Team:DTU-Denmark/HelloWorld

From 2013.igem.org

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== Introduction ==
== Introduction ==
-
‘Hello World!’ are the first words a programmer prints when learning a new programming language. In analogy to this our team decided to do a ‘Hello World’ project in order to familiarize ourselves with lab techniques that we used later on to construct plasmids. Specifically we were performing PCR with uracil-containing primers, purifying PCR products and ligating them by means of USER cloning (Nour-Eldin, H. H.).
+
‘Hello World!’ are the first words a programmer prints when learning a new programming language. Analogously, our team decided to do a ‘Hello World’ project in order to familiarize ourselves with lab techniques that we used later on to construct plasmids. Specifically we were performing PCR with uracil-containing primers, purifying PCR products and ligating them by means of USER cloning [1].
-
 
+
-
Since we are working with many periplasmic proteins, we wanted to try to target proteins to the periplasm. To do this, we used periplasmic signal peptides from the TAT and Sec pathways, and with a translational fusion of the signal peptide to GFP, we expressed GFP in the periplasm. Simultaneously, we expressed RFP in the cytoplasm as a background color, inspired by Skoog, Karl, et al.
+
 +
Since we are working with many periplasmic proteins, we wanted to try to target proteins to the periplasm. To do this, we used periplasmic signal peptides from the TAT and Sec pathways, and with a translational fusion of the signal peptide to GFP, we expressed GFP in the periplasm. Simultaneously, we expressed RFP in the cytoplasm as a background color, inspired by Skoog, Karl, et al. [2].
== Methods ==
== Methods ==
===Construction===
===Construction===
-
The overal goal was to test the twin arginine pathway (TAT) and whether this signal peptide could transport GFP SF into the periplasm. The reason why we choose to use GFP superfolder (SF) was that this variant has been shown to fold faster than the E. coli transport system is at translocation, (Fisher, Adam C., and Matthew P. DeLisa.). This assures that the GFP will form its fluorophore before translocation to the more reductive periplasmic space. Thus it will not be inactivated by the inhibition of fluorophore formation as seen in other oxidative compartments like ER (Aronson, Deborah E., Lindsey M. Costantini, and Erik L. Snapp.).  
+
The overal goal was to test the twin arginine pathway (TAT) and whether this signal peptide could transport GFP SF into the periplasm. The reason why we choose to use GFP superfolder (SF) was that this variant has been shown to fold faster than the ''E. coli'' transport system is at translocation, [3]. This assures that the GFP will form its fluorophore before translocation to the more reductive periplasmic space. Thus it will not be inactivated by the inhibition of fluorophore formation as seen in other oxidative compartments like the ER [4].
Construction of the plasmids was done with USER-cloning and assembly of 3 fragments. The starting point was a plasmid construct with RFP and GFP SF respectively. The RFP and GFP SF were amplified out with their associated RBS (the same in both cases).  
Construction of the plasmids was done with USER-cloning and assembly of 3 fragments. The starting point was a plasmid construct with RFP and GFP SF respectively. The RFP and GFP SF were amplified out with their associated RBS (the same in both cases).  
 +
[[File:Both.png|680px]]
[[File:Both.png|680px]]
-
The TAT signal peptide was bought as a gBlock from IDT. All fragments were assembled into an expression vector specially designed to have a tight on/off mechanism ([http://parts.igem.org/Part:BBa_K1067007 BBa_K1067007]). Primers were design by the program [http://www.cbs.dtu.dk/services/PHUSER-2.0/web/ PHUSER] (Olsen, Lars Rønn, et al.) so that we got a seamless assembly.
+
The TAT signal peptide was bought as a gBlock from IDT. All fragments were assembled into an expression vector specially designed to have a tight on/off mechanism.  For this we used a promoter constructed from our [[Team:DTU-Denmark/pBAD_SPL|synthetic promoter library]] ([http://parts.igem.org/Part:BBa_K1067007 BBa_K1067007]). Primers were design by the program [http://www.cbs.dtu.dk/services/PHUSER-2.0/web/ PHUSER] [5] so that we got a seamless assembly.
[[File:PZA21-MCS TAT araBAD.png|680px|alt=Alt|"Hello World"" construct]]
[[File:PZA21-MCS TAT araBAD.png|680px|alt=Alt|"Hello World"" construct]]
===Visualization===
===Visualization===
-
To visualize that GFP SF actually is exported we constructed a procedure for growing the cells and tracing the GFP SF to the periplasm (Skoog, Karl, et al.). It turns out that if you just grow cells in LB and induce the GFP SF/RFP expression there will be too much GFP SF in the cytoplasm to get a good resolution between cytoplasm and periplasm. That is why it’s important to devise a procedure for stopping the production for GFP SP and thereafter tracing it from the cytoplasm into the periplasm. This underlines the importance of having a non-leaky inducible expression system; when expression is stopped by removing the inducer it would spoil the procedure if the system kept leaking out GFP SF into the cytoplasm.
+
To visualize that GFP SF actually is exported, we constructed a procedure for growing the cells and tracing the GFP SF to the periplasm (Skoog, Karl, et al.). As we initially found, if you just grow cells in LB and induce the GFP SF/RFP expression, there will be too much GFP SF in the cytoplasm to get a good resolution between cytoplasm and periplasm. That is why it’s important to devise a procedure for stopping the production for GFP SP and thereafter tracing it from the cytoplasm into the periplasm. This underlines the importance of having a non-leaky inducible expression system; when expression is stopped by removing the inducer it would spoil the procedure if the system kept leaking out GFP SF into the cytoplasm.
After optimizing the procedure we made a final version which can be found in the [https://2013.igem.org/Team:DTU-Denmark/Methods/Visualizing_GFP_in_the_periplasm methods page]. This also includes how to use background subtraction to get a better resolution.
After optimizing the procedure we made a final version which can be found in the [https://2013.igem.org/Team:DTU-Denmark/Methods/Visualizing_GFP_in_the_periplasm methods page]. This also includes how to use background subtraction to get a better resolution.
-
 
