Difference between revisions of "Team:Freiburg/Project/Cellfree Expression"

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<h1 class="sectionedit1">Methodology Cell-Free Expression</h1>
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<h1>Cell-Free Expression</h1>
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<h3 class="sectionedit2">Why Do We Use Cell-Free Expression?</h3>
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<h2>Why Do We Use Cell-Free Expression?</h2>
  
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<strong> Cell-based</strong> protein expression is a well established method to obtain large amounts of a target protein. It enables accumulation and purification of the protein in quantities sufficient for various <i>in vitro</i> applications.  
 
<strong> Cell-based</strong> protein expression is a well established method to obtain large amounts of a target protein. It enables accumulation and purification of the protein in quantities sufficient for various <i>in vitro</i> applications.  
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For translating DNA templates into protein microarrays in a microfluidic set-up, cell-free expression is the method of choice. This system is capable of expressing many different sequences at once. Additionally, the microfluidic setup provides the opportunity to constantly supplement the expression. Replacing depleted components, like dNTPs, amino acids or energy sources like creatine phosphate, allows higher protein yields.  
 
For translating DNA templates into protein microarrays in a microfluidic set-up, cell-free expression is the method of choice. This system is capable of expressing many different sequences at once. Additionally, the microfluidic setup provides the opportunity to constantly supplement the expression. Replacing depleted components, like dNTPs, amino acids or energy sources like creatine phosphate, allows higher protein yields.  
 
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<h3 class="sectionedit4">Basics of Cell-Free Expression</h3>
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<h2>Basics of Cell-Free Expression</h2>
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<h3>The Components</h3>
  
 
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                       <p><strong>Figure 1: Basic Components of a Cell-Free Expression Mix.</strong> A standard cell-free expression systems consist of a DNA template, the cell extract and additives containing all the components needed for energy regeneration, buffering and generation of the protein. </p>
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                       <p><strong>Figure 1: Basic Components of a Cell-Free Expression Mix.</strong> A standard cell-free expression systems consists of a DNA template, the cell extract and additives containing all the components needed for energy regeneration, buffering and generation of the protein. </p>
 
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<li>a reaction solution containing the transcriptional and translational molecular machineries </li>
 
<li>a reaction solution containing the transcriptional and translational molecular machineries </li>
 
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Cell extracts supply the reaction with most of the molecules, including:
 
Cell extracts supply the reaction with most of the molecules, including:
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<p>
Regular cell lysate already contains most of the components needed for cell-free expression. The machineries that usually conduct the translation and transcription of various proteins in the organism can be 'reprogrammed' to produce only the protein of choice. Our building blocks, the amino acids and <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">NTPs</a>, are already present but are also supplemented to raise the efficiency. As the normal energy regeneration system is missing in a cell lysate, an artificial one is added; e.g. here we use creatine phosphokinase.  
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Regular cell lysate already contains most of the components needed for cell-free expression. The machineries that usually conduct the translation and transcription of various proteins in the organism can be 'reprogrammed' to produce only the protein of choice. Our building blocks, the amino acids and NTPs, are already present but are also supplemented to raise the efficiency. As the normal energy regeneration system is missing in a cell lysate, an artificial one is added; e.g. here we use creatine phosphokinase.  
 
Other components present in a cell-free expression mix buffer the sensitive system and imitate the cytosolic environment.   
 
Other components present in a cell-free expression mix buffer the sensitive system and imitate the cytosolic environment.   
 
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                       <p><strong>Figure 2: Prokaryotic vs eukaryotic cell-free expression.</strong> text. This is a test if  more text will eventually make this text box wider and the page look better.</p>
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                       <p><strong>Figure 2: Prokaryotic vs eukaryotic cell-free expression.</strong></p>
 
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<h3>The Reaction</h3>
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                       <p><strong>Figure 3: Batch vs Dialysis mode.</strong> text. This is a test if  more text will eventually make this text box wider and the page look better.</p>
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                       <p><strong>Figure 3: Batch vs Dialysis mode.</strong> </p>
 
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<p>
 
<p>
There are two ways of performing a cell-free reaction. In batch reactions, transcription and translation are carried out in a reaction vessel containing all necessary components. Due to different reasons like fast depletion of energy supply, degradation of components (e.g. nucleotides), and decreasing concentrations of free Mg<sup>2+</sup>-ions, the reaction in the batch system usually reaches a plateau after about 1-2 hours.
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There are two ways of performing a cell-free reaction. In <b>batch reactions</b>, transcription and translation are carried out in a reaction vessel containing all necessary components. Due to different reasons like fast depletion of energy supply, degradation of components (e.g. nucleotides), and decreasing concentrations of free Mg<sup>2+</sup>-ions, the reaction in the batch system usually reaches a plateau after about 1-2 hours.
 
