Difference between revisions of "Team:Ionis Paris/Biobrick Design"

 
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                             <h1>Biobrick design</h1>
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                             <h1 id="back_to_the_top">Biobrick design</h1>
 
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                                 <h3>Biobrick definition</h3>
 
                                 <h3>Biobrick definition</h3>
 
<br/>
 
<br/>
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<p>In an IGEM context, our genetic circuit, our plasmid, is defined as a biobrick. The different elements of the genetic circuit participate to the specificity of the biobrick. In the IGEM registry, we distinguish 2 components that participate to the composition of a plasmid: the plasmid backbone and the biobrick part (see Figure 2).</p><br/> </div>
+
<p>In the context of iGEM, our genetic circuit, encoded as a plasmid, is defined as a BioBrick. The different elements of the genetic circuit contribute to the function of the BioBrick. In the iGEM registry, we can distinguish 2 components that compose a plasmid: the plasmid backbone and the BioBrick part (see Figure 2).</p><br/> </div>
 
   
 
   
 
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                                 </figure>
 
                                 </figure>
 
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                                       <div class="blog_heading">
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                                         <h4><a href="http://parts.igem.org/Plasmid_backbones/Assembly">Figure 1: General structure of a Biobrick.</a></h4>  
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                                         <h4><a href="https://static.igem.org/mediawiki/2016/8/81/T--Ionis_Paris--AtthelabFig1.png"></a></h4>
 
                                             </div>
 
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<br/>                                                     
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<p><i>Figure 1: General structure of a BioBrick (source <a href="http://parts.igem.org/Plasmid_backbones/Assembly">here </a>)</i></p><br/>                                                     
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<p>For the assembly of our biobrick we use the BioBrick RFC[10] assembly standard because it is the standard of the IGEM competition and most of the parts available on the registry match this standard. The BioBrick RFC[10] assembly standard is based on the use of a prefix and a suffix placed at the extremities of each part to be assembled in order to obtain standard biobricks that are compatible and thus can be easily assembled.</p><br/>
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<p>For the assembly of our biobrick we use the BioBrick RFC[10] assembly standard because it is the standard of the IGEM competition and most of the parts available on the registry match this standard. The BioBrick RFC[10] assembly standard is based on the use of a prefix and a suffix placed at the extremities of each part to be assembled in order to obtain standard BioBricks that are compatible and thus can be easily assembled.</p><br/>
 
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                               </li>
 
                               </li>
  
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                                 <p>Prefix and suffix provide a method to obtain standard genetic construction. Their exact sequences are available in Figure 3. Each one includes two different restriction sites: </p>
+
                                 <p>Prefix and suffix provide a method to obtain standard genetic construction. Their exact sequences are available in Figure 2. Each one includes two different restriction sites: </p>
 
                               <ul><li><p> - EcoRI and XbaI in the prefix</p>
 
                               <ul><li><p> - EcoRI and XbaI in the prefix</p>
 
                               </li>
 
                               </li>
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                     <p>For protein coding regions (that starts with ATG), there is an adapted prefix.</p>
 
                     <p>For protein coding regions (that starts with ATG), there is an adapted prefix.</p>
 
                                     <figure class="postImg waves-effect">
 
                                     <figure class="postImg waves-effect">
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                                     <img src="https://static.igem.org/mediawiki/2016/4/45/IONIS_IGEM_Fig_2_Prefix_and_suffix_sequences_%28version_1%29.png" alt="">
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                                     <img src="https://static.igem.org/mediawiki/2016/e/e7/T--Ionis_Paris--AtthelabFig2.png" alt="">
 
                                 </figure>
 
                                 </figure>
 +
<p><i>Figure 2: Prefix and suffix sequences</i></p><br/>   
 
                     <p>All components of the genetic circuit are added to the system with these prefix and suffix. Once added to the system, in order to be compatible with the RFC[10] standard, a part does not have to contain these four restriction sites, they have to be unique to the prefix and suffix.</p>
 
                     <p>All components of the genetic circuit are added to the system with these prefix and suffix. Once added to the system, in order to be compatible with the RFC[10] standard, a part does not have to contain these four restriction sites, they have to be unique to the prefix and suffix.</p>
 
                               <li><p>Assembling method</p>
 
                               <li><p>Assembling method</p>
 
                               </li>
 
                               </li>
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                                    <img src="https://static.igem.org/mediawiki/2016/8/82/T--Ionis_Paris--AtthelabFig3.png" alt="">
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                                </figure>
 +
<p><i>Figure 3: Assembling method</i></p><br/>
 
                              
 
                              
 
                               <li><p>Scar</p>
 
                               <li><p>Scar</p>
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   - 5'  [part A]  TACTAG  [part B, that starts with ATG] 3’.
 
   - 5'  [part A]  TACTAG  [part B, that starts with ATG] 3’.
 
</p>
 
</p>
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                     <p>The only disadvantage of the RFC[10] assembly standard is the impossibility to make protein fusion. Indeed the 6bp scar includes a stop codon and the 8bp scar includes a frame-shift and a stop codon. The alternative to this problem is to use a scar-less assembly method or DNA synthesis. </p><br/>
+
                     <p>The only disadvantage of the RFC[10] assembly standard is the impossibility to make fusion proteins. The 6bp scar includes a stop codon and the 8bp scar includes a frame-shift and a stop codon. The alternative to this problem is to use a scar-less assembly method or DNA synthesis. </p><br/>
  
 
                                
 
                                
 
                                           <h3>Biobrick part</h3>
 
                                           <h3>Biobrick part</h3>
 
                            
 