-
===Modeling===
 
-
To assess the ability to distinguish the periplasmic from the cytoplasmic space we made a model which is based on a perfect spherical cell with and even layer between inner and outer membrane.
 
-
[[File:Cell model.png|300px|center|Conceptual drawing for the model]]
 
-
 
-
To get a value of the RFP and GFP signal we used a cross section of the spherical cell and measured the length of RFP and GFP going across this section; see the measurement bars at the figure.  The make a graph of this we set the middle of the cell to be 0 on the x-axis. On the y-axis we let two lines show the value of GFP and RFP in the cross section.
 
-
 
-
The first graph can be seen below:
 
-
[[File:First model.png|thumb|center|upright=2|The first model was done i Maple.]]
 
-
 
-
 
== Results ==
== Results ==
We used different methods for testing that our construct actually did work and also for verifying the model we did before the test.  
We used different methods for testing that our construct actually did work and also for verifying the model we did before the test.  
 +
===Periplasmic vs. cytoplasmic fraction===
===Periplasmic vs. cytoplasmic fraction===
-
The first test we did was to purify the periplasmic fraction of the cells and then comparing with the cytoplasmic ([https://2013.igem.org/Team:DTU-Denmark/Notebook/6_July_2013 link to notebook]). We did this with the cold osmotic shock method and viewed the fraction under UV-light.  
+
The first test we did was to purify the periplasmic fraction of the cells and then to compare them with the cytoplasmic fraction ([https://2013.igem.org/Team:DTU-Denmark/Notebook/6_July_2013 lab notebook entry]). We did this with the cold osmotic shock method and viewed the fraction under UV-light.  
-
[[File:Sucrose A+D+C.JPG|thumb|center|upright=3|Periplasmic fractions are clear green fluorescent while the pellet with the cytoplasmic fraction is red fluorescent]]
+
[[File:DTU-Denmark_HelloWorld_Sucrose_A+D+C_2.jpg|thumb|center|upright=3|Periplasmic fractions are clear green fluorescent while the pellet with the cytoplasmic fraction is red fluorescent]]
-
 
