Difference between revisions of "Team:Tianjin"

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<!-------------- Team Tianjin WIKI Page: Overview ---------------->
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                             <h1>Team Tianjin</h1>
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                             <h1>Plasterminator</h1>
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                                 <div class="separator line-separator">∎</div>
 
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                             <h5>"Plastics taste good." &nbsp; --- &nbsp; <i>Yeast</i></h5>
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                             <h5>"Plastic tastes good."</h5>
 
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                                <h2>A brief description</h2>
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                                 <p class="TeamTianjin-text-main">
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                                     This March our team paid much attention to an article <i class="ref-title">A bacterium that degrades and assimilates poly(ethylene terephthalate)</i><a class="btn popover-info ref-title-link" data-toggle="popover" data-placement="top" title="Reference" data-content="Yoshida, Shosuke, et al. 'A bacterium that degrades and assimilates poly (ethylene terephthalate).' Science 351.6278 (2016): 1196-1199.">1</a> published in Science in the same month. A new kind of bacteria that can decompose PET was found and studied in detail. We plan to express its unique genes in some commonly used mode organisms such as yeasts and E.colis to enhance its activities of decomposition significantly since they are relatively low at present.
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                                     Since 1964, plastics production has increased 20-fold, reaching 311 million tonnes in 2014, the equivalent of more than 900 Empire State Buildings. Plastics production is expected to double again in 20 years and almost quadruple by 2050.
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                                  <a class="btn popover-info ref-title-link" data-toggle="popover" data-placement="top" title="Source" data-content="The New Plastics Economy: Rethinking the future of plastics (World Economic Forum, 2016)">1</a>
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                                 </p><br/><br/><br/>
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                                    <div class="revealOnScroll TeamTianjin-text-animNum" data-animation="fadeInUp" data-timeout="5"><p class="NumHide" data-num="20">20</p><span class="NumHide">Folds</span></div>
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                                    <div class="revealOnScroll TeamTianjin-text-animNum" data-animation="fadeInUp" data-timeout="5"><p class="NumHide" data-num="311">311</p><span class="NumHide">MT</span></div>
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                                    <h2>Polyethylene  terephthalate</h2>
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                                  <b>A</b>
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                                    <p class="TeamTianjin-text-main">
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                                        Plastics have been intensively developed during the last 50 years, among which poly(ethylene terephthalate) (PET) is one of the most widely used polymers worldwide. From daily containers to medical implements, from fibers for textile to ‘space blanket’, nowadays PET is used in almost every single area of our life due to its premium performance, such as durability and the easiness to be molded into different shapes. However, the durability of PET was found to become the biggest drawback, non-degradable, which leads to a global accumulation of plastic waste.
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                                    <p class="TeamTianjin-text-main">
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                                        With the increasing awareness of the worldwide problems associated with white pollution, many solutions have been brought up in dealing with the plastic waste. Compared to the traditional chemical recycling processes which have been considered extremely harmful to the environment, enzymatic hydrolysis of PET is presently evaluated as an environmentally friendly strategy for recycling post-consumer PET wastes. And during the last 15 years, many natural enzymes extracted from microorganisms have been found to be capable of decomposing PET.
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                                    <h2>A New Solution</h2>
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                                    <p class="TeamTianjin-text-main">
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                                        The biodegradation of PET has much more advantages than traditional ways of degrading PET for its low cost and low harm to environment. In recent decades, many labs around the world have proposed a variety of ways to degrade PET biologically. The most inspiring one is the biodegradation ability of a recently found bacterial, called <i class="emphasize">Ideonella sakaiensis</i> <span class="emphasize">201-F6</span>, by Shosuke Yoshida and his colleagues from Japan, which has been studied and published in <i class="ref-title">Science</i> this March<a class="btn popover-info ref-title-link" data-toggle="popover" data-placement="top" title="Reference" data-content="Yoshida, Shosuke, et al. 'A bacterium that degrades and assimilates poly (ethylene terephthalate).' Science 351.6278 (2016): 1196-1199.">2</a>. They analyzed the degrading pathways and isolated two kinds of enzymes, PETase and MHETase. The PETase degrades PET into MHET (mono(2-hydroxyethyl) terephthalic acid) and MHETase degrades MHET into TPA (terephthalic acid) and EG (ethylene glycol).
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                                 <h2>Current situation</h2>
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                                 <h2>Design</h2>
 