<br>
 
<br>
In dialysis mode, the cell-free transcription and translation reaction is carried out in a small reaction chamber that is separated by a dialysis membrane from a 10-20x larger reservoir containing low molecular weight reagents. The reservoir supplies the reaction chamber with ions, energy substrates, nucleotides and amino acids. In turn, the low molecular weight by-products are efficiently diluted via the membrane from the reaction chamber into the reservoir. This setup will drive the reaction longer (usually 20-24 hrs) and results in higher levels of produced protein.  
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In <b>dialysis mode</b>, the cell-free transcription and translation reaction is carried out in a small reaction chamber that is separated by a dialysis membrane from a 10-20x larger reservoir containing low molecular weight reagents. The reservoir supplies the reaction chamber with ions, energy substrates, nucleotides and amino acids. In turn, the low molecular weight by-products are efficiently diluted via the membrane from the reaction chamber into the reservoir. This setup will drive the reaction longer (usually 20-24 hrs) and results in higher levels of produced protein.  
 
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<h3>The Design of the DNA Template</h3>
 
<p>
 
<p>
The design of the DNA template is one more aspect that deserves attention.
 
</br>
 
 
In general, it is possible to use RNA, plasmids, or linear templates (e.g. PCR products). In all cases, the structural design of the DNA or RNA is of great importance for the yield and quality of the protein produced.
 
In general, it is possible to use RNA, plasmids, or linear templates (e.g. PCR products). In all cases, the structural design of the DNA or RNA is of great importance for the yield and quality of the protein produced.
In bacterial <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">5'-UTRs</a> the optimization can be achieved by placing the <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">Shine-Dalgarno (SD)</a> sequence at an optimal distance, typically eight nucleotides, from the AUG start codon. The SD sequence interacts with the 3'-end of 16S ribosomal RNA (rRNA) that is part of the small ribosomal (30S) subunit, to facilitate initiation. Furthermore, the integration of an A/U-rich enhancer sequence further upstream allows the SD sequence to interact more effectively with the rRNA.  
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In bacterial 5'-UTRs the optimization can be achieved by placing the Shine-Dalgarno (SD) sequence at an optimal distance, typically eight nucleotides, from the AUG start codon. The SD sequence interacts with the 3'-end of 16S ribosomal RNA (rRNA) that is part of the small ribosomal (30S) subunit, to facilitate initiation. Furthermore, the integration of an A/U-rich enhancer sequence further upstream allows the SD sequence to interact more effectively with the rRNA.  
 
Another attempt in this context is the use of different tags to enhance expression, as reported by Haberstock et al. (2012)<sup><a class="fn_top" href="#fn__3" id="fnt__3" name="fnt__3">3)</a></sup>.  
 
Another attempt in this context is the use of different tags to enhance expression, as reported by Haberstock et al. (2012)<sup><a class="fn_top" href="#fn__3" id="fnt__3" name="fnt__3">3)</a></sup>.  
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<br>
 
In eukaryotes, the Internal Ribosome Entry Site (IRES) is a highly structured element found within viral mRNA that is able to induce eukaryotic initiation. This solves the problem of ineffective capping, which presents a major restriction of high production. For example, the IRES of the <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">Cricket Paralysis Virus (CrPV)</a> showed the ability to increase expression substantially across several species. <sup><a class="fn_top" href="#fn__4" id="fnt__4" name="fnt__4">4)</a></sup>
 
In eukaryotes, the Internal Ribosome Entry Site (IRES) is a highly structured element found within viral mRNA that is able to induce eukaryotic initiation. This solves the problem of ineffective capping, which presents a major restriction of high production. For example, the IRES of the <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">Cricket Paralysis Virus (CrPV)</a> showed the ability to increase expression substantially across several species. <sup><a class="fn_top" href="#fn__4" id="fnt__4" name="fnt__4">4)</a></sup>
 