                            
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                     <p>The biobrick part is composed by the sequence located between the prefix and the suffix. This sequence includes the devices that will realize given functions in the cell (e.g protein production).  
+
                     <p>The biobrick part is composed of the sequence located between the prefix and the suffix. This sequence includes the devices that will perform the given functions in the cell (i.e protein production).<br/>
−
Each device is a composite part, which means it is composed of several basic parts assembled together to ensure a specific function. A basic part is a single functional unit coding for a basic biological function and cannot be split into smaller units. Promoters, coding gene or RBSs are examples of basic parts. Two devices make up our biobrick part, one in charge of the XylR protein synthesis and one in charge of the Gaussia luciferase synthesis.</p><br/>
+
Each device is a composite part, which means it is composed of several basic parts assembled together to ensure a specific function. A basic part is a single functional unit coding for a basic biological function and cannot be split into smaller units. Promoters, coding sequences or RBSs are examples of basic parts. Two parts make up our device: one in charge of the XylR protein synthesis and one in charge of the<i>Gaussia</i> luciferase synthesis.</p><br/>
  
 
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                                 </div>
 
                                 </div>
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                     <p>The plasmid backbone is the sequence that begins with the suffix and ends with the prefix. The plasmid backbone mainly serves as support for the propagation of the biobrick part. It includes the replication origin and the antibiotic resistance marker.<br/>
+
                     <p>The plasmid backbone is the sequence that begins with the suffix and ends with the prefix. The plasmid backbone mainly serves as support for the propagation of the biobrick part. It includes the origin of replication and the antibiotic resistance marker.<br/>
−
The presence of the antibiotic resistance marker in the backbone allows, after the bacterial transformation, the selection of only clones that incorporate the plasmid thanks to a medium containing the antibiotic. Clones that do not incorporate the plasmid do not have the antibiotic resistance and thus cannot survive in the selective medium.  
+
The presence of the antibiotic resistance marker in the backbone allows the selection of only clones that incorporate the plasmid thanks to an antibiotic in the medium. Clones that do not incorporate the plasmid do not have the antibiotic resistance and thus cannot survive in the selective medium.  
 
In the iGEM competition, a set of 4 linearized plasmid backbones is sent to each team: pSB1A3, pSB1C3, pSB1K3.m1, and pSB1T3. They respectively include these 4 antibiotics: Ampicillin, Chloramphenicol, Kanamycin and Tetracycline.
 
In the iGEM competition, a set of 4 linearized plasmid backbones is sent to each team: pSB1A3, pSB1C3, pSB1K3.m1, and pSB1T3. They respectively include these 4 antibiotics: Ampicillin, Chloramphenicol, Kanamycin and Tetracycline.
 
</p><br/>     
 
</p><br/>     
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                               <div class="blog_top">
 
                               <div class="blog_top">
 
                                     <h4 class="blog_topHd">
 
                                     <h4 class="blog_topHd">
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                                       PRINCIPLE AND FUNCTIONING OF OUT "BIOSENSOR" PLASMID
+
                                       PRINCIPLE AND FUNCTIONING OF OUR "BIOSENSOR" PLASMID
 
                                     </h4>
 
                                     </h4>
 
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                       <br/>
 
                       <br/>
 
                     <p>The biosensor cell contains a genetic circuit, located on a plasmid support, allowing the expression of genes involved in the detection of the pollutant.  
 
                     <p>The biosensor cell contains a genetic circuit, located on a plasmid support, allowing the expression of genes involved in the detection of the pollutant.  
−
The Pr promoter is a constitutive promoter allowing the transcription of the XylR gene, coding for the XylR protein. The XylR protein, a transcriptional regulatory protein for the Pu promoter, is activated by aromatic hydrocarbons that carry a methyl group (as the toluene and xylene). In our biosensor, the Pu promoter allows the transcription of the bioluminescent reporter gene GLuc, coding for the Gaussia luciferase. When this enzyme reacts with its substrate, the Coelenterazine, it emits luminescence.</p>
+
The Pr promoter is a constitutive promoter driving the transcription of the XylR gene, coding for the XylR protein. The XylR protein, a transcriptional regulatory protein for the Pu promoter, is activated by aromatic hydrocarbons that carry a methyl group (like toluene and xylene). In our biosensor, the Pu promoter allows the transcription of the bioluminescent reporter gene GLuc, coding for the <i>Gaussia luciferase</i>. When this enzyme reacts with its substrate, a substance called the Coelenterazine, it emits luminescence.</p>
 
                                     <figure class="postImg waves-effect">
 
                                     <figure class="postImg waves-effect">
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                                     <img src="https://static.igem.org/mediawiki/2016/1/1c/Biosensor_mechanism.jpg" alt="">
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                                     <img src="https://static.igem.org/mediawiki/2016/d/d6/T--Ionis_Paris--AtthelabFig4.png" alt="">
 
                                 </figure>
 
                                 </figure>
 
                                 <div class="blog">
 
                                 <div class="blog">
 +
<p><i>Figure 4: The biosensor mechanism</i></p>
 
                                           <h3>Plasmid map</h3>
 
                                           <h3>Plasmid map</h3>
 
                                 </div>
 
                                 </div>
  
 
                     <p>For the construction of our plasmid, we selected parts that are RFC[10] compatible.
 