                                 <p class="TeamTianjin-text-main">
 
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                                     We have synthesized the gene sequences of the PETase and MHETase based on the supplementary materials of the original paper after several months’ literature reviewing. And we began several preliminary experiments to figure out if those exogenous genes could be well expressed in the host cells. We decide to enhance the activities of these two enzymes via surface display, protein scaffold and fusion expression. Another way to enhance the rate of reactions is to put the first (hydrolysis of PET) and the second step (hydrolysis of MHET) together by cascade catalysis.
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                                     We synthetize the two genes according to the sequences from NCBI, and our project aims to improve the degrading abilities of the two enzymes, especially the key enzyme, PETase, which degrades macromolecule PET with significantly low rate (60mg PET film (20 × 15 × 0.2 mm) was degraded totally by PETase after 60 days according to the Supplementary Materials<a class="btn popover-info ref-title-link" href="http://science.sciencemag.org/content/suppl/2016/03/09/351.6278.1196.DC1">3</a>). We designed a microbial consortia to degrade PET and its products TPA and EG completely, as well as a reporting and regulation system <span class="emphasize">R-R System</span> to make the expression visible and controllable. When we assay the enzyme activities, we use unconventional method, <span class="emphasize">Cell-Free</span> protein expression system
 
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                                    <a class="projecticon" href="#"><img class="img-responsive" data-animation="zoomIn" src="https://static.igem.org/mediawiki/2016/8/8a/T--Tianjin--Protein_Engineering_ICON.svg" width="60%" alt="Protein Engineering"></a><br/>
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                                    We hope to construct a system that can efficiently express and secrete (or display) these two enzymes. The system will be able to hydrolyze PET with a much higher rate than the Ideonella sakaiensis reported in the thesis.  
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                                    <h2>Rational Design</h2>
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                                      As is known to all, the activity of enzyme depends on the interaction of enzyme molecules and substrate molecules. However, the structure of PETase has not been determined yet, so we do not know how the enzyme interacts with substrate PET. The lack of enzyme structure causes serious problems to our project. We had to apply another way to rationally design our enzyme molecule to achieve higher activity. We used a kind of PET hydrolase, LC_Cutinase (LCC), whose structure had been determined correctly, as our reference. We speculated the active sites of PETase according to the structure of LCC. In order to increase the activity of PETase, we come up with two ways. First, we should make the active sites more exposed so that the reaction will be easier to take place. Second, we should increase the hydrophobicity near the active sites because of the high hydrophobicity of PET surface. We totally designed 22 site-directed mutants and expressed them in Saccharomyces cerevisiae and then assay their activity to determine which design is valid.
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                                  <a class="projecticon" href="#"><img class="img-responsive" src="https://static.igem.org/mediawiki/2016/4/49/T--Tianjin--Consortium_ICON.svg" width="60%" alt="Microbial consortia"></a><br/>
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                                    <h2>Microbial consortia</h2>
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                                    <p class="TeamTianjin-text-main">
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                                      The product of degradation are TPA and EG, which are also toxic to environment. The best way to solve this problem is to continue degrading them biologically. We found that <i class="emphasize">Rhodococcus jostii</i> RHA1 owned the ability of degrading TPA into acetyl coenzyme A that can enter the tricarboxylic acid cycle to be transformed into carbon dioxide, and the <i class="emphasize">Pseudomonas putida</i> KT2440 can utilize EG as its sole carbon source. Therefore, we could mix the <i class="emphasize">Rhodococcus jostii</i> RHA1, <i class="emphasize">Pseudomonas putida</i> KT2440, and another kind of organism which can secrete the two enzymes together so that we can successively degrade PET into carbon dioxide. To reduce the difficulty of constructing a microbial consortia, we used a kind of prokaryote, <i class="emphasize">Bacillus subtilis</i>, which also has strong secretion ability, to express the two enzymes. We changed the culture conditions and culture mediums to avoid the competition among the three kinds of bacterial. We assayed the PET, TPA and EG degrading ability in respect to prove the advantage of this system.
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                                  <a class="projecticon" href="#"><img class="img-responsive" src="https://static.igem.org/mediawiki/2016/e/e0/T--Tianjin--Reporting_Regulation_ICON.svg" width="60%" alt="R-R System"></a><br/>
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                                    <h2>Reporting-Regulation System</h2>
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                                    <p class="TeamTianjin-text-main">
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                                      In order to express PETase in a visible and controllable way, we build the reporting-regulation system (R-R System). The reporting system is based on the promoter CpxR from iGEM official kit, which can be indirectly induced by inclusion body in periplasm of E.coli. We use RFP as the reporting protein for its visible red fluorescence under natural light. If the PETase was overexpressed, the inclusion body will unavoidably form in periplasm and the RFP will express. The regulation system has two parts. The first is based on the regulation system, we change the RFP gene to ddpX gene, which can degrade the peptidoglycan in cell wall to cause lysis of <i class="emphasize">E.coli</i> so that the accumulated enzyme can be released. The second is based on the TPA positive feedback system. We insert a leader sequence which can be regulated the TPA before promoter to make the promoter inducible by TPA. We test this system in <i class="emphasize">Saccharomyces cerevisiae</i>.
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                                  <a class="projecticon" href="#"><img class="img-responsive" src="https://static.igem.org/mediawiki/2016/5/5d/T--Tianjin--Cell_Free_System_ICON.svg" width="60%" alt="Cell-Free Protein Expression System"></a><br/>
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                                    <h2>Cell-Free Protein Expression System</h2>
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                                    <p class="TeamTianjin-text-main">
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                                      Besides the works above, we try to find a new method to assay the activity of enzyme. Due to the simple constituent, fast expression speed, and low disturbance of cell-free protein expression system, it becomes our first choice. We used the <i class="emphasize">E.coli</i> CFPS to express modifided PETase and compared them to the wild type as a assay method. The PETase gene is fused with a CFP(Cyan Fluorescence Protein) gene so that the cyan fluorescence signal can act as a reporter of PETase expression level. And than we used the enzymes we had got to degrade PET and detected the degradation products.  
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  <b>Notice:</b> This page is currently under construction. Contents in this page are temporaory and will be modified several times before the final release. &nbsp;&nbsp;&nbsp; &#8212; 2016 iGEM Team Tianjin
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{{:Team:Tianjin/Templates/Sponsor|}}
 