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<h3 id="diamix" class="sectionedit3">Our DiaMIX</h3>
 
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<h2 id="diamix" class="sectionedit3">Our DiaMIX</h2>
  
 
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                       <p><strong>Figure 4: <i>E. coli </i> lysate production. </strong> Add procedure description.</p>
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                       <p><strong>Figure 4: <i>E. coli </i> lysate production. </strong></p>
 
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<p>  
 
<p>  
To produce the DiaMIX we used the <i>E. coli</i> strain <a href="https://2015.igem.org/Team:Freiburg/Project/Coli_Strains" target="blank">BL21</a>, as it is carrying a gene coding for the T7 RNA polymerase, which facilitates an improved expression of proteins. The cells were induced with IPTG prior to further treatment to initialize T7 polymerase expression, therefore allowing a high rate of protein synthesis.  
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For producing the DiaMIX we used the <i>E. coli</i> strain <a href="https://2015.igem.org/Team:Freiburg/Project/Coli_Strains" target="blank">BL21</a>, as it is carrying a gene coding for the T7 RNA polymerase, which facilitates an improved expression of proteins. The cells were induced with IPTG prior to further treatment to initialize T7 polymerase expression, therefore allowing a high rate of protein synthesis.  
 
Since all the coding sequences used in our project were manufactured synthetically, the <i>E. coli</i> BL21 cells were additionally transformed with the plasmid <a href="https://2015.igem.org/Team:Freiburg/Labjournals/Plasmids>pRARE2</a>  containing the coding sequence of tRNAs for the translation of rare codons (AGA, AGG, AUA, CUA, GGA, CCC and CGG). According to an <a class=Wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/Cellfex" title="cellfree_protocol" target="blank">optimized protocol</a> adapted from the <a class="media" href="http://www.embl.de/" target="_blank" title="EMBL" target="blank">European Molecular Biology Lab</a> (EMBL) Heidelberg, the lysate was prepared from <i>E. coli</i> BL21 cells, frozen in liquid nitrogen and afterwards stored at -80°C.  
 
Since all the coding sequences used in our project were manufactured synthetically, the <i>E. coli</i> BL21 cells were additionally transformed with the plasmid <a href="https://2015.igem.org/Team:Freiburg/Labjournals/Plasmids>pRARE2</a>  containing the coding sequence of tRNAs for the translation of rare codons (AGA, AGG, AUA, CUA, GGA, CCC and CGG). According to an <a class=Wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/Cellfex" title="cellfree_protocol" target="blank">optimized protocol</a> adapted from the <a class="media" href="http://www.embl.de/" target="_blank" title="EMBL" target="blank">European Molecular Biology Lab</a> (EMBL) Heidelberg, the lysate was prepared from <i>E. coli</i> BL21 cells, frozen in liquid nitrogen and afterwards stored at -80°C.  
 
This lysate contains the whole transcription and translation apparatus of the cell, allowing successful expression of proteins from DNA templates.
 
This lysate contains the whole transcription and translation apparatus of the cell, allowing successful expression of proteins from DNA templates.
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To verify the functionality of our system, we <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Results#own_mix_anchor" target="blank">compared it</a> to a commercially available kit.
 
To verify the functionality of our system, we <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Results#own_mix_anchor" target="blank">compared it</a> to a commercially available kit.
 
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<h2>Verification of Protein Expression</h2>
<h3 class="sectionedit4">Verification of Protein Expression</h3>
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<p>
 
<p>
 
To validate whether the expression in the DiaMIX yields correctly folded proteins, we used various methods like <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/MesurementGFP" target="blank">fluorescence measurements</a>, <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/LUC" target="blank">luciferase assays</a> and <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/Western_Blot" target="blank">Western Blots</a>. Our first approach was the expression of <a href="https://2015.igem.org/Team:Freiburg/Results/Cellfree" target="blank">GFP</a>, which can be detected via its fluorescence. We used a plasmid template (LINK) that was added to the self-prepared expression mix. The expression was then visualized via a microplate reader measurement. Measurement of the increase in emitted light at a wavelength of 520 nm monitored the progression of expression. We verified the results with a Western Blot using an antibody against GFP.</br>
 
