Team:SJTU-BioX-Shanghai/Part2 Extension

From 2014.igem.org

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<h2 id="alignright" align="right">——Polymerization and Maximization</h2>
<h2 id="alignright" align="right">——Polymerization and Maximization</h2>
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<!--<p><strong>The ''Crown''</strong></p>-->
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<h2 id="Crown">Crown</h2>
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<p>This Crown will help us achieve the goal of selective polymerization of enzymes. Polymerized enzymes, different from normal scattered condition, has much more opportunities to contact with the substrates. Therefore, our project aims to increase as well as to control the efficiency of complex reactions. We'll build a framework that make multi-enzyme complex easy to form, which we call a Crown.</p>
+
<br/>
 +
<p>This <strong><em>Crown</strong></em> will help us achieve the goal of selective polymerization of enzymes.</p>
 +
<p>Polymerized enzymes, different from normal scattered condition, has much more opportunities to contact with the substrates. Therefore, our project aims to increase as well as to control the efficiency of complex reactions. We'll build a framework that make multi-enzyme complex easy to form, which we call a <strong><em>Crown</strong></em>.</p>
-
<p>And based on the success of the individual fusion protein (The first jewel) expression, we tried to add more jewels on the Crown. (fig.1)</p>
+
<br/>
 +
<center><img src="http://2014.igem.org/wiki/images/2/2e/SJTU14_Part2%281-3%29.jpg"></img></center>
 +
<br/>
 +
<p>And based on the success of the individual fusion protein (The first jewel) expression, we tried to add more jewels on the <strong><em>Crown</strong></em>.</p>
-
<p>In order to build a polymerase system, we make more fusion proteins bind to the same Connector. Then by adding enzymes, it has the practical effect of accelerating the reactions and enhancing efficiency of the production. So far, the Crown is built with more than one jewel shining on it.</p>
+
<p>In order to build a polymerase system, we make more fusion proteins bind to the same <strong><em>Connector</strong></em>. Then by adding enzymes, it has the practical effect of accelerating the reactions and enhancing efficiency of the production. So far, the <strong><em>Crown</strong></em> is built with more than one jewel shining on it.</p>
<br/>
<br/>
-
<h2>Selective Polymerization</h2>
 
-
<p>Our fused protein can not only be used to polymerize enzymes but also to control selective combinations. As the pathway showed in the picture, we can get different product by combining E1 and E2 together or combining E1 and E3 together. Therefore, we can control the direction of pathway by simply transforming different Connectee plasmid. </p>
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<h2 id="SelectivePolymerization">Selective Polymerization</h2>
 +
<br/>
 +
<p>Our fused protein can not only be used to polymerize enzymes but also to control selective combinations. As the pathway showed in the picture, we can get different product by combining E1 and E2 together or combining E1 and E3 together. Therefore, we can control the direction of pathway by simply transforming different <strong><em>Connectee</strong></em> plasmid. </p>
 +
<br/>
 +
<center><img src="http://2014.igem.org/wiki/images/3/38/SJTU14_Part2%28Selective_Polymerization%29.jpg"></img></center>
 +
<br/>
 +
<p>All the three enzymes involves are expressed in the bacteria. Each of fused protein contain ssDsbA,Lgt,FL3,enzyme,HL and TAL while the TAL part can recognize three different sites. We design two <strong><em>Connectee</strong></em> plasmids. <strong><em>Connectee1</strong></em> has TAL recognition sites for E1 and E2 and <strong><em>Connectee2</strong></em> has recognition sites for E1 and E3. By transforming P1 only into the bacteria, the fused proteins containing E1 and E2 will bind to the plasmid, thus produce S3 efficiently. Analogously, by transforming P2 into the bacteria, we can expect to get higher yield of product S4.</p>
-
<p>All the three enzymes involves are expressed in the bacteria. Each of fused protein contain ssDsbA,Lgt,FL3,enzyme,HL and TAL while the TAL part can recognize three different sites. We design two Connectee plasmids. Connectee1 has TAL recognition sites for E1 and E2 and Connectee2 has recognition sites for E1 and E3. By transforming P1 only into the bacteria, the fused proteins containing E1 and E2 will bind to the plasmid, thus produce S3 efficiently. Analogously, by transforming P2 into the bacteria, we can expect to get higher yield of product S4.</p>
+
<br/>
 +
<h2 id="HowtobeaCraftsmen">How to be a Craftsmen</h2>
 +
<br/>
 +
<p>A compact machine requires bold ideas and careful practicing. Here comes how we built our <strong><em>Crown</strong></em>.</p>
-
<h2>How to be a Craftsmen</h2>
 