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Revision as of 14:50, 11 October 2016

TEAM TIANJIN

LOGO


Team Tianjin Background

Plasterminator

∎
"Plastic tastes good."

Since 1964, plastics production has increased 20-fold, reaching 311 million tonnes in 2014, the equivalent of more than 900 Empire State Buildings. Plastics production is expected to double again in 20 years and almost quadruple by 2050. 1




20

Folds

311

MT
Overview Fig1

Polyethylene terephthalate

A

Plastics have been intensively developed during the last 50 years, among which poly(ethylene terephthalate) (PET) is one of the most widely used polymers worldwide. From daily containers to medical implements, from fibers for textile to ‘space blanket’, nowadays PET is used in almost every single area of our life due to its premium performance, such as durability and the easiness to be molded into different shapes. However, the durability of PET was found to become the biggest drawback, non-degradable, which leads to a global accumulation of plastic waste.

With the increasing awareness of the worldwide problems associated with white pollution, many solutions have been brought up in dealing with the plastic waste. Compared to the traditional chemical recycling processes which have been considered extremely harmful to the environment, enzymatic hydrolysis of PET is presently evaluated as an environmentally friendly strategy for recycling post-consumer PET wastes. And during the last 15 years, many natural enzymes extracted from microorganisms have been found to be capable of decomposing PET.


A New Solution

The biodegradation of PET has much more advantages than traditional ways of degrading PET for its low cost and low harm to environment. In recent decades, many labs around the world have proposed a variety of ways to degrade PET biologically. The most inspiring one is the biodegradation ability of a recently found bacterial, called Ideonella sakaiensis 201-F6, by Shosuke Yoshida and his colleagues from Japan, which has been studied and published in Science this March2. They analyzed the degrading pathways and isolated two kinds of enzymes, PETase and MHETase. The PETase degrades PET into MHET (mono(2-hydroxyethyl) terephthalic acid) and MHETase degrades MHET into TPA (terephthalic acid) and EG (ethylene glycol).