To validate whether the expression in the DiaMIX yields correctly folded proteins, we used various methods like <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/MesurementGFP" target="blank">fluorescence measurements</a>, <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/LUC" target="blank">luciferase assays</a> and <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Protocols/Western_Blot" target="blank">Western Blots</a>. Our first approach was the expression of <a href="https://2015.igem.org/Team:Freiburg/Results/Cellfree" target="blank">GFP</a>, which can be detected via its fluorescence. We used a plasmid template (LINK) that was added to the self-prepared expression mix. The expression was then visualized via a microplate reader measurement. Measurement of the increase in emitted light at a wavelength of 520 nm monitored the progression of expression. We verified the results with a Western Blot using an antibody against GFP.</br>
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<h2>Step by Step Validation</h2>
<h3 class="sectionedit5">Step by Step Validation</h3>
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<p>
 
Since we aimed at using cell-free expression in combination with the DiaCHIP, we decided to validate the <a href="https://2015.igem.org/Team:Freiburg/Project/System" target="blank">process</a> in individual steps.  
 
Since we aimed at using cell-free expression in combination with the DiaCHIP, we decided to validate the <a href="https://2015.igem.org/Team:Freiburg/Project/System" target="blank">process</a> in individual steps.  
 
Starting with cell-free expression in a tube, we spotted the produced proteins on iRIf slides to check whether we detect their interaction with the respective antibodies.
 
Starting with cell-free expression in a tube, we spotted the produced proteins on iRIf slides to check whether we detect their interaction with the respective antibodies.
In the next step, we spotted our expression system on the slide without starting the reaction beforehand. Then we added the plasmid template, an let the mix incubate on the slide. The proteins produced in the cell-free expression should directly bind to the specific surface since they carry the respective tag.  
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In the next step, we spotted our expression system on the slide without starting the reaction beforehand. Then we added the plasmid template and let the mix incubate on the slide. The proteins produced by cell-free expression should directly bind to the specific surface since they carry the respective tag.  
 
Finally, we performed a cell-free expression from immobilized DNA in the finished setup of glass and PDMS slide.  
 
Finally, we performed a cell-free expression from immobilized DNA in the finished setup of glass and PDMS slide.  
 
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<h4>Immobilizing DNA on PDMS</h4>
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<h3>Immobilizing DNA on PDMS</h3>
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<p>
 
<p>
 
One of the core components of the DiaCHIP is the copying mechanism that allows production of a protein microarray from a DNA template. In summary, we established a <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Project/Cellfree_Expression" title="cellfree" target="blank">cell-free expression system</a> that can be used to translate proteins from DNA immobilized on a PDMS slide.  
 
One of the core components of the DiaCHIP is the copying mechanism that allows production of a protein microarray from a DNA template. In summary, we established a <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Project/Cellfree_Expression" title="cellfree" target="blank">cell-free expression system</a> that can be used to translate proteins from DNA immobilized on a PDMS slide.  
 
<br>
 
<br>
The first step needed for copying DNA arrays is to genetically fuse antigen coding sequences to a His tag that is used for surface immobilization later on. The whole expression cassette including promoter and terminator regions is amplified by PCR using an amino-labeled reverse primer. Via this amino group, the DNA is immobilized on an activated PDMS surface. The forward primer used for this PCR is labeled with <a class=wikilink1" href="https://2015.igem.org/Team:Freiburg/Glossary" title="glossary">Cy3</a>.  
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The first step needed for copying DNA arrays is to genetically fuse antigen coding sequences to a His-Tag that is used for surface immobilization later on. The whole expression cassette including promoter and terminator regions is amplified by PCR using an amino-labeled reverse primer. Via this amino group, the DNA is immobilized on an activated PDMS surface. In order to check for successful binding, the forward primer used for this PCR is labeled with the dye Cy3.  
 
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<h4>Spotting of Expressed GFP on Slide</h4>
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<h3>Spotting of Expressed GFP on Slide</h3>
 
<p>
 
<p>
 
To test whether our cell-free expression system reaches protein concentration high enough for detection with iRIf, we spotted cell-free expressed GFP on iRIf slides. We then measured the binding of anti-GFP to the cell-free expressed GFP to assess the amount of expressed protein and its folding status.
 