-
<p>A compact machine requires bold ideas and careful practicing. Here comes how we built our Crown.</p>
+
<h3 id="ConstructionMethod">Construction Method</h3>
-
<h3>Construction Method:</h3>
+
<p>Above all, we use 3 sets of <strong><em>Connectee1</strong></em> to build polymerization system. There are four main parts in a <strong><em>Connectee1</strong></em> for testing.</p>
-
<p>Above all, we use 3sets of Connector 1 to build polymerization system. There are four main parts in a Connector 1 for testing.</p>
+
<p>ssDsbA: SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of <em>E.coli</em>.</p>
-
<p>ssDsbA: SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of E.coli .</p>
+
<p>FP: To visualize the localization of fusion protein with fluorescence test , we added FP in the <strong><em>Connectee1</strong></em> and placed it just after the ssDsbA. We chose mRFP,CFP,YFP in our system.</p>
-
 
+
-
<p>FP: To visualize the localization of fusion protein with fluorescence test , we added FP in the Connectee 1 and placed it just after the ssDsbA. We chose mRFP,CFP,YFP in our system.</p>
+
<p>Lgt: Phosphatidylglycerol prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein act as an membrane anchor of E.coli with seven transmembrane segments and has been successfully overexpressed in E. coli without causing harm to cells.</p>
<p>Lgt: Phosphatidylglycerol prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein act as an membrane anchor of E.coli with seven transmembrane segments and has been successfully overexpressed in E. coli without causing harm to cells.</p>
-
<p>TAL effectors:As mentioned earlier,we choose three kinds of combinations to build three different TAL proteins, which is based on the parts that the team of Freiburg offered in 2012. These three TAL proteins can identify three different 14bp nucleotide sequences on a Connector. Note that we added a His Tag at the end of TAL protein to facilitate separation and purification.</p>
+
<p>TAL effectors:As mentioned earlier,we choose three kinds of combinations to build three different TAL proteins, which is based on the parts that the team of Freiburg offered in 2012. These three TAL proteins can identify three different 14bp nucleotide sequences on a <strong><em>Connector</strong></em>. Note that we added a His Tag at the end of TAL protein to facilitate separation and purification.</p>
-
<p>For the three kinds of corresponding Connectoe 2, we did not introduced ssDsbA-Lgt section to keep them in a free intracellular state.</p>
+
<p>For the three kinds of corresponding <strong><em>Connector2</strong></em>, we did not introduced ssDsbA-Lgt section to keep them in a free intracellular state.</p>
-
<p>In the final production of our construction, we add an easy-to-hand interface sequence between the Lgt and TAL protein in Connector 1 or just before the TAL protein in Connector 2, as sites to adding enzymes.</p>
+
<p>In the final production of our construction, we add an easy-to-hand interface sequence between the Lgt and TAL protein in <strong><em>Connector1</strong></em> or just before the TAL protein in Connector 2, as sites to adding enzymes.</p>
-
 
