3vw;"> In order to have control over the different culture perameters we also decided to use M63 culture medium. This is the medium which is used for Curdlan production in <i> Agrobacterium </i> and is also interesting since it is a minimal medium which allows us to easily vary parameters and optimize production. Furthermore, since Curdlan is a glucose derivative, being able to control the amount of sugar in the medium is interesting for production optimization. <b>We plan on testing the effect of the following parameters on Curdlan production</b>: </p> | <p align="justify" style="text-indent: 3vw;"> In order to have control over the different culture perameters we also decided to use M63 culture medium. This is the medium which is used for Curdlan production in <i> Agrobacterium </i> and is also interesting since it is a minimal medium which allows us to easily vary parameters and optimize production. Furthermore, since Curdlan is a glucose derivative, being able to control the amount of sugar in the medium is interesting for production optimization. <b>We plan on testing the effect of the following parameters on Curdlan production</b>: </p> | ||
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− | <p align="justify" style="text-indent: 3vw;"> 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 (1→6)-β-glucans(1→3)-β-D-glucans. (aimanianda et al 2009) In order to separate the two we plan on using <b>(1→6)-β-glucanases</b> in order to obtain a solution of (1→3)-β-glucans and therefore our Curdlan molecule. </p> | + | <p align="justify" style="text-indent: 3vw;"> 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 (1→6)-β-glucans(1→3)-β-D-glucans. (aimanianda et al 2009) In order to separate the two compounds, we plan on using <b>(1→6)-β-glucanases</b> in order to obtain a solution of (1→3)-β-glucans and therefore our Curdlan molecule. </p> |
− | <p align="justify" style="text-indent: 3vw;"> We therefore decided to over-express the Curdlan metabolic pathway by inserting into yeast (<i>INVSC1</i> strain ) an inducible promoter (<i>Gal1</i>) for the β-glucan synthase gene (<i>Fks1</i>) hoping that this would allow the cell to produce | + | <p align="justify" style="text-indent: 3vw;"> We therefore decided to over-express the Curdlan metabolic pathway by inserting into yeast (<i>INVSC1</i> strain ) an inducible promoter (<i>Gal1</i>) for the β-glucan synthase gene (<i>Fks1</i>) 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. </p> |
− | <p align="justify" style="text-indent: 3vw;"> To do this , we will extract the <b><i>FKS1</i> gene</b> from yeast DNA by amplifying the genomic DNA | + | <p align="justify" style="text-indent: 3vw;"> To do this , we will extract the <b><i>FKS1</i> gene</b> from yeast DNA by amplifying the genomic DNA by PCR. We will then insert <i>FKS1</i gene in one hand, into <b>pYES2 plasmid</b> with the <i>Gal1</i> inductive promoter to then integrate the modified plasmid in <i>Saccharomyces cerevisiae </i> and boost the production of Curdlan. This strategy did not work. We then tried to put a inductive promoter ahead of the relevant gene by homologous recombination. We put the <i>Gal1</i> promoter and a selective gene <i>HIS3</i> (to select our successful transformants) in front of <i>FKS1</i>. <i>Gal1</i> promoter and <i>HIS3</i> was extract by PCR from <b>pFA 6a-HIS3MX6-pGAL-3HA</b> . |
On the other hand, we will integrate the <i>FKS1</i> gene into the iGEM plasmid pSB1C3 to get our BioBrick that we'll send to Boston. This genetic construction with <i>HIS3</i> gene and <i>GAL1</i> promoter was inserted in pSB1C3 by Gibson assembly. However, site-directed mutagenesis may be necessary when integrating the gene into the plasmid because there are restriction sites (EcoR1) that are unwanted within the <i>HIS3</i> gene. </p> | On the other hand, we will integrate the <i>FKS1</i> gene into the iGEM plasmid pSB1C3 to get our BioBrick that we'll send to Boston. This genetic construction with <i>HIS3</i> gene and <i>GAL1</i> promoter was inserted in pSB1C3 by Gibson assembly. However, site-directed mutagenesis may be necessary when integrating the gene into the plasmid because there are restriction sites (EcoR1) that are unwanted within the <i>HIS3</i> gene. </p> | ||
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<p class="reference" align="left"> [16]Menard R, Alban S, (2004) β-1,3 Glucan Sulfate, but not β-1,3 Glucan, Induces the Salicylic Acid Signaling Pathway in Tobacco and Arabidopsis </p> | <p class="reference" align="left"> [16]Menard R, Alban S, (2004) β-1,3 Glucan Sulfate, but not β-1,3 Glucan, Induces the Salicylic Acid Signaling Pathway in Tobacco and Arabidopsis </p> | ||
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<h6> <a href= "https://2015.igem.org/Team:Bordeaux/Problem" style=" color: #FF5E00;"> Problem ☚ </a> Previous Page . Next Page <a href= "https://2015.igem.org/Team:Bordeaux/AchievementsNotebook" style=" color: #FF5E00;"> ☛ Notebook & Protocols </h6> | <h6> <a href= "https://2015.igem.org/Team:Bordeaux/Problem" style=" color: #FF5E00;"> Problem ☚ </a> Previous Page . Next Page <a href= "https://2015.igem.org/Team:Bordeaux/AchievementsNotebook" style=" color: #FF5E00;"> ☛ Notebook & Protocols </h6> | ||
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Latest revision as of 02:24, 19 September 2015