                     <p>For the construction of our plasmid, we selected parts that are RFC[10] compatible.
−
In Figure 4 below, the map of our plasmid is represented in a simplified way, composed of the pSB1C3 backbone and the biosensor part.</p>
+
In Figure 4 below, the map of our plasmid is represented in a simplified way, and is composed of the pSB1C3 backbone and the biosensor part.</p>
 
                                 <figure class="postImg waves-effect">
 
                                 <figure class="postImg waves-effect">
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                                     <img src="https://static.igem.org/mediawiki/2016/e/e1/Plasmid_map.jpg" alt="">
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                                     <img src="https://static.igem.org/mediawiki/2016/8/87/T--Ionis_Paris--AtthelabFig5.png" alt="">
 
                                 </figure>
 
                                 </figure>
 +
<p><i>Figure 4: Our plasmid map</i></p>
 
                                
 
                                
 
                                 <div class="blog_top">
 
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                                 </div>  
 
                    
 
                    
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                     <p>We chose to use Escherichia Coli strain DH5α as chassis for our plasmid. Indeed, this bacterium grows easily and has several mutations that make it an excellent choice for cloning procedures with a high efficiency transformation. All our parts are optimized for E. Coli. Moreover, E. Coli is the model organism, entirely sequenced.</p><br/>
+
                     <p>We chose to use Escherichia Coli strain DH5α as chassis for our plasmid. Indeed, this bacterium grows easily and has several mutations that make it an excellent choice for cloning procedures with a high efficiency transformation. All our parts are optimized for E. Coli. Moreover, E. Coli is a model organism, entirely sequenced.</p><br/>
 
                                 <div class="blog">
 
                                 <div class="blog">
 
                                           <h3>Plasmid Backbone</h3>
 
                                           <h3>Plasmid Backbone</h3>
 
                                 </div>  
 
                                 </div>  
−
                                 <p>The chosen plasmid backbone is pSB1C3, a high copy number assembly plasmid backbone of 2070 pb, because this type of plasmid backbone is the most used to assemble BioBrick standard biological parts together. This plasmid backbone includes a high copy replication origin that allows the obtaining of a high copy number per cell, which facilitates the DNA purification. The ccdb gene ensures to not transform the uncut plasmid during the assembly of two BioBrick parts. As already specified, the presence of the antibiotic resistance marker in the backbone allows the selection of clones that incorporated the plasmid.</p>
+
                                 <p>We selected the pSB1C3 plasmid, a high copy number assembly plasmid, as a backbone of 2070 pb, because it is the most used type of backbone to assemble BioBricks. This plasmid backbone includes a high copy replication origin that allows a high copy number per cell which facilitates DNA purification. All the plasmid backbone used for the competition are provided with a default insert: the ccdb gene. This gene can be used as a marker to establish whether the plasmid backbone have been successfully digested. If not, the cell death gene will remain in the plasmid backbone and kill the kill the transformed bacteria. The ccdb gene ensures to not keep cells transformed with the uncut plasmid during the assembly of two BioBrick parts.<br/>
−
                                <p>This plasmid is also the designated plasmid backbone required for the registry shipping during the IGEM competition.</p>
+
As already specified, the presence of the antibiotic resistance marker in the backbone allows the selection of clones that incorporated the plasmid. <br/>
−
                                <p>The pSB1C3 plasmid backbone confers Chloramphenicol resistance and includes the pUC19-derived pMB1, replication origin with a copy number of 100-300 per cell. The map of pSB1C3 plasmid is available below in Figure 2.</p><br/>
+
This plasmid is also the designated plasmid backbone required for the registry shipping during the IGEM competition.</p>
 +
                               
 +
 
 
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                                                 <figure class="postImg waves-effect">
 
                                                 <figure class="postImg waves-effect">
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                                     <img src="https://static.igem.org/mediawiki/2016/4/47/IONIS_IGEM_plasmid_biobricks.jpg" alt="">
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                                     <img src="https://static.igem.org/mediawiki/2016/9/9e/T--Ionis_Paris--AtthelabFig6.png" alt="">
 
                                 </figure>
 
                                 </figure>
 
                                       <div class="blog_heading">
 
                                       <div class="blog_heading">
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                                         <h4><a href="http://parts.igem.org/Plasmid_backbones/Assembly">
+
                                         <p><i>Figure 6: Standard structure of high copy number assembly plasmid backbone. (source <a href="http://parts.igem.org/Plasmid_backbones/Assembly">here</a>)</i></p>
−
Figure 6: Standard structure of high copy number assembly plasmid backbone.</a></h4>  
+
 
                                             </div>
 
                                             </div>
 
                                           </div>
 
                                           </div>
 +
 +
<p>The pSB1C3 plasmid backbone confers Chloramphenicol resistance and includes the pUC19-derived pMB1, replication origin with a copy number of 100-300 per cell. The map of pSB1C3 plasmid is available below in Figure 2.</p><br/>
 +
 
                                             <div class="col-md-4">
 
                                             <div class="col-md-4">
 
                                                 <a href="http://parts.igem.org/Part:pSB1C3">
 
                                                 <a href="http://parts.igem.org/Part:pSB1C3">
 
                                                     <figure class="postImg waves-effect">
 
                                                     <figure class="postImg waves-effect">
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                                                         <img src="https://static.igem.org/mediawiki/2016/a/a2/IONIS_IGEM_biobricks_plasmid.jpg" alt="">
+
                                                         <img src="https://static.igem.org/mediawiki/2016/8/8a/T--Ionis_Paris--AtthelabFig7.png" alt="">
 
                                                     </figure>
 
                                                     </figure>
 
                                                 </a>
 
                                                 </a>
 
                                                 <div class="blog_heading">
 
                                                 <div class="blog_heading">
−
                                                     <h4><a href="http://parts.igem.org/Part:pSB1C3" >Figure 7: Map of pSB1C3 plasmid.</a></h4>
+
                                                     <h4><a href="http://parts.igem.org/Part:pSB1C3" ></a></h4>
 +
<p><i>Figure 7: Map of the pSB1C3 plasmid (source <a href="http://parts.igem.org/Part:pSB1C3">here</a>)</i></p>
 
