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Team:UC Davis - 2012.igem.org

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Modules

We have created several modules and biobrick parts for the degradation and utilization of PET. The PET degradation can be seen below.

LC-Cutinase and Initial PET Degradation

When looking for a catalyst capable of breaking down PET, we came across a paper that conducted a metagenomic analysis of leaf-branch compost, identified a cutinase homolog, and demonstrated its PET-degrading activity [1]. It was found that this catalyst broke PET down into two by-products: ethylene glycol and terepthalic acid (TPA). We chose to use this leaf-branch compost cutinase (LC-Cutinase) in our module as it was reported to have a high activity and showed potential for use in PET degradation and surface modification.

Design
We had the LC-Cutinase gene synthesized with a pelB leader sequence and a 6-his tag and labeled it Bba_K936014. The pelB leader sequence is a protein tag that directs the protein to the periplasmic space. The tag is removed by a pelB peptidase once in the periplasm. The LC-cutinase paper used a pelB tag and reported that once the cutinase was brought to the membrane, there is a leakage that helps the catalyst to be secreted into the extracellular matrix [1]. This secretion is desirable for both the purification of the enzyme and for future applications where the bacterial culture would be directly incubated with the PET. We included a his-tag to the end of the sequence so that we could purify the cutinase for incubation with PET as well as identify where it goes after production (i.e. extracellular space or inside the cell). We have two different constructs expressing this part: one with a constitutive promoter (J23101) and one with the inducible pBad promoter (k206000)allowing for induction of the cutinase gene.

Experiments
We have designed and conducted an experiment to determine how much of the protein is being secreted and how much is remaining inside of the cell, the results of which can be found here (link coming soon).

Ethylene Glycol Modules

In [2], the authors report that E. coli can grow with ethylene glycol as a sole carbon source by expressing two enzymes, glycolaldehyde reductase and glycolaldehyde dehydrogenase. While ethylene glycol is toxic for vertebrates because of the kidney damage that it confers, E. coli strains such as the MG1655 strain can use it as an energy source.

Glycolaldehyde reductase (DL-1,2-propanediol oxidoreductase) is normally an anaerobic protein that reduces L-lactaldehyde into L-1,2-propanediol, an excreted product. In addition, a mutant from the paper aforementioned was able to live on L-1,2-propanediol as a sole carbon source. Not only are there mutants that live on the L-1,2-propanediol, but there are also mutants selected for growth on ethylene glycol. We are working to mutate the reductase to work aerobically, rather than anaerobically [3].

In contrast to the reductase, glycolaldehyde dehydrogenase is an aerobic protein that oxidizes glycolaldehyde further to glycolate. The glycolate will be used further downstream in metabolism to provide the carbon source for the E. coli to live.

We are using these enzymes polycistronically with the Bba_J23101 and Bba_K206000 promoters to see the difference in overproduction of the enzymes and modulating the production. Our modular efforts in plasmids will eventually be applied toward a rational strain engineering approach, where we manipulate the MG1655 chromosome to optimize the degradation of ethylene glycol.

References

1. S. Sulaiman, S. Yamato, E. Kanaya, J. Kim, Y. Koga, K. Takano, S. Kanaya. "Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach." Applied and Environment Microbiology, vol. 78 no. 5, pp. 1556-1562, March 2012.
2. Boronat, Albert, Caballero, Estrella, and Juan Aguilar. “Experimental Evolution of a Metabolic Pathway for Ethylene Glycol Utilization by Escherichia coli.” Journal of Bacteriology, Vol. 153 No. 1, pp. 134-139, January 1983.
3. Lu, Zhe, Elisa Cabiscol, Nuria Obradors, Jordi Tamarit, Joaquim Ros, Juan Aguilar, and E.C.C. Lin. "Evolution of an Escherichia coli Protein with Increased Resistance to Oxidative Stress." Journal of Biological Chemistry. 273.14 (1998): n. page. Print.

@@ Line 1,203: / Line 1,203: @@
 <h1> LC-Cutinase and Initial PET Degradation </h1>
 <article>
-When looking for a catalyst capable of breaking down PET, we came across a paper that conducted a metagenomic analysis of leaf-branch compost, identified a cutinase homolog, and demonstrated its PET-degrading activity [1]. It was found that this catalyst broke PET down into two by-products: ethylene glycol and terepthalic acid (TPA).
+When looking for a catalyst capable of breaking down PET, we came across a paper that conducted a metagenomic analysis of leaf-branch compost, identified a cutinase homolog, and demonstrated its PET-degrading activity [1]. It was found that this catalyst broke PET down into two by-products: ethylene glycol and terepthalic acid (TPA). We chose to use this leaf-branch compost cutinase (LC-Cutinase) in our module as it was reported to have a high activity and showed potential for use in PET degradation and surface modification.
 <br>
 <center><img src="https://static.igem.org/mediawiki/2012/6/62/UCDavisLCCutinase_Process.png"></center>
 <br>
-We had the LC-Cutinase gene synthesized with a pelB leader sequence and a 6-his tag and labeled it <a href="http://partsregistry.org/Part:BBa_K936014">Bba_K936014</a>. It has been placed the following construct where it is promoted by a pBad variant Bba_K206000.
+<b>Design</b><br>
+We had the LC-Cutinase gene synthesized with a pelB leader sequence and a 6-his tag and labeled it <a href="http://partsregistry.org/Part:BBa_K936014">Bba_K936014</a>. The pelB leader sequence is a protein tag that directs the protein to the periplasmic space. The tag is removed by a pelB peptidase once in the periplasm. The LC-cutinase paper used a pelB tag and reported that once the cutinase was brought to the membrane, there is a leakage that helps the catalyst to be secreted into the extracellular matrix [1]. This secretion is desirable for both the purification of the enzyme and for future applications where the bacterial culture would be directly incubated with the PET. We included a his-tag to the end of the sequence so that we could purify the cutinase for incubation with PET as well as identify where it goes after production (i.e. extracellular space or inside the cell). We have two different constructs expressing this part: one with a constitutive promoter (J23101) and one with the inducible pBad promoter (k206000)allowing for induction of the cutinase gene.
 <center><br><img src="https://static.igem.org/mediawiki/2012/2/28/UCDavisNew_pBAD_B34_Cutinase.png"></center>
 <br>
-The pelB leader sequence on the cutinase gene directs the enzyme to the periplasmic space [1] . Once the enzyme is led towards the membrane, there is a leakage that helps it be secreted into the extracellular matrix [1]. We hoped that this sequence would help the enzyme be secreted so the PET would more easily be degraded. When we ordered the cutinase sequence, we added pelB to the front of the sequence, in hopes of repeating the secretion shown in previous results.
+<b>Experiments</b><br>
-The inclusion of a his-tag allows us to purify the cutinase protein and identify where it is after it is produced. We have designed and conducted an experiment to determine how much of the protein is being secreted and how much is remaining inside of the cell, the results of which can be found here (link coming soon).
+We have designed and conducted an experiment to determine how much of the protein is being secreted and how much is remaining inside of the cell, the results of which can be found here (link coming soon).
 </article>

Team:UC Davis/Project/Catalyst

From 2012.igem.org