Bottle 1
Bottle 2
Bottle 3
Team Tianjin Overview

Design

We synthetize the two genes according to the sequences from NCBI, and our project aims to improve the degrading abilities of the two enzymes, especially the key enzyme, PETase, which degrades macromolecule PET with significantly low rate (60mg PET film (20 × 15 × 0.2 mm) was degraded totally by PETase after 60 days according to the Supplementary Materials3). We designed a microbial consortia to degrade PET and its products TPA and EG completely, as well as a reporting and regulation system R-R System to make the expression visible and controllable. When we assay the enzyme activities, we use unconventional method, Cell-Free protein expression system

Protein Engineering

Rational Design

As is known to all, the activity of enzyme depends on the interaction of enzyme molecules and substrate molecules. However, the structure of PETase has not been determined yet, so we do not know how the enzyme interacts with substrate PET. The lack of enzyme structure causes serious problems to our project. We had to apply another way to rationally design our enzyme molecule to achieve higher activity. We used a kind of PET hydrolase, LC_Cutinase (LCC), whose structure had been determined correctly, as our reference. We speculated the active sites of PETase according to the structure of LCC. In order to increase the activity of PETase, we come up with two ways. First, we should make the active sites more exposed so that the reaction will be easier to take place. Second, we should increase the hydrophobicity near the active sites because of the high hydrophobicity of PET surface. We totally designed 22 site-directed mutants and expressed them in Saccharomyces cerevisiae and then assay their activity to determine which design is valid.

Microbial consortia

Microbial consortia

The product of degradation are TPA and EG, which are also toxic to environment. The best way to solve this problem is to continue degrading them biologically. We found that Rhodococcus jostii RHA1 owned the ability of degrading TPA into acetyl coenzyme A that can enter the tricarboxylic acid cycle to be transformed into carbon dioxide, and the Pseudomonas putida KT2440 can utilize EG as its sole carbon source. Therefore, we could mix the Rhodococcus jostii RHA1, Pseudomonas putida KT2440, and another kind of organism which can secrete the two enzymes together so that we can successively degrade PET into carbon dioxide. To reduce the difficulty of constructing a microbial consortia, we used a kind of prokaryote, Bacillus subtilis, which also has strong secretion ability, to express the two enzymes. We changed the culture conditions and culture mediums to avoid the competition among the three kinds of bacterial. We assayed the PET, TPA and EG degrading ability in respect to prove the advantage of this system.

R-R System

Reporting-Regulation System

In order to express PETase in a visible and controllable way, we build the reporting-regulation system (R-R System). The reporting system is based on the promoter CpxR from iGEM official kit, which can be indirectly induced by inclusion body in periplasm of E.coli. We use RFP as the reporting protein for its visible red fluorescence under natural light. If the PETase was overexpressed, the inclusion body will unavoidably form in periplasm and the RFP will express. The regulation system has two parts. The first is based on the regulation system, we change the RFP gene to ddpX gene, which can degrade the peptidoglycan in cell wall to cause lysis of E.coli so that the accumulated enzyme can be released. The second is based on the TPA positive feedback system. We insert a leader sequence which can be regulated the TPA before promoter to make the promoter inducible by TPA. We test this system in Saccharomyces cerevisiae.

Cell-Free Protein Expression System

Cell-Free Protein Expression System

Besides the works above, we try to find a new method to assay the activity of enzyme. Due to the simple constituent, fast expression speed, and low disturbance of cell-free protein expression system, it becomes our first choice. We used the E.coli CFPS to express modifided PETase and compared them to the wild type as a assay method. The PETase gene is fused with a CFP(Cyan Fluorescence Protein) gene so that the cyan fluorescence signal can act as a reporter of PETase expression level. And than we used the enzymes we had got to degrade PET and detected the degradation products.

Team Tianjin Sponsor Alltech
Team Tianjin Sponsor GenScript
Team Tianjin Sponsor SynbioTech