                                                      
 
                                                      
 
                                                 </div>   
 
                                                 </div>   
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  </div>
 
  </div>
  
−
                      <div class="col-xs-12 col-sm-7">
 
 
                          
 
                          
 
                                 <div class="blog">
 
                                 <div class="blog">
 
                                           <h3>Constitutive Pr promoter</h3>
 
                                           <h3>Constitutive Pr promoter</h3>
 
                                 </div>
 
                                 </div>
−
                                   <p>The Pr promoter is found in the toluene recognition system and is composed of 410 bp. It has a constitutive expression. This promoter is available on the iGEM registry at this ID access: BBa_I723018.</p>
+
                                   <p>The Pr promoter is found in the toluene recognition system and is composed of 410 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723018.</p>
−
                                   <p>We chose to use this promoter because it is the specific promoter for the XylR gene. This promoter is naturally constitutive. It leads to the permanent production of the XylR protein. Indeed, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein has to be present in sufficient amount.</p><br/>
+
                                   <p>We chose to use this promoter because it is the specific promoter for the XylR gene. This promoter is naturally constitutive. It leads to the permanent production of the XylR protein. Indeed, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein should be present in sufficient amount.</p><br/>
  
 
                                 <div class="blog">
 
                                 <div class="blog">
 
                                           <h3>XylR gene</h3>
 
                                           <h3>XylR gene</h3>
 
                                 </div>
 
                                 </div>
−
                                   <p>The XylR gene, a gene of 1795 bp, encodes for the XylR protein and is regulated by the Pr promoter in its natural organization. This gene is available on the iGEM registry at this ID access: BBa_K1834844.</p>
+
                                   <p>The 1704 bp XylR gene, encodes for the XylR protein and is regulated by the Pr promoter in its native context. This gene is available on the iGEM Registry of Standard Biological Parts (<a href="http://parts.igem.org/Part:BBa_K1834844" ><font color="DeepPink">BBa_K1834844</font></a>). The XylR that we designed for our biosensor is a bit different because it is optimized for E.Coli DH5-Alpha and for IDT synthesis. .</p>
−
                                   <p>The XylR protein, mined from Pseudomonas putida, is involved in the transcriptional activation of the toluene recognition system. This regulatory protein allows the detection of aromatic hydrocarbons that carry a methyl group, i.e. xylene, toluene and 1-chloro-3-methyl-benzene. The A domain of the XylR protein (sensing domain), reacts with the pollutant molecule by binding to its methyl group. This leads to the formation of a tetramer. The C domain is involved in the dimerization of XylR, which is ATP dependent. The made up tetramer acts as an activator transcriptional factor for the Pu promoter, through the DNA binding D domain.</p><br/>
+
                                   <p>The XylR protein, mined from <i>Pseudomonas putida</i>, is involved in the transcriptional activation of the toluene recognition system. This regulatory protein allows the detection of aromatic hydrocarbons that carry a methyl group, i.e. xylene, toluene and 1-chloro-3-methyl-benzene. The A domain of the XylR protein (sensing domain), binds to the pollutant molecule. This leads to the formation of a tetramer. The C domain is involved in the dimerization of XylR, which is ATP dependent. The made up tetramer acts as an activator transcriptional factor for the Pu promoter through the DNA binding D domain.</p><br/>
 +
 
 +
                                <figure class="postImg waves-effect">
 +
                                    <img src="https://static.igem.org/mediawiki/2016/5/58/T--Ionis_Paris--AtthelabFig8.png" alt="">
 +
                                </figure>
 +
<p><i>Figure 8: The XylR CDS structure</i></p>
  
 
                                 <div class="blog">
 
                                 <div class="blog">
 +
<p></
 
                                           <h3>Pu promoter</h3>
 
                                           <h3>Pu promoter</h3>
 
                                 </div>
 
                                 </div>
−
                                   <p>Pu is a promoter found in the toluene recognition system and is composed of 320 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723020.
+
                                   <p>Pu is a promoter found in the toluene recognition system and is composed of 320 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723020.<br/>
−
<br/>We chose to use this promoter because of its sensibility to the tetramer formed by the transcriptional regulator XylR coupled with xylene, toluene or 1-chloro-3-methyl-benzene, in response to the detection of one of these environmental pollutants.</p><br/>
+
We chose to use this promoter because of its sensibility to the transcriptional regulator XylR bound to xylene, toluene or 1-chloro-3-methyl-benzene.</p><br/>
  
 
                                 <div class="blog">
 
                                 <div class="blog">
 
                                           <h3>GLuc gene</h3>
 
                                           <h3>GLuc gene</h3>
 
                                 </div>
 
                                 </div>
−
                                   <p>This gene is found in a well-known organism, the copepod Gaussia princeps. It encodes for a Luciferase enzyme, the Gaussia Luciferase, also known as GLuc, which is involved in a bioluminescence process. This enzyme degrades its substrate, the Coelenterazine, into a product, the Coelenteramide. With an optimal substrate level, this step produces energy in the form of protons that can be recovered with a fixed spectrophotometer at 475nm (green light).</p>
+
                                   <p>This gene is found in a well-known organism, the copepod Gaussia princeps. It encodes for the Gaussia luciferase enzyme, also known as GLuc, which is involved in a bioluminescence process. This enzyme degrades its substrate, coelenterazine, into a product, celenteramide. With an optimal substrate level, this step produces energy in the form of light that can be detected with a fixed spectrophotometer at 488nm.</p>
−
                                   <p>We chose to use the GLuc-His part, a gene of 522 bp, available on the iGEM registry at the BBa_K1732027 ID access. It is an optimized version for E.Coli of its twin the GLUCCO-His part (BBa_K1732003), which codes for the Gaussia luciferase following by 6 histidines. In our plasmid, this gene is positioned after an induced promoter, known as Pu promoter to report the activation of the toluene recognition system.
+
                                   <p>We chose to use the GLuc-His part, a gene of 522 bp, available on the iGEM registry at the (BBa_K1732027) which codes for the Gaussia luciferase followed by 6 histidines and optimized it for E.coli. In our plasmid, this gene is positioned after an inducible promoter, the Pu promoter, to report the activation of the toluene recognition system.<br/>
−
The Gaussia luciferase needs the addition of substrate to ensure its activity because this molecule is not synthetized by our biosensor. Due to its secreted form, lysing cells in order to assay GLuc activity is not necessary.</p>
+
 