+
-
 
+
-
 
+
===Fluorescent microscope images===  
===Fluorescent microscope images===  
-
Next test was the "real thing". We wanted bulletproof evidences that GFP SF was actually exported; and what better way to do this than getting pictures of it? After following the our procedure for chasing GFP SF to the periplasm the could see these images after background subtraction. Following is an image with no zoom:
+
Next test was the "real thing". We wanted water-tight evidence that GFP SF was actually exported; and what better way to do this than getting pictures of it? After following our procedure for chasing GFP SF to the periplasm, we observed these images after background subtraction. Following is an image with no zoom:
[[File:GFP in perimplasm RFP in cytoplasm.png|thumb|center|upright=3|Transformed ''E. coli'' taken with a Fluorescence microscope]]
[[File:GFP in perimplasm RFP in cytoplasm.png|thumb|center|upright=3|Transformed ''E. coli'' taken with a Fluorescence microscope]]
Line 56: Line 43:
-
For this cell a line profile was made that shows both the GFP- and RFP signal across the cell:
+
For this cell a linear profile was made that shows both the GFP and RFP signal across the cell:
[[File:Graf.PNG|thumb|center|upright=3|Line profile of the cross section of the cell seen in the above close up]]
[[File:Graf.PNG|thumb|center|upright=3|Line profile of the cross section of the cell seen in the above close up]]
-
This was staggeringly close to our model seen in next section.
+
These profiles closely resemble our model seen in next section.
 +
 
 +
 
 +
==Modeling==
 +
 
 +
===Modeling Methods===
 +
To assess the ability to distinguish the periplasmic from the cytoplasmic space we made a model which is based on a perfect spherical cell with and even layer between inner and outer membrane.
 +
[[File:Cell model.png|300px|center|Conceptual drawing for the model]]
 +
 
 +
To get a value of the RFP and GFP signal we used a cross section of the spherical cell and measured the length of RFP and GFP going across this section; see the measurement bars at the figure.  The make a graph of this we set the middle of the cell to be 0 on the x-axis. On the y-axis we let two lines show the value of GFP and RFP in the cross section.
 +
 
 +
The first graph can be seen below:
 +
[[File:First model.png|thumb|center|upright=2|The first model was done in Maple.]]
 +
 
===Model of "Hello World" construct===
===Model of "Hello World" construct===
 +
With the mathematical equations made for making the graph above we made a interactive model that enables the user to set their own settings with regard to GFP and RFP intensity and cytoplasmic vs. periplasmic fraction. If the parameters are set well the model reassembles the images we acquired with the fluorescence microscope. 
 +
<html>
<html>
-
            <form>
 
-
                <label for="inner_cell_prop_slider">Cell membrane size:</label>
 
-
                <input type="range" name="inner_cell_prop_slider" id="inner_cell_prop_slider" min="0" max="1" step=".01" value="0.5">
 
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                <label for="red_intensity_slider">Red intesity:</label>
 
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                <input type="range" name="red_intensity_slider" id="red_intensity_slider" min="0" max="255" step="1" value="200">
 
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                <label for="green_intensity_slider">Green intensity:</label>
 
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                <input type="range" name="green_intensity_slider" id="green_intensity_slider" min="0" max="255" step="1" value="200">
 