+
<br/>
-
<h3>Co-Transformation & Induced expression:</h3>
+
 +
<h3 id="Co-Transformation&InducedExpression">Co-Transformation & Induced Expression</h3>
<p>Expression vectors used in the project for membrane protein expression are modified versions of pRSFDuet-1, pETDuet-1,pACYCDuet-1(NOVAGEN), which are originally regulated by T7 promoter. These plasmids can coexist in one cell.</p>
<p>Expression vectors used in the project for membrane protein expression are modified versions of pRSFDuet-1, pETDuet-1,pACYCDuet-1(NOVAGEN), which are originally regulated by T7 promoter. These plasmids can coexist in one cell.</p>
-
<p>The Connector is pBluescript II KS(+) .</p>
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<p>The <strong><em>Connector</strong></em> is pBluescript II KS(+) .</p>
-
<p>We used the four reformed plasmids to co-transform and induced the Connectors to express. Now the structure of the crown appears in the E. coli cell membrane or cytoplasm.</p>
+
<p>We used the four reformed plasmids to co-transform and induced the <strong><em>Connectors</strong></em> to express. Now the structure of the crown appears in the E. coli cell membrane or cytoplasm.</p>
 +
<br/>
-
<h2>Test methods</h2>
+
<h3 id="Testmethods">Test methods</h3>
-
 
+
<p>We use formaldehyde to stabilize the connected fusion proteins and <strong><em>Connector</strong></em>, then separate the proteins-Connector complexes and digest the protein. Finally use PCR to detect the three sequences of the <strong><em>Connector</strong></em> which TAL proteins are designed to bind to.</p>
-
<p>We use formaldehyde to stabilize the connected fusion proteins and Connector, then separate the proteins-Connector complexes and digest the protein. Finally use PCR to detect the three sequences of the Connector which TAL proteins are designed to bind to.</p>
+
<p>Then, we can test the yield of different product to determine the efficiency of selective combination.</p>
<p>Then, we can test the yield of different product to determine the efficiency of selective combination.</p>
 +
<br/>
-
<h2>What’s more ?</h2>
+
<h2 id="What'smore">What’s more ?</h2>
 +
<br/>
 +
<center><img src="http://2014.igem.org/wiki/images/a/a5/SJTU14_Part2%281-3-5%29.jpg"></img></center>
 +
<br/>
 +
<p>We are trying to put more enzymes into the polymerization system, which makes the <strong><em>Crown</strong></em> more practical and brilliant. And with more enzymes on the <strong><em>Crown</strong></em>, there will be more possible choices for selective combination.</p>
-
<p>We are trying to put more enzymes into the polymerization system, which makes the Crown more practical and brilliant. (fig.3) And with more enzymes on the Crown, there will be more possible choices for selective combination.</p>
+
<br/>
 +
<br/>
-
 
+
<h2 id=Reference>Reference</h2>
-
<h2>Reference: </h2>
+
<br/>
<ol>
<ol>
<li>Pailler, Jérémy, et al. "Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane." Journal of bacteriology 194.9 (2012): 2142-2151.</li>
<li>Pailler, Jérémy, et al. "Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane." Journal of bacteriology 194.9 (2012): 2142-2151.</li>
-
 
<li>Schierle, Clark F., et al. "The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway." Journal of bacteriology 185.19 (2003): 5706-5713.</li>
<li>Schierle, Clark F., et al. "The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway." Journal of bacteriology 185.19 (2003): 5706-5713.</li>
-
 
<li>Katsuyama, Tomonori, et al. "An efficient strategy for TALEN-mediated genome engineering in Drosophila." Nucleic acids research 41.17 (2013): e163-e163.</li>
<li>Katsuyama, Tomonori, et al. "An efficient strategy for TALEN-mediated genome engineering in Drosophila." Nucleic acids research 41.17 (2013): e163-e163.</li>
-
 
<li>Bogdanove, Adam J., Sebastian Schornack, and Thomas Lahaye. "TAL effectors: finding plant genes for disease and defense." Current opinion in plant biology 13.4 (2010): 394-401.</li>
<li>Bogdanove, Adam J., Sebastian Schornack, and Thomas Lahaye. "TAL effectors: finding plant genes for disease and defense." Current opinion in plant biology 13.4 (2010): 394-401.</li>
 +
</ol>
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 +
   </article>
   </article>
   </div></html>
   </div></html>
{{Team:SJTU-BioX-Shanghai/footer}}
{{Team:SJTU-BioX-Shanghai/footer}}

Revision as of 18:21, 16 October 2014

More than One Jewel on the Crown

——Polymerization and Maximization

Crown


This Crown will help us achieve the goal of selective polymerization of enzymes.