To test whether our cell-free expression system reaches protein concentration high enough for detection with iRIf, we spotted cell-free expressed GFP on iRIf slides. We then measured the binding of anti-GFP to the cell-free expressed GFP to assess the amount of expressed protein and its folding status.
 
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<h4>On-slide Expression of GFP</h4>
 
<h4>On-slide Expression of GFP</h4>
  
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To estimate the specificity of our surface, we evaluated the proportion of cell-free expressed GFP that bound to the surface. We determined the amount of unspecific binding of non-target proteins to the surface with iRIf using anti-GFP antibodies. Unspecific binding of proteins present in the DiaMIX would lead to decrease in signal, whereas a highly specific surface only binds GFP and thus shows a strong signal at the GFP spot.
 
To estimate the specificity of our surface, we evaluated the proportion of cell-free expressed GFP that bound to the surface. We determined the amount of unspecific binding of non-target proteins to the surface with iRIf using anti-GFP antibodies. Unspecific binding of proteins present in the DiaMIX would lead to decrease in signal, whereas a highly specific surface only binds GFP and thus shows a strong signal at the GFP spot.
 
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<h4>In-chamber Expression of GFP</h4>
 
<h4>In-chamber Expression of GFP</h4>
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<h3 class="sectionedit6">Cell-free Expression of Antigens</h3>
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<h2>Cell-free Expression of Antigens</h2>
  
 
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An important goal was to express antigens with the required tags in a concentration and folding state that suffices for an iRIf measurement. Here we focused on a <a href="https://2015.igem.org/Team:Freiburg/Project/Diseases#Tetanus_anchor" target="blank"><i>C. tetani</i></a> epitope flagged by a double <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">His and a Spy-tag</a>. For cloning of this construct we used a newly designed <a href="https://2015.igem.org/Team:Freiburg/Methods/Cloning" target="blank">cloning site</a> and a vector that we had optimized for cell-free expression.</br>
 
An important goal was to express antigens with the required tags in a concentration and folding state that suffices for an iRIf measurement. Here we focused on a <a href="https://2015.igem.org/Team:Freiburg/Project/Diseases#Tetanus_anchor" target="blank"><i>C. tetani</i></a> epitope flagged by a double <a href="https://2015.igem.org/Team:Freiburg/Glossary" target="blank">His and a Spy-tag</a>. For cloning of this construct we used a newly designed <a href="https://2015.igem.org/Team:Freiburg/Methods/Cloning" target="blank">cloning site</a> and a vector that we had optimized for cell-free expression.</br>
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<h3 class="sectionedit7">Testing Different Conditions</h3>
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<h2>Testing Different Conditions</h2>
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To identify the optimal DNA concentration that results in a maximum protein expression, we tested different conditions. For this experiment, we used DNA coding for the enzyme luciferase. The protein concentration could then be measured using the <a href="https://2015.igem.org/Team:Freiburg/Protocols/LUC" target="blank" target="blank">luciferase assay</a>.</br>
 
To identify the optimal DNA concentration that results in a maximum protein expression, we tested different conditions. For this experiment, we used DNA coding for the enzyme luciferase. The protein concentration could then be measured using the <a href="https://2015.igem.org/Team:Freiburg/Protocols/LUC" target="blank" target="blank">luciferase assay</a>.</br>
 
Another component whose concentration is crucial for optimal cell-free expression is magnesium. To evaluate the effects of different magnesium concentrations, we started multiple cell-free expression mixes using different magnesium starting concentrations. Magnesium was added to the mix in the form of magnesium acetate. </br>
 
Another component whose concentration is crucial for optimal cell-free expression is magnesium. To evaluate the effects of different magnesium concentrations, we started multiple cell-free expression mixes using different magnesium starting concentrations. Magnesium was added to the mix in the form of magnesium acetate. </br>
 
After expression, a luciferase assay could visualize the protein concentration in the different reaction mixes.
 
After expression, a luciferase assay could visualize the protein concentration in the different reaction mixes.
 
 
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Revision as of 03:00, 18 September 2015

""

(MU) Habe es nun mal durchgekuckt und einige Saetze geaendert.
Die Sachen muessen auf jedenFall noch ergaenzt werden:
Der Titel Methodology Cell-Free Expression - da muss noch irgendwas gemacht werden.
pRARE2 link (done LK)
GFP template link
Alle Figs haben falsche Nummern (also fast alle). (done LK)
Dann auch den Text entsprechend aendern, dass er sich auf die richtigen figs bezieht.
zweite und dritte Fig. 1 Legenden
Fig. 6 Tetanus Antigen, da stimmt was nicht am Bild, das ist Tetanus. (done LK)

(LK) Labjournal-Links, im Text auf figures eingehen.