-
            </form>
 
-
            <div id="visualization">
+
<script src="http://ajax.aspnetcdn.com/ajax/modernizr/modernizr-2.0.6-development-only.js"></script>
 +
<div id="browser_too_old" >
 +
<table>
 +
<tr>
 +
<td style="text-align: center">
 +
          <h4>Warning</h4>
 +
              <img src="/wiki/images/c/cb/Warning.png" height="70" width="70">
 +
              <h3>Oh no! Your browser is too old to display this content</h3>
 +
              <p><b>Please install the newest version of any of these: </b></p>
 +
              <p><b><i>Chrome, Safari, Internet Explorer (Windows 7 or later only), Firefox, Opera</i></b></p>
 +
              <p><b>And please come back! It's worth it!</b></p>
 +
</td>
 +
</tr>
 +
</table>
 +
</div>
-
            </div>
+
<div id="visualization_complete" class="display:none">
-
            <div id="cell_image">
+
-
            </div>
+
<table style="border: 0px">
 +
<tr>
 +
<td>
 +
                Cell membrane size:
 +
</td>
 +
<td>
 +
                <input type="range" name="inner_cell_prop_slider" id="inner_cell_prop_slider" min="0" max="1" step=".01" value="0.5">
 +
</td>
 +
<td id="inner_cell_prop_num">
 +
</td>
 +
</tr>
 +
<tr>
 +
<td>
 +
                Red intesity:
 +
</td>
 +
<td>
 +
                <input type="range" name="red_intensity_slider" id="red_intensity_slider" min="0" max="255" step="1" value="255">
 +
</td>
 +
<td id="red_intensity_num">
 +
</td>
 +
</tr>
 +
<tr>
 +
<td>
 +
                Green intensity:
 +
</td>
 +
<td>
 +
                <input type="range" name="green_intensity_slider" id="green_intensity_slider" min="0" max="255" step="1" value="255">
 +
</td>
 +
<td id="green_intensity_num">
 +
</td>
 +
</tr>
 +
</table>
-
            <script src="http://cdnjs.cloudflare.com/ajax/libs/d3/3.2.2/d3.v3.min.js" charset="utf-8"></script>
+
          <div id="visualization">
-
           
+
          </div>
 +
          <div id="cell_image">
 +
          </div>
 +
</div>
 +
<!--End of visualization_complete -->
-
            <script src="http://dworzynski.eu/main.js"></script>
 
 +
            <script src="http://cdnjs.cloudflare.com/ajax/libs/d3/3.2.2/d3.v3.min.js" charset="utf-8"></script>
 +
 +
            <script src="http://dworzynski.eu/visualization_logic.js"></script>
 +
            <script src="http://dworzynski.eu/visualization_main.js"></script>
-
                  <script>
 
-
        //  $(document).bind('pageinit', function(){
 
-
                $('#inner_cell_prop_slider').change(function(event){
 
-
                    inner_cell_proportion = parseFloat($("#inner_cell_prop_slider")[0].value);
 
-
                    update();
 
-
                });
 
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                $('#red_intensity_slider').change(function(event){
 
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                    red_intensity = parseFloat($("#red_intensity_slider")[0].value);
 
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                    update();
 
-
                });
 
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                $('#green_intensity_slider').change(function(event){
 
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                    green_intensity = parseFloat($("#green_intensity_slider")[0].value);
 
-
                    update();
 
-
                });
 
-
//});
 
