Difference between revisions of "Team:RHIT/Design"

Line 162: Line 162:
  
 
<div class="column full_size">
 
<div class="column full_size">
 +
 +
<p>For our project, we have designed a plasmid that secretes MHETase and the double mutant PETase to increase the rate at which PET is degraded compared to the previous PETase sequence. We inserted the plasmid into an E. coli MG1655 strain. Because of the toxicity of ethylene glycol, a second plasmid was designed to allow the bacteria to break down the ethylene glycol and utilize its products as a carbon source. These enzymes include glycolaldehyde reductase, glycolaldehyde dehydrogenase, glycolate oxidase, and malate synthase. This series of enzymes will turn the ethylene glycol, released from the breakdown of PET, into malate which can be used by the cell as a carbon source via the citric acid cycle. <br><br>
 +
 +
Our E. coli will degrade PET into terephthalic acid (TPA)  and ethylene glycol (EG) utilizing the PETase and MHETase enzymes, as shown in Figure 1 below. </p>
 +
<center>
 +
<img src = "https://static.igem.org/mediawiki/2018/9/9d/T--RHIT--design1.jpg">
 +
</center>
 +
<center> Figure 1 </center>
 +
<br><br>
 +
 +
<p>Terephthalic acid is recyclable when purified and is relatively nontoxic. Ethylene glycol, on the other hand, is extremely toxic to humans, although it has been proven to be safe for E. coli cells.
 +
<br><br>
 +
The E. coli will then take the ethylene glycol and utilize it as a carbon source using glycolaldehyde reductase, glycolaldehyde dehydrogenase, glycolate oxidase, and malate synthase. This will result in intermediates of glycolaldehyde, glycolate, and glyoxylate, as well as the product of malate which will be used in the citric acid cycle, as shown in Figure 2 below. </p>
 +
<center>
 +
<img src = "https://static.igem.org/mediawiki/2018/3/30/T--RHIT--design2_.jpg">
 +
</center>
 +
<center> Figure 2 </center>
 +
<br><br>
 +
 +
<p>Two plasmids were designed to accomplish our goals. The first plasmid (Figure 3) contains PETase and MHETase. The second plasmid (Figure 4) contains the enzyme series for the breakdown of ethylene glycol. </p>
 +
 +
</div>
 +
 +
<div class ="column half_size">
 +
<center>
 +
<img src = "https://static.igem.org/mediawiki/2018/e/ec/T--RHIT--plasmid1.jpg">
 +
</center>
 +
<center> Figure 3 </center>
 +
</div>
 +
 +
<div class = "column half_size">
 +
<center>
 +
<img src = "https://static.igem.org/mediawiki/2018/c/c9/T--RHIT--plasmid2.jpg">
 +
</center>
 +
<center> Figure 4 </center>
 +
</div>
 +
 +
<div class = "column full_size">
 +
<br><br>
 +
<p> Our team selected the W159H/S238F double mutated enzyme based on the article released in April of 2018. The article analyzed the structure of PETase to design the specific double amino acid mutation. PETase was found to have similar common features to cutinases and lipases, which are also shown to partially degrade PET. The double mutation changes the PETase structure by narrowing the binding cleft to better resemble cutinase. In Figure 5 below, which comes from the article, E shows the proposed structure of the binding site in wild-type PETase, while F shows the proposed structure of the binding site in the W159H/S238F double mutated PETase. [1] </p>
 +
 +
<center>
 +
<img src = "https://static.igem.org/mediawiki/2018/2/2e/T--RHIT--doublemutant.jpg">
 +
</center>
 +
<center> Figure 5 </center>
 +
 +
<br><br>
 +
 +
<h5> References </h5>
 +
<ul>
 +
<li>[1]Austin, H., Allen, M., Donohoe, B., Rorrer, N., Kearns, F., Silveira, R., Pollard, B., Dominick, G., Duman, R., El Omari, K., Mykhaylyk, V., Wagner, A., Michener, W., Amore, A., Skaf, M., Crowley, M., Thorne, A., Johnson, C., Woodcock, H., McGeehan, J. and Beckham, G. (2018). Characterization and engineering of a plastic-degrading aromatic polyesterase. Proceedings of the National Academy of Sciences, 115(19), pp.E4350-E4357.</li>
 +
</ul>
 +
 +
</div>
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 
<h1>Design</h1>
 
<h1>Design</h1>
 
<p>
 
<p>

Revision as of 20:03, 2 August 2018




Connect with us on Facebook!
Contact Us!

patekm@rose-hulman.edu
5500 Wabash Ave.
Terre Haute, IN 47803

Description
Design
Experiments
Notebook
Results
Achievements
InterLab
Attributions

For our project, we have designed a plasmid that secretes MHETase and the double mutant PETase to increase the rate at which PET is degraded compared to the previous PETase sequence. We inserted the plasmid into an E. coli MG1655 strain. Because of the toxicity of ethylene glycol, a second plasmid was designed to allow the bacteria to break down the ethylene glycol and utilize its products as a carbon source. These enzymes include glycolaldehyde reductase, glycolaldehyde dehydrogenase, glycolate oxidase, and malate synthase. This series of enzymes will turn the ethylene glycol, released from the breakdown of PET, into malate which can be used by the cell as a carbon source via the citric acid cycle.

Our E. coli will degrade PET into terephthalic acid (TPA) and ethylene glycol (EG) utilizing the PETase and MHETase enzymes, as shown in Figure 1 below.

Figure 1


Terephthalic acid is recyclable when purified and is relatively nontoxic. Ethylene glycol, on the other hand, is extremely toxic to humans, although it has been proven to be safe for E. coli cells.

The E. coli will then take the ethylene glycol and utilize it as a carbon source using glycolaldehyde reductase, glycolaldehyde dehydrogenase, glycolate oxidase, and malate synthase. This will result in intermediates of glycolaldehyde, glycolate, and glyoxylate, as well as the product of malate which will be used in the citric acid cycle, as shown in Figure 2 below.

Figure 2


Two plasmids were designed to accomplish our goals. The first plasmid (Figure 3) contains PETase and MHETase. The second plasmid (Figure 4) contains the enzyme series for the breakdown of ethylene glycol.

Figure 3
Figure 4


Our team selected the W159H/S238F double mutated enzyme based on the article released in April of 2018. The article analyzed the structure of PETase to design the specific double amino acid mutation. PETase was found to have similar common features to cutinases and lipases, which are also shown to partially degrade PET. The double mutation changes the PETase structure by narrowing the binding cleft to better resemble cutinase. In Figure 5 below, which comes from the article, E shows the proposed structure of the binding site in wild-type PETase, while F shows the proposed structure of the binding site in the W159H/S238F double mutated PETase. [1]

Figure 5


References
  • [1]Austin, H., Allen, M., Donohoe, B., Rorrer, N., Kearns, F., Silveira, R., Pollard, B., Dominick, G., Duman, R., El Omari, K., Mykhaylyk, V., Wagner, A., Michener, W., Amore, A., Skaf, M., Crowley, M., Thorne, A., Johnson, C., Woodcock, H., McGeehan, J. and Beckham, G. (2018). Characterization and engineering of a plastic-degrading aromatic polyesterase. Proceedings of the National Academy of Sciences, 115(19), pp.E4350-E4357.

Design

Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.

This page is different to the "Applied Design Award" page. Please see the Applied Design page for more information on how to compete for that award.

What should this page contain?

  • Explanation of the engineering principles your team used in your design
  • Discussion of the design iterations your team went through
  • Experimental plan to test your designs

Inspiration