Cell-Free Expression

Why Do We Use Cell-Free Expression?

Cell-based protein expression is a well established method to obtain large amounts of a target protein. It enables accumulation and purification of the protein in quantities sufficient for various in vitro applications. Nevertheless, it is a tedious task to generate all the genetically modified organisms if many different proteins need to be expressed. Additionally, purification cannot be performed with a generalized protocol, but usually requires separate optimization for each protein.
Cell-free expression offers a possibility to overcome several challenges of conventional protein expression and has many advantages, in particular for our project.1)
Generally speaking, it saves a lot of time and money to avoid the generation of genetically modified organisms for every protein. Suitable DNA sequences are only constructed once, for example by custom synthesis by a company, and can be stored until needed. At the purification step, cell-free expression avoids the need for cell lysis and therefore circumvents this harsh procedure, thus preserving the integrity of the protein. In cell-based expression, too strong induction often results in aggregation of protein, rendering it non-functional. This risk is minimized by using cell-free expression, since the expressed protein is dispersed in a far larger volume than the intracellular space.2)
For translating DNA templates into protein microarrays in a microfluidic set-up, cell-free expression is the method of choice. This system is capable of expressing many different sequences at once. Additionally, the microfluidic setup provides the opportunity to constantly supplement the expression. Replacing depleted components, like dNTPs, amino acids or energy sources like creatine phosphate, allows higher protein yields.

Basics of Cell-Free Expression

The Components

Figure 1: Basic Components of a Cell-Free Expression Mix. A standard cell-free expression systems consists of a DNA template, the cell extract and additives containing all the components needed for energy regeneration, buffering and generation of the protein.

Two basic components are needed to conduct in vitro protein expression:

  • the genetic template (mRNA or DNA) encoding the target protein
  • a reaction solution containing the transcriptional and translational molecular machineries

Cell extracts supply the reaction with most of the molecules, including:

  • RNA polymerases for mRNA transcription
  • ribosomes for polypeptide translation
  • tRNA and amino acids
  • enzymatic cofactors and an energy source
  • cellular components essential for proper protein folding

Regular cell lysate already contains most of the components needed for cell-free expression. The machineries that usually conduct the translation and transcription of various proteins in the organism can be 'reprogrammed' to produce only the protein of choice. Our building blocks, the amino acids and NTPs, are already present but are also supplemented to raise the efficiency. As the normal energy regeneration system is missing in a cell lysate, an artificial one is added; e.g. here we use creatine phosphokinase. Other components present in a cell-free expression mix buffer the sensitive system and imitate the cytosolic environment.

Figure 2: Prokaryotic vs eukaryotic cell-free expression.

Besides bacteria-based systems, there are several other possibilities with specific advantages and disadvantages. An E. coli system convinces with easiness, cost-efficiency and high yield. However, for the production of complex eukaryotic proteins, it might not be the best option since eukaryotic cell-free lysates provide post-translational modifications such as core glycosylation or phosphorylation, and natural membrane components (e.g. microsomes) for membrane protein insertion. These systems are based on wheat germ embryos, rabbit reticulocytes, insect cells or other animal and human cell lines.



The Reaction

Figure 3: Batch vs Dialysis mode.

There are two ways of performing a cell-free reaction. In batch reactions, transcription and translation are carried out in a reaction vessel containing all necessary components. Due to different reasons like fast depletion of energy supply, degradation of components (e.g. nucleotides), and decreasing concentrations of free Mg2+-ions, the reaction in the batch system usually reaches a plateau after about 1-2 hours.
In dialysis mode, the cell-free transcription and translation reaction is carried out in a small reaction chamber that is separated by a dialysis membrane from a 10-20x larger reservoir containing low molecular weight reagents. The reservoir supplies the reaction chamber with ions, energy substrates, nucleotides and amino acids. In turn, the low molecular weight by-products are efficiently diluted via the membrane from the reaction chamber into the reservoir. This setup will drive the reaction longer (usually 20-24 hrs) and results in higher levels of produced protein.