-
        </script>
 
</html>
</html>
== Conclusions ==
== Conclusions ==
-
Biobrick [[Team:DTU-Denmark/Parts|BBa_K1067009]] successfully directs GFP SF to the periplasm of ''E. coli''. This experiment is a proof of concept that proteins can be exported to the periplasm. There have in previous iGEM project been a confusing whether or not it was possible to export GFP to the periplasm; this experiment verifies just that and gives a procedure on how to reproduce this.  
+
Biobrick [[Team:DTU-Denmark/Parts|BBa_K1067009]] successfully directs GFP SF to the periplasm of ''E. coli''. This experiment is a proof of concept that proteins can be exported to the periplasm. In previous iGEM projects, there has been confusion as to whether or not it is possible to export GFP to the periplasm; this experiment verifies just that and gives a procedure on how to reproduce this.
 +
==References==
 +
[1] Nour-Eldin, H. H., Geu-Flores, F., & Halkier, B. A. (2010). USER cloning and USER fusion: the ideal cloning techniques for small and big laboratories. In Plant Secondary Metabolism Engineering (pp. 185-200). Humana Press.
 +
[2] Skoog, Karl, et al. "Sequential Closure of the Cytoplasm and Then the Periplasm during Cell Division in Escherichia coli." Journal of bacteriology 194.3 (2012): 584-586.
-
==References==
+
[3] Fisher, Adam C., and Matthew P. DeLisa. "Laboratory evolution of fast-folding green fluorescent protein using secretory pathway quality control." PLoS One 3.6 (2008): e2351.
-
<html>
+
-
<ul>
+
[4] Aronson, Deborah E., Lindsey M. Costantini, and Erik L. Snapp. "Superfolder GFP is fluorescent in oxidizing environments when targeted via the Sec translocon." Traffic 12.5 (2011): 543-548.
-
<li>Skoog, Karl, et al. "Sequential Closure of the Cytoplasm and Then the Periplasm during Cell Division in Escherichia coli." Journal of bacteriology 194.3 (2012): 584-586.
+
-
<li>Nour-Eldin, H. H., Geu-Flores, F., & Halkier, B. A. (2010). USER cloning and USER fusion: the ideal cloning techniques for small and big laboratories. In Plant Secondary Metabolism Engineering (pp. 185-200). Humana Press.
+
-
<li>Olsen, Lars Rønn, et al. "PHUSER (Primer Help for USER): a novel tool for USER fusion primer design." Nucleic acids research 39.suppl 2 (2011): W61-W67.
+
-
<li>Fisher, Adam C., and Matthew P. DeLisa. "Laboratory evolution of fast-folding green fluorescent protein using secretory pathway quality control." PLoS One 3.6 (2008): e2351.
+
-
<li>Aronson, Deborah E., Lindsey M. Costantini, and Erik L. Snapp. "Superfolder GFP is fluorescent in oxidizing environments when targeted via the Sec translocon." Traffic 12.5 (2011): 543-548.
+
-
</ul>
+
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</td>
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<td width="163px" height="100%" valign="top">
+
-
</td>
+
-
</tr>
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-
</font>
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-
</table>
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<!-- Main content area -->
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[5] Olsen, Lars Rønn, et al. "PHUSER (Primer Help for USER): a novel tool for USER fusion primer design." Nucleic acids research 39.suppl 2 (2011): W61-W67.
-
</body>
 
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</html>
 
{{:Team:DTU-Denmark/Templates/EndPage}}
{{:Team:DTU-Denmark/Templates/EndPage}}

Latest revision as of 18:01, 4 October 2013

Hello World Pilot Project

Contents


Introduction

‘Hello World!’ are the first words a programmer prints when learning a new programming language. Analogously, our team decided to do a ‘Hello World’ project in order to familiarize ourselves with lab techniques that we used later on to construct plasmids. Specifically we were performing PCR with uracil-containing primers, purifying PCR products and ligating them by means of USER cloning [1].

Since we are working with many periplasmic proteins, we wanted to try to target proteins to the periplasm. To do this, we used periplasmic signal peptides from the TAT and Sec pathways, and with a translational fusion of the signal peptide to GFP, we expressed GFP in the periplasm. Simultaneously, we expressed RFP in the cytoplasm as a background color, inspired by Skoog, Karl, et al. [2].

Methods

Construction

The overal goal was to test the twin arginine pathway (TAT) and whether this signal peptide could transport GFP SF into the periplasm. The reason why we choose to use GFP superfolder (SF) was that this variant has been shown to fold faster than the E. coli transport system is at translocation, [3]. This assures that the GFP will form its fluorophore before translocation to the more reductive periplasmic space. Thus it will not be inactivated by the inhibition of fluorophore formation as seen in other oxidative compartments like the ER [4].

Construction of the plasmids was done with USER-cloning and assembly of 3 fragments. The starting point was a plasmid construct with RFP and GFP SF respectively. The RFP and GFP SF were amplified out with their associated RBS (the same in both cases).

Both.png


The TAT signal peptide was bought as a gBlock from IDT. All fragments were assembled into an expression vector specially designed to have a tight on/off mechanism. For this we used a promoter constructed from our synthetic promoter library ([http://parts.igem.org/Part:BBa_K1067007 BBa_K1067007]). Primers were design by the program [http://www.cbs.dtu.dk/services/PHUSER-2.0/web/ PHUSER] [5] so that we got a seamless assembly.

Alt

Visualization

To visualize that GFP SF actually is exported, we constructed a procedure for growing the cells and tracing the GFP SF to the periplasm (Skoog, Karl, et al.). As we initially found, if you just grow cells in LB and induce the GFP SF/RFP expression, there will be too much GFP SF in the cytoplasm to get a good resolution between cytoplasm and periplasm. That is why it’s important to devise a procedure for stopping the production for GFP SP and thereafter tracing it from the cytoplasm into the periplasm. This underlines the importance of having a non-leaky inducible expression system; when expression is stopped by removing the inducer it would spoil the procedure if the system kept leaking out GFP SF into the cytoplasm.