 +
The Gaussia luciferase needs the addition of substrate to ensure its activity because this molecule is not synthetized by our biosensor. Therefore, in the laboratory, luciferase substrate can be added at the same time in each sample ensuring that every measurement will be taken at the same time. This allow a better consistency between our different results. Also, due to its secreted form, lysing cells in order to assay GLuc activity is not necessary.</p>
 +
 
 +
                                  <p>The Gaussia luciferase is an ideal reporter gene because of its stability at high temperature thanks to disulfide bonds and because it has extremely high activity in light production for very sensitive assays. When compared to Firefly and Renilla luciferase, GLuc generates over 1000-fold higher bioluminescent signal intensity[1][2]. The NanoLuc has an activity a little higher but this luciferase is very recent and thus less characterized.</p>
 +
                                  <p>Advantages of luminescence, over fluorescence, include the absence of background noise, the amplification of signal and a high dynamic range that spans many orders of magnitude. Indeed, since light emission depends strictly on the chemical reaction between the substrate and the luciferase, there is no background noise originating from the sample [3]. Furthermore, the turnover of the light reaction significantly amplifies the reporter signal. Even though bioluminescence is currently used mainly for transcription study and cell imaging, this method become increasingly popular for quantitative analysis.</p>
 +
 
 +
                                  <p>Even though bioluminescence is currently used mainly for transcription study and cell imaging, this method become increasingly popular for quantitative analysis. [3] For more information about bioluminescence and the Gaussia luciferase, <a href="https://2016.igem.org/Single_blog-full.html">click here ! </a></p><br/>
 +
 
 +
<p>[1] Inouye, S., Sahara-Miura, Y., Sato, J., Iimori, R., Yoshida, S., and Hosoya, T. (2013). Expression, purification and luminescence properties of coelenterazine-utilizing luciferases from Renilla, Oplophorus and Gaussia: Comparison of substrate specificity for C2-modified coelenterazines. Protein Expression and Purification 88, 150–156.<br/>
 +
[2] S. Inouye, Y. Sahara, Identification of two catalytic domains in a luciferase secreted by the copepod Gaussia princeps, Biochem. Biophys. Res. Commun. 365 (2008) 96–101<br/>
 +
[3]Wood, K (2011), The bioluminescence advantage, laboratorynews, available on: http://www.labnews.co.uk/features/the-bioluminescence-advantage-13-09-2011/</p>
  
−
                                  <p>The Gaussia luciferase is an ideal reporter gene because of its stability at high temperature thanks to disulfide bonds and because it has extremely high activity in light production for very sensitive assays. When compared to Firefly and Renilla luciferase, GLuc generates over 1000-fold higher bioluminescent signal intensity. The NanoLuc has an activity a little higher but this luciferase is very recent and thus less characterized.</p>
 
−
                                  <p>Advantages of luminescence, over fluorescence, include the absence of background noise, the amplification of signal and a high dynamic range that spans many orders of magnitude. Indeed, since light emission depends strictly on the chemical reaction between the substrate and the luciferase, there is no background noise originating from the sample. Furthermore, the turnover of the light reaction significantly amplifies the reporter signal.Even though bioluminescence is currently used mainly for transcription study and cell imaging, this method become increasingly popular for quantitative analysis.<br/>Moreover, the fact that the luciferase substrate have to be added in the laboratory present an interesting way to control the reaction. Indeed the luciferase substrate can be added at the same time for each samples allowing a better compliance between the different samples.</p>
 
−
                                  <p>The transcription of luciferase in the presence of specific pollutants and the use of its substrate as a manner to assess pollutant concentration is an innovative approach , yet poorly studied.</p>
 
−
                                  <p>For more information about bioluminescence and the Gaussia luciferase, <a href="https://2016.igem.org/Single_blog-full.html">click here ! </a></p><br/>
 
  
 
                                 <div class="blog">
 
                                 <div class="blog">
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                                   <p>The weaker RBS is a sequence of 11 bp with an efficiency of 0.01, derivative of BBa_B0030. This RBS is available on the iGEM registry at this ID access: BBa_0033. <br/>An other weak RBS is available on the iGEM registry at this ID access: BBa_B0031. This RBS, a sequence of 14 bp derivative of BBa_B0030, has an efficiency of 0.07.</p><br/>
 
                                   <p>The weaker RBS is a sequence of 11 bp with an efficiency of 0.01, derivative of BBa_B0030. This RBS is available on the iGEM registry at this ID access: BBa_0033. <br/>An other weak RBS is available on the iGEM registry at this ID access: BBa_B0031. This RBS, a sequence of 14 bp derivative of BBa_B0030, has an efficiency of 0.07.</p><br/>
  
−
                                     <blockquote>
+
                                     <p>
 
In our project, we chose to use the stronger RBS, the Elowitz RBS (BBa_B0034), in order to have a maximal production rate. Indeed, as we already specified, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein has to be present in an enough amount and the Gaussia luciferase has to be produced rapidly in an amount that is proportional to the pollutant amount. This allows a luminescent response corresponding to the pollutant rate.
 