Polymerized enzymes, different from normal scattered condition, has much more opportunities to contact with the substrates. Therefore, our project aims to increase as well as to control the efficiency of complex reactions. We'll build a framework that make multi-enzyme complex easy to form, which we call a Crown.



And based on the success of the individual fusion protein (The first jewel) expression, we tried to add more jewels on the Crown.

In order to build a polymerase system, we make more fusion proteins bind to the same Connector. Then by adding enzymes, it has the practical effect of accelerating the reactions and enhancing efficiency of the production. So far, the Crown is built with more than one jewel shining on it.


Selective Polymerization


Our fused protein can not only be used to polymerize enzymes but also to control selective combinations. As the pathway showed in the picture, we can get different product by combining E1 and E2 together or combining E1 and E3 together. Therefore, we can control the direction of pathway by simply transforming different Connectee plasmid.



All the three enzymes involves are expressed in the bacteria. Each of fused protein contain ssDsbA,Lgt,FL3,enzyme,HL and TAL while the TAL part can recognize three different sites. We design two Connectee plasmids. Connectee1 has TAL recognition sites for E1 and E2 and Connectee2 has recognition sites for E1 and E3. By transforming P1 only into the bacteria, the fused proteins containing E1 and E2 will bind to the plasmid, thus produce S3 efficiently. Analogously, by transforming P2 into the bacteria, we can expect to get higher yield of product S4.


How to be a Craftsmen


A compact machine requires bold ideas and careful practicing. Here comes how we built our Crown.

Construction Method

Above all, we use 3 sets of Connectee1 to build polymerization system. There are four main parts in a Connectee1 for testing.

ssDsbA: SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of E.coli.

FP: To visualize the localization of fusion protein with fluorescence test , we added FP in the Connectee1 and placed it just after the ssDsbA. We chose mRFP,CFP,YFP in our system.

Lgt: Phosphatidylglycerol prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein act as an membrane anchor of E.coli with seven transmembrane segments and has been successfully overexpressed in E. coli without causing harm to cells.

TAL effectors:As mentioned earlier,we choose three kinds of combinations to build three different TAL proteins, which is based on the parts that the team of Freiburg offered in 2012. These three TAL proteins can identify three different 14bp nucleotide sequences on a Connector. Note that we added a His Tag at the end of TAL protein to facilitate separation and purification.

For the three kinds of corresponding Connector2, we did not introduced ssDsbA-Lgt section to keep them in a free intracellular state.

In the final production of our construction, we add an easy-to-hand interface sequence between the Lgt and TAL protein in Connector1 or just before the TAL protein in Connector 2, as sites to adding enzymes.


Co-Transformation & Induced Expression

Expression vectors used in the project for membrane protein expression are modified versions of pRSFDuet-1, pETDuet-1,pACYCDuet-1(NOVAGEN), which are originally regulated by T7 promoter. These plasmids can coexist in one cell.

The Connector is pBluescript II KS(+) .

We used the four reformed plasmids to co-transform and induced the Connectors to express. Now the structure of the crown appears in the E. coli cell membrane or cytoplasm.


Test methods

We use formaldehyde to stabilize the connected fusion proteins and Connector, then separate the proteins-Connector complexes and digest the protein. Finally use PCR to detect the three sequences of the Connector which TAL proteins are designed to bind to.

Then, we can test the yield of different product to determine the efficiency of selective combination.


What’s more ?



We are trying to put more enzymes into the polymerization system, which makes the Crown more practical and brilliant. And with more enzymes on the Crown, there will be more possible choices for selective combination.



Reference


  1. Pailler, Jérémy, et al. "Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane." Journal of bacteriology 194.9 (2012): 2142-2151.
  2. Schierle, Clark F., et al. "The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway." Journal of bacteriology 185.19 (2003): 5706-5713.
  3. Katsuyama, Tomonori, et al. "An efficient strategy for TALEN-mediated genome engineering in Drosophila." Nucleic acids research 41.17 (2013): e163-e163.
  4. Bogdanove, Adam J., Sebastian Schornack, and Thomas Lahaye. "TAL effectors: finding plant genes for disease and defense." Current opinion in plant biology 13.4 (2010): 394-401.