After optimizing the procedure we made a final version which can be found in the methods page. This also includes how to use background subtraction to get a better resolution.

Results

We used different methods for testing that our construct actually did work and also for verifying the model we did before the test.


Periplasmic vs. cytoplasmic fraction

The first test we did was to purify the periplasmic fraction of the cells and then to compare them with the cytoplasmic fraction (lab notebook entry). We did this with the cold osmotic shock method and viewed the fraction under UV-light.

Periplasmic fractions are clear green fluorescent while the pellet with the cytoplasmic fraction is red fluorescent

Fluorescent microscope images

Next test was the "real thing". We wanted water-tight evidence that GFP SF was actually exported; and what better way to do this than getting pictures of it? After following our procedure for chasing GFP SF to the periplasm, we observed these images after background subtraction. Following is an image with no zoom:

Transformed E. coli taken with a Fluorescence microscope


Next to test our model we picked a cell this good resolution and zoomed in on this:

Close up of several cells, showing GFP expression in the periplasm


For this cell a linear profile was made that shows both the GFP and RFP signal across the cell:

Line profile of the cross section of the cell seen in the above close up

These profiles closely resemble our model seen in next section.


Modeling

Modeling Methods

To assess the ability to distinguish the periplasmic from the cytoplasmic space we made a model which is based on a perfect spherical cell with and even layer between inner and outer membrane.

Conceptual drawing for the model

To get a value of the RFP and GFP signal we used a cross section of the spherical cell and measured the length of RFP and GFP going across this section; see the measurement bars at the figure. The make a graph of this we set the middle of the cell to be 0 on the x-axis. On the y-axis we let two lines show the value of GFP and RFP in the cross section.

The first graph can be seen below:

The first model was done in Maple.


Model of "Hello World" construct

With the mathematical equations made for making the graph above we made a interactive model that enables the user to set their own settings with regard to GFP and RFP intensity and cytoplasmic vs. periplasmic fraction. If the parameters are set well the model reassembles the images we acquired with the fluorescence microscope.

Warning

Oh no! Your browser is too old to display this content

Please install the newest version of any of these:

Chrome, Safari, Internet Explorer (Windows 7 or later only), Firefox, Opera

And please come back! It's worth it!
Cell membrane size:
Red intesity:
Green intensity:

Conclusions

Biobrick BBa_K1067009 successfully directs GFP SF to the periplasm of E. coli. This experiment is a proof of concept that proteins can be exported to the periplasm. In previous iGEM projects, there has been confusion as to whether or not it is possible to export GFP to the periplasm; this experiment verifies just that and gives a procedure on how to reproduce this.

References

[1] Nour-Eldin, H. H., Geu-Flores, F., & Halkier, B. A. (2010). USER cloning and USER fusion: the ideal cloning techniques for small and big laboratories. In Plant Secondary Metabolism Engineering (pp. 185-200). Humana Press.

[2] Skoog, Karl, et al. "Sequential Closure of the Cytoplasm and Then the Periplasm during Cell Division in Escherichia coli." Journal of bacteriology 194.3 (2012): 584-586.

[3] Fisher, Adam C., and Matthew P. DeLisa. "Laboratory evolution of fast-folding green fluorescent protein using secretory pathway quality control." PLoS One 3.6 (2008): e2351.

[4] Aronson, Deborah E., Lindsey M. Costantini, and Erik L. Snapp. "Superfolder GFP is fluorescent in oxidizing environments when targeted via the Sec translocon." Traffic 12.5 (2011): 543-548.

[5] Olsen, Lars Rønn, et al. "PHUSER (Primer Help for USER): a novel tool for USER fusion primer design." Nucleic acids research 39.suppl 2 (2011): W61-W67.


Retrieved from "http://2013.igem.org/Team:DTU-Denmark/HelloWorld"