In our project, we chose to use the stronger RBS, the Elowitz RBS (BBa_B0034), in order to have a maximal production rate. Indeed, as we already specified, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein has to be present in an enough amount and the Gaussia luciferase has to be produced rapidly in an amount that is proportional to the pollutant amount. This allows a luminescent response corresponding to the pollutant rate.
−
                                     </blockquote>
+
                                     </p>
 
                                 <div class="blog">
 
                                 <div class="blog">
 
                                           <h3>Double terminator</h3>
 
                                           <h3>Double terminator</h3>
 
                                 </div>
 
                                 </div>
−
                                 <p>A terminator is a genetic part placed at the end of a gene, in order to end transcription thanks to a stop codon. It exists several types of terminators but the most used are forward terminators. In general, some RNA polymerases will continue the transcription after the terminator, thus the terminator efficiency is not 100% in the most cases.<br/>In order to increase the terminator efficiency in our plasmid we chose to use a double terminator. We selected two different double terminators that we have to test.<br/>The first one of 129 bp, consisting of BBa_B0010 and BBa_B0012 as shown in Figure 4, available on the iGEM registry at this ID access: BBa_B0015. It is the most used terminator for forward transcription with a forward-efficiency of 0,984 according to measurements done by Caitlin Conboy, and of 0,97 according to measurements done by Jason Kelly. Procedures used for these measurements are explained in the <a href="http://parts.igem.org/Help:Terminators/Measurement">IGEM registry</a>.
+
                                 <p>A terminator is a genetic part placed at the end of a gene, in order to end transcription thanks to a stop codon. Several types of terminators exists but the most used are forward terminators. In general, some RNA polymerases will continue the transcription after the terminator, thus the terminator efficiency is not 100% in the most cases.<br/>
 +
In order to increase the terminator efficiency in our plasmid we chose to use a double terminator. We selected two different double terminators that we have to test.<br/>
 +
The first one of 129 bp, consisting of BBa_B0010 and BBa_B0012 as shown in Figure 4, available on the iGEM registry at this ID access: BBa_B0015. It is the most used terminator for forward transcription with a forward-efficiency of 0,984 according to measurements done by Caitlin Conboy, and of 0,97 according to measurements done by Jason Kelly. Procedures used for these measurements are explained in the <a href="http://parts.igem.org/Help:Terminators/Measurement">IGEM registry</a>.</p>
  
−
</p>
 
  
 +
                                <figure class="postImg waves-effect">
 +
                                    <img src="https://static.igem.org/mediawiki/2016/4/4a/T--Ionis_Paris--AtthelabFig9.png" alt="">
 +
                                </figure>
 +
 +
 +
 +
<p><i>Figure 9: B0015 double terminator structure (Source <a href="http://parts.igem.org/Part:BBa_B0015">here</a>)</i></p>
 +
 +
<p>The second one of 95 bp, consisting of BBa_B0011 and BBa_B0012 as shown in Figure 9, available on the iGEM registry at this ID access: BBa_B0014. It is a bidirectional terminator with a forward-efficiency of 0,604 according to measurements done by Caitlin Conboy and of 0,96 according to measurements done by Jason Kelly, and with a reverse-efficiency of 0,86 according to measurements done by Jason Kelly.</p>
 +
 +
                                <figure class="postImg waves-effect">
 +
                                    <img src="https://static.igem.org/mediawiki/2016/c/c4/T--Ionis_Paris--AtthelabFig10.png" alt="">
 +
                                </figure>
 +
 +
 +
 +
<p><i>Figure 10: B0014 double terminator structure (Source <a href="http://parts.igem.org/Part:BBa_B0014">here</a>)</i></p>
  
 
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Latest revision as of 20:51, 19 October 2016

Principle OF THE BIOBRICK DESIGN IN AN IGEM CONTEXT

Biobrick definition


In the context of iGEM, our genetic circuit, encoded as a plasmid, is defined as a BioBrick. The different elements of the genetic circuit contribute to the function of the BioBrick. In the iGEM registry, we can distinguish 2 components that compose a plasmid: the plasmid backbone and the BioBrick part (see Figure 2).


Figure 1: General structure of a BioBrick (source here )


For the assembly of our biobrick we use the BioBrick RFC[10] assembly standard because it is the standard of the IGEM competition and most of the parts available on the registry match this standard. The BioBrick RFC[10] assembly standard is based on the use of a prefix and a suffix placed at the extremities of each part to be assembled in order to obtain standard BioBricks that are compatible and thus can be easily assembled.


Biobrick RFC[10] assembly standard

  • Prefix and suffix

    • Prefix and suffix provide a method to obtain standard genetic construction. Their exact sequences are available in Figure 2. Each one includes two different restriction sites:

    • - EcoRI and XbaI in the prefix

    • - SpeI and PstI in the suffix

    For protein coding regions (that starts with ATG), there is an adapted prefix.

    Figure 2: Prefix and suffix sequences


    All components of the genetic circuit are added to the system with these prefix and suffix. Once added to the system, in order to be compatible with the RFC[10] standard, a part does not have to contain these four restriction sites, they have to be unique to the prefix and suffix.

  • Assembling method

    • Figure 3: Assembling method


  • Scar

    • The use of this assembling method leaves a scar between the 2 assembled parts, with the following DNA sequence:
    - 5' [part A] TACTAGAG [part B] 3’. When using the alternate prefix in the case of the assembling of a RBS with a protein coding region, the scar DNA sequence would be:
    - 5' [part A] TACTAG [part B, that starts with ATG] 3’.