The Design of the DNA Template

In general, it is possible to use RNA, plasmids, or linear templates (e.g. PCR products). In all cases, the structural design of the DNA or RNA is of great importance for the yield and quality of the protein produced. In bacterial 5'-UTRs the optimization can be achieved by placing the Shine-Dalgarno (SD) sequence at an optimal distance, typically eight nucleotides, from the AUG start codon. The SD sequence interacts with the 3'-end of 16S ribosomal RNA (rRNA) that is part of the small ribosomal (30S) subunit, to facilitate initiation. Furthermore, the integration of an A/U-rich enhancer sequence further upstream allows the SD sequence to interact more effectively with the rRNA. Another attempt in this context is the use of different tags to enhance expression, as reported by Haberstock et al. (2012)3).
In eukaryotes, the Internal Ribosome Entry Site (IRES) is a highly structured element found within viral mRNA that is able to induce eukaryotic initiation. This solves the problem of ineffective capping, which presents a major restriction of high production. For example, the IRES of the Cricket Paralysis Virus (CrPV) showed the ability to increase expression substantially across several species. 4)

Our DiaMIX

We developed a low-budget protocol for expressing proteins in a prokaryotic cell-free expression system based on an Escherichia coli lysate. Most of the established cell-free expression systems are based on rabbit reticulocytes, wheat germ cells, insect cells or E. coli cells. Due to the prokaryotic origin of most of the proteins expressed during our project, we decided to base our low-budget prokaryotic cell-free expression system, the DiaMIX, on an E. coli cell culture.


Figure 4: E. coli lysate production.

For producing the DiaMIX we used the E. coli strain BL21, as it is carrying a gene coding for the T7 RNA polymerase, which facilitates an improved expression of proteins. The cells were induced with IPTG prior to further treatment to initialize T7 polymerase expression, therefore allowing a high rate of protein synthesis. Since all the coding sequences used in our project were manufactured synthetically, the E. coli BL21 cells were additionally transformed with the plasmid optimized protocol adapted from the European Molecular Biology Lab (EMBL) Heidelberg, the lysate was prepared from E. coli BL21 cells, frozen in liquid nitrogen and afterwards stored at -80°C. This lysate contains the whole transcription and translation apparatus of the cell, allowing successful expression of proteins from DNA templates.

However, the E. coli lysate is just one of the main components of the DiaMIX. Additional ingredients required for expression are buffering agents, amino acids, nucleotides and energy sources. We obtained an L-amino acid kit from Sigma-Aldrich and mixed them together in the proper amounts. The energy generating system based on creatine phosphate and phosphokinases, as well as the mix containing nucleotides, amino acids and buffers (see protocol) were prepared and added to the lysate directly before expression.

After adding all three components, the complete cell-free expression mix was subsequently used to express proteins. Therefore, the reaction was started by adding DNA coding for the respective proteins. To verify the functionality of our system, we compared it to a commercially available kit.

Verification of Protein Expression

To validate whether the expression in the DiaMIX yields correctly folded proteins, we used various methods like fluorescence measurements, luciferase assays and Western Blots. Our first approach was the expression of GFP, which can be detected via its fluorescence. We used a plasmid template (LINK) that was added to the self-prepared expression mix. The expression was then visualized via a microplate reader measurement. Measurement of the increase in emitted light at a wavelength of 520 nm monitored the progression of expression. We verified the results with a Western Blot using an antibody against GFP.
For further results of this experiment, have a look here.
As a second test we performed a luciferase assay. In contrast to the expression of GFP which can be followed by a gradual rise of GFP over time, the luciferase assay is based on the emission of light when the substrate luciferin is converted into oxyluciferin. This reaction is catalyzed by the enzyme luciferase. Therefore it does not allow a tracking of expression over time. Moreover it is not dependent on correct folding and offers detection within seconds. We used a plasmid with the firefly luciferase (pBESTlucTM) to express luciferase with our cell-free expression system. The substrate luciferin was added to the mix after expression had finished. The luminescence was measured using a microplate reader.
For more information about the outcome of this analysis, check out our results. This analysis helped us to evaluate the concentration of expressed protein in the cell-free expression system.