    The only disadvantage of the RFC[10] assembly standard is the impossibility to make fusion proteins. The 6bp scar includes a stop codon and the 8bp scar includes a frame-shift and a stop codon. The alternative to this problem is to use a scar-less assembly method or DNA synthesis.


    Biobrick part

    The biobrick part is composed of the sequence located between the prefix and the suffix. This sequence includes the devices that will perform the given functions in the cell (i.e protein production).
    Each device is a composite part, which means it is composed of several basic parts assembled together to ensure a specific function. A basic part is a single functional unit coding for a basic biological function and cannot be split into smaller units. Promoters, coding sequences or RBSs are examples of basic parts. Two parts make up our device: one in charge of the XylR protein synthesis and one in charge of theGaussia luciferase synthesis.


    Plasmid backbone

    The plasmid backbone is the sequence that begins with the suffix and ends with the prefix. The plasmid backbone mainly serves as support for the propagation of the biobrick part. It includes the origin of replication and the antibiotic resistance marker.
    The presence of the antibiotic resistance marker in the backbone allows the selection of only clones that incorporate the plasmid thanks to an antibiotic in the medium. Clones that do not incorporate the plasmid do not have the antibiotic resistance and thus cannot survive in the selective medium. In the iGEM competition, a set of 4 linearized plasmid backbones is sent to each team: pSB1A3, pSB1C3, pSB1K3.m1, and pSB1T3. They respectively include these 4 antibiotics: Ampicillin, Chloramphenicol, Kanamycin and Tetracycline.


    PRINCIPLE AND FUNCTIONING OF OUR "BIOSENSOR" PLASMID


    The biosensor cell contains a genetic circuit, located on a plasmid support, allowing the expression of genes involved in the detection of the pollutant. The Pr promoter is a constitutive promoter driving the transcription of the XylR gene, coding for the XylR protein. The XylR protein, a transcriptional regulatory protein for the Pu promoter, is activated by aromatic hydrocarbons that carry a methyl group (like toluene and xylene). In our biosensor, the Pu promoter allows the transcription of the bioluminescent reporter gene GLuc, coding for the Gaussia luciferase. When this enzyme reacts with its substrate, a substance called the Coelenterazine, it emits luminescence.

    Figure 4: The biosensor mechanism

    Plasmid map

    For the construction of our plasmid, we selected parts that are RFC[10] compatible. In Figure 4 below, the map of our plasmid is represented in a simplified way, and is composed of the pSB1C3 backbone and the biosensor part.

    Figure 4: Our plasmid map

    Details on the used parts


    Chassis

    We chose to use Escherichia Coli strain DH5α as chassis for our plasmid. Indeed, this bacterium grows easily and has several mutations that make it an excellent choice for cloning procedures with a high efficiency transformation. All our parts are optimized for E. Coli. Moreover, E. Coli is a model organism, entirely sequenced.


    Plasmid Backbone

    We selected the pSB1C3 plasmid, a high copy number assembly plasmid, as a backbone of 2070 pb, because it is the most used type of backbone to assemble BioBricks. This plasmid backbone includes a high copy replication origin that allows a high copy number per cell which facilitates DNA purification. All the plasmid backbone used for the competition are provided with a default insert: the ccdb gene. This gene can be used as a marker to establish whether the plasmid backbone have been successfully digested. If not, the cell death gene will remain in the plasmid backbone and kill the kill the transformed bacteria. The ccdb gene ensures to not keep cells transformed with the uncut plasmid during the assembly of two BioBrick parts.
    As already specified, the presence of the antibiotic resistance marker in the backbone allows the selection of clones that incorporated the plasmid.
    This plasmid is also the designated plasmid backbone required for the registry shipping during the IGEM competition.

    Figure 6: Standard structure of high copy number assembly plasmid backbone. (source here)

    The pSB1C3 plasmid backbone confers Chloramphenicol resistance and includes the pUC19-derived pMB1, replication origin with a copy number of 100-300 per cell. The map of pSB1C3 plasmid is available below in Figure 2.

    Figure 7: Map of the pSB1C3 plasmid (source here)

    Constitutive Pr promoter

    The Pr promoter is found in the toluene recognition system and is composed of 410 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723018.

    We chose to use this promoter because it is the specific promoter for the XylR gene. This promoter is naturally constitutive. It leads to the permanent production of the XylR protein. Indeed, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein should be present in sufficient amount.


    XylR gene

    The 1704 bp XylR gene, encodes for the XylR protein and is regulated by the Pr promoter in its native context. This gene is available on the iGEM Registry of Standard Biological Parts (BBa_K1834844). The XylR that we designed for our biosensor is a bit different because it is optimized for E.Coli DH5-Alpha and for IDT synthesis. .

    The XylR protein, mined from Pseudomonas putida, is involved in the transcriptional activation of the toluene recognition system. This regulatory protein allows the detection of aromatic hydrocarbons that carry a methyl group, i.e. xylene, toluene and 1-chloro-3-methyl-benzene. The A domain of the XylR protein (sensing domain), binds to the pollutant molecule. This leads to the formation of a tetramer. The C domain is involved in the dimerization of XylR, which is ATP dependent. The made up tetramer acts as an activator transcriptional factor for the Pu promoter through the DNA binding D domain.


    Figure 8: The XylR CDS structure

    Pu promoter

    Pu is a promoter found in the toluene recognition system and is composed of 320 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723020.
    We chose to use this promoter because of its sensibility to the transcriptional regulator XylR bound to xylene, toluene or 1-chloro-3-methyl-benzene.


    GLuc gene

    This gene is found in a well-known organism, the copepod Gaussia princeps. It encodes for the Gaussia luciferase enzyme, also known as GLuc, which is involved in a bioluminescence process. This enzyme degrades its substrate, coelenterazine, into a product, celenteramide. With an optimal substrate level, this step produces energy in the form of light that can be detected with a fixed spectrophotometer at 488nm.

    We chose to use the GLuc-His part, a gene of 522 bp, available on the iGEM registry at the (BBa_K1732027) which codes for the Gaussia luciferase followed by 6 histidines and optimized it for E.coli. In our plasmid, this gene is positioned after an inducible promoter, the Pu promoter, to report the activation of the toluene recognition system.
    The Gaussia luciferase needs the addition of substrate to ensure its activity because this molecule is not synthetized by our biosensor. Therefore, in the laboratory, luciferase substrate can be added at the same time in each sample ensuring that every measurement will be taken at the same time. This allow a better consistency between our different results. Also, due to its secreted form, lysing cells in order to assay GLuc activity is not necessary.

    The Gaussia luciferase is an ideal reporter gene because of its stability at high temperature thanks to disulfide bonds and because it has extremely high activity in light production for very sensitive assays. When compared to Firefly and Renilla luciferase, GLuc generates over 1000-fold higher bioluminescent signal intensity[1][2]. The NanoLuc has an activity a little higher but this luciferase is very recent and thus less characterized.

    Advantages of luminescence, over fluorescence, include the absence of background noise, the amplification of signal and a high dynamic range that spans many orders of magnitude. Indeed, since light emission depends strictly on the chemical reaction between the substrate and the luciferase, there is no background noise originating from the sample [3]. Furthermore, the turnover of the light reaction significantly amplifies the reporter signal. Even though bioluminescence is currently used mainly for transcription study and cell imaging, this method become increasingly popular for quantitative analysis.

    Even though bioluminescence is currently used mainly for transcription study and cell imaging, this method become increasingly popular for quantitative analysis. [3] For more information about bioluminescence and the Gaussia luciferase, click here !


    [1] Inouye, S., Sahara-Miura, Y., Sato, J., Iimori, R., Yoshida, S., and Hosoya, T. (2013). Expression, purification and luminescence properties of coelenterazine-utilizing luciferases from Renilla, Oplophorus and Gaussia: Comparison of substrate specificity for C2-modified coelenterazines. Protein Expression and Purification 88, 150–156.
    [2] S. Inouye, Y. Sahara, Identification of two catalytic domains in a luciferase secreted by the copepod Gaussia princeps, Biochem. Biophys. Res. Commun. 365 (2008) 96–101
    [3]Wood, K (2011), The bioluminescence advantage, laboratorynews, available on: http://www.labnews.co.uk/features/the-bioluminescence-advantage-13-09-2011/

    Elowitz RBS

    In our plasmid, all genes, XylR and GLuc, are preceded by a sequence that can easily affect the rate of translation: the Ribosome binding Sequence (RBS).

    There are different types of RBS, depending on their binding strength:

  • Strong RBS:

    • The Elowitz RBS is the stronger RBS with an efficiency of 1.0. This RBS is a sequence of 12 bp and is available on the iGEM registry at this ID access: BBa_B0034.
    An other strong RBS, based on Ron Weiss thesis, is available on the iGEM registry at this ID access: BBa_B0030. This RBS, a sequence of 15 bp, has an efficiency of 0.6.
    This type of RBS allows a high translation rate that leads to a high protein production. However, a too high production can be harmful for the organism because a lot of proteins could be unfolded or misfolded.

  • Middle RBS:

    • An example of Middle RBS is available on the iGEM registry at this ID access: BBa_B0032. This RBS, a sequence of 13 bp derivative of BBa_B0030, has an efficiency of 0.3.

  • Weak RBS:

    • The weaker RBS is a sequence of 11 bp with an efficiency of 0.01, derivative of BBa_B0030. This RBS is available on the iGEM registry at this ID access: BBa_0033.
    An other weak RBS is available on the iGEM registry at this ID access: BBa_B0031. This RBS, a sequence of 14 bp derivative of BBa_B0030, has an efficiency of 0.07.


    In our project, we chose to use the stronger RBS, the Elowitz RBS (BBa_B0034), in order to have a maximal production rate. Indeed, as we already specified, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein has to be present in an enough amount and the Gaussia luciferase has to be produced rapidly in an amount that is proportional to the pollutant amount. This allows a luminescent response corresponding to the pollutant rate.

    Double terminator

    A terminator is a genetic part placed at the end of a gene, in order to end transcription thanks to a stop codon. Several types of terminators exists but the most used are forward terminators. In general, some RNA polymerases will continue the transcription after the terminator, thus the terminator efficiency is not 100% in the most cases.
    In order to increase the terminator efficiency in our plasmid we chose to use a double terminator. We selected two different double terminators that we have to test.
    The first one of 129 bp, consisting of BBa_B0010 and BBa_B0012 as shown in Figure 4, available on the iGEM registry at this ID access: BBa_B0015. It is the most used terminator for forward transcription with a forward-efficiency of 0,984 according to measurements done by Caitlin Conboy, and of 0,97 according to measurements done by Jason Kelly. Procedures used for these measurements are explained in the IGEM registry.

    Figure 9: B0015 double terminator structure (Source here)

    The second one of 95 bp, consisting of BBa_B0011 and BBa_B0012 as shown in Figure 9, available on the iGEM registry at this ID access: BBa_B0014. It is a bidirectional terminator with a forward-efficiency of 0,604 according to measurements done by Caitlin Conboy and of 0,96 according to measurements done by Jason Kelly, and with a reverse-efficiency of 0,86 according to measurements done by Jason Kelly.

    Figure 10: B0014 double terminator structure (Source here)