Figure 5: Luciferase reaction. The enzyme luciferase catalyzes the reaction of D-luciferin to D-luciferyl using ATP as an energy source. D-luciferyl is instantly converted into oxyluciferin, whereby energy is emitted as light. The intensity of bioluminescence is proportional to the amount of expressed luciferase.

Step by Step Validation

Since we aimed at using cell-free expression in combination with the DiaCHIP, we decided to validate the process in individual steps. Starting with cell-free expression in a tube, we spotted the produced proteins on iRIf slides to check whether we detect their interaction with the respective antibodies. In the next step, we spotted our expression system on the slide without starting the reaction beforehand. Then we added the plasmid template and let the mix incubate on the slide. The proteins produced by cell-free expression should directly bind to the specific surface since they carry the respective tag. Finally, we performed a cell-free expression from immobilized DNA in the finished setup of glass and PDMS slide.

Figure 6: Immobilization of DNA. PCR product coding for GFP with a Cy3 and an amino label was spotted onto the activated PDMS slide. Binding of the amino group to the specific surface allows direct DNA immobilization.

Immobilizing DNA on PDMS

One of the core components of the DiaCHIP is the copying mechanism that allows production of a protein microarray from a DNA template. In summary, we established a cell-free expression system that can be used to translate proteins from DNA immobilized on a PDMS slide.
The first step needed for copying DNA arrays is to genetically fuse antigen coding sequences to a His-Tag that is used for surface immobilization later on. The whole expression cassette including promoter and terminator regions is amplified by PCR using an amino-labeled reverse primer. Via this amino group, the DNA is immobilized on an activated PDMS surface. In order to check for successful binding, the forward primer used for this PCR is labeled with the dye Cy3.


Figure 7: Spotting of expressed GFP. Cell-free expressed GFP lysate was spotted on the activated glass slide after expression was performed for 2 hours at 37°C. For detailed reaction check our lab journal.

Spotting of Expressed GFP on Slide

To test whether our cell-free expression system reaches protein concentration high enough for detection with iRIf, we spotted cell-free expressed GFP on iRIf slides. We then measured the binding of anti-GFP to the cell-free expressed GFP to assess the amount of expressed protein and its folding status.




Figure 8: On-slide expression of GFP. Cell-free expression mix was spotted on the activated glass slide and expression was performed. For details on the reaction check our lab journal.


On-slide Expression of GFP

To estimate the specificity of our surface, we evaluated the proportion of cell-free expressed GFP that bound to the surface. We determined the amount of unspecific binding of non-target proteins to the surface with iRIf using anti-GFP antibodies. Unspecific binding of proteins present in the DiaMIX would lead to decrease in signal, whereas a highly specific surface only binds GFP and thus shows a strong signal at the GFP spot.



Figure 9: In-chamber expression of GFP. Cell-free expression mix was pipetted into the flow chamber with immobilized DNA on the silicone slide and an activated glass slide. Then the expression was performed. For detailed reaction check our lab journal.

In-chamber Expression of GFP

This step would show if our entire system, from cell-free expression to detection of the expressed proteins with antibodies actually works. Expression of the antigens inside the flow chamber with our DiaMIX and subsequent diffusion of the His-tagged proteins through the chamber will result in a distinct spot of bound protein on the glass slide. When cell-free expression is completed, the bound antigens would form an antigen array that can be used for detection of antigen-antibody binding events.

Cell-free Expression of Antigens

Figure 10: Tetanus

An important goal was to express antigens with the required tags in a concentration and folding state that suffices for an iRIf measurement. Here we focused on a C. tetani epitope flagged by a double His and a Spy-tag. For cloning of this construct we used a newly designed cloning site and a vector that we had optimized for cell-free expression.
The antigen was expressed in a tube reaction and afterwards spotted onto a Ni-NTA surface.

Testing Different Conditions

To identify the optimal DNA concentration that results in a maximum protein expression, we tested different conditions. For this experiment, we used DNA coding for the enzyme luciferase. The protein concentration could then be measured using the luciferase assay.
Another component whose concentration is crucial for optimal cell-free expression is magnesium. To evaluate the effects of different magnesium concentrations, we started multiple cell-free expression mixes using different magnesium starting concentrations. Magnesium was added to the mix in the form of magnesium acetate.
After expression, a luciferase assay could visualize the protein concentration in the different reaction mixes.