Each year, 130 million tons of fossil plastics are produced in the world, which take 500-1000 years to degrade, and pollute the environment; 1,5 millions of marine animals were killed in 2014 and we will eventually kill us too (Figure 1, Project). A sustainable initiative is to produce biodegradable plastics; however its synthesis process (chemical and biological) is complex and expensive. The team UChile-OpenBio designed two populations of bacteria to achieve this: the team will use Escherichia coli to produce a biodegradable plastic called PLA (Polylactic acid) from easy to assimilate renewable resources. The first population will convert glucose into lactate and will self-regulate its production by sensing the pH. The second population will polymerize lactate into PLA and will export it into the medium. In addition the team is planning to replace the glucose by Chilean brown macroalgae (kelp), a renewable resource to sustainably produce PLA. In this way, the team would help fighting against pollution, contributing to a better world!
Difference between revisions of "Team:UChile-OpenBio"
| Line 65: | Line 65: | ||
<span class="titulo_seccion" >Overview: Background</span> | <span class="titulo_seccion" >Overview: Background</span> | ||
<article> | <article> | ||
| − | <p>Each year, 130 million tons of fossil plastics are produced in the world, which take 500-1000 years to degrade, and pollute the environment; 1,5 millions of marine animals were killed in 2014 and we will eventually kill us too ( | + | <p>Each year, 130 million tons of fossil plastics are produced in the world, which take 500-1000 years to degrade, and pollute the environment; 1,5 millions of marine animals were killed in 2014 and we will eventually kill us too (Figure 1, Project). A sustainable initiative is to produce biodegradable plastics; however its synthesis process (chemical and biological) is complex and expensive. The team UChile-OpenBio designed two populations of bacteria to achieve this: the team will use Escherichia coli to produce a biodegradable plastic called PLA (Polylactic acid) from easy to assimilate renewable resources. The first population will convert glucose into lactate and will self-regulate its production by sensing the pH. The second population will polymerize lactate into PLA and will export it into the medium. In addition the team is planning to replace the glucose by Chilean brown macroalgae (kelp), a renewable resource to sustainably produce PLA. In this way, the team would help fighting against pollution, contributing to a better world! </p> |
| Line 91: | Line 91: | ||
<p>The transcription can be regulated by different factors (repressors, pH, light, etc) which are detected by the <span class="destacado">promotor</span>. These signals induce or inhibit the activation of the module.</p> | <p>The transcription can be regulated by different factors (repressors, pH, light, etc) which are detected by the <span class="destacado">promotor</span>. These signals induce or inhibit the activation of the module.</p> | ||
<p>If the module is activated then the transcription process begins, in which several copies of the message are made.</p> | <p>If the module is activated then the transcription process begins, in which several copies of the message are made.</p> | ||
| − | <p>The <span class="destacado">RBS</span> (Ribosomal Bonding Site) intervenes in the translation process: if it is strong many proteins will be synthesised. If it is weak, few proteins will be synthetized. So the function of RBS is | + | <p>The <span class="destacado">RBS</span> (Ribosomal Bonding Site) intervenes in the translation process: if it is strong, many proteins will be synthesised. If it is weak, few proteins will be synthetized. So the function of RBS is regulate the quantity of produced proteins.</p> |
<p>The <span class="destacado">coding sequence</span> is the message, the recipe that shall be translated to protein.</p> | <p>The <span class="destacado">coding sequence</span> is the message, the recipe that shall be translated to protein.</p> | ||
<p>The <span class="destacado">terminator</span> is a DNA sequence that puts an end to the transcription process.</p> | <p>The <span class="destacado">terminator</span> is a DNA sequence that puts an end to the transcription process.</p> | ||
| Line 105: | Line 105: | ||
<div class="division"> | <div class="division"> | ||
<div class="half"> | <div class="half"> | ||
| − | <p>The team decided to used legos to explain the pla project due to | + | <p>The team decided to used legos to explain the pla project due to different reasons.</p> |
</div> | </div> | ||
</div> | </div> | ||
| Line 143: | Line 143: | ||
<div class="division"> | <div class="division"> | ||
<div class="half"> | <div class="half"> | ||
| − | <h3>E. Coli 1 | + | <h3>E. Coli 1 Population: “Lactadora”</h3> |
<img class="" alt="Lactadora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" /> | <img class="" alt="Lactadora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" /> | ||
<p>In our project we used two bacterias « Escherichia coli »: name and first name of the bacteria.<br>This population are responsible for lactate production.</p> | <p>In our project we used two bacterias « Escherichia coli »: name and first name of the bacteria.<br>This population are responsible for lactate production.</p> | ||
</div> | </div> | ||
<div class="half last"> | <div class="half last"> | ||
| − | <h3>E. Coli 2 | + | <h3>E. Coli 2 Population: “PLAdora”</h3> |
<img class="" alt="PLAdora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" /> | <img class="" alt="PLAdora" src="https://static.igem.org/mediawiki/2015/0/0b/Lego_description-bacteria_lego.png" /> | ||
<p>« Escherichia coli »: name and first name of the bacteria. « 1 » y « 2 » only mean that these bacteria, in this process, are responsible for different functions (but they belong the same bacteria strain).<br>This population are responsible for process the lactate into PLA.</p> | <p>« Escherichia coli »: name and first name of the bacteria. « 1 » y « 2 » only mean that these bacteria, in this process, are responsible for different functions (but they belong the same bacteria strain).<br>This population are responsible for process the lactate into PLA.</p> | ||
| Line 172: | Line 172: | ||
</div> | </div> | ||
<div class="one_third last"> | <div class="one_third last"> | ||
| − | <p>Finally, lactate can be obtained from glucose thanks to LDH, which gene we insert into the | + | <p>Finally, lactate can be obtained from glucose thanks to LDH, which gene we insert into the bacterium.</p> |
</div> | </div> | ||
</div> | </div> | ||
| Line 188: | Line 188: | ||
<div class="division"> | <div class="division"> | ||
<div class="half"> | <div class="half"> | ||
| − | <p>The lactate produced by the <span class="destacado">E.coli 1 Population</span> is secreted into the medium and enters in the | + | <p>The lactate produced by the <span class="destacado">E.coli 1 Population</span> is secreted into the medium and enters in the bacteria of the E.coli 2 Population</p> |
</div> | </div> | ||
<div class="half last"> | <div class="half last"> | ||
| Line 210: | Line 210: | ||
</div> | </div> | ||
<div class="one_third"> | <div class="one_third"> | ||
| − | <p>PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together...</p> | + | <p>PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together. . .</p> |
</div> | </div> | ||
<div class="one_third last"> | <div class="one_third last"> | ||
| Line 233: | Line 233: | ||
</article> | </article> | ||
<article> | <article> | ||
| − | <h3> | + | <h3>Important Modules of the process</h3> |
<div class="division"> | <div class="division"> | ||
<div class="half"> | <div class="half"> | ||
| Line 266: | Line 266: | ||
<h3>Regulation of lactate production in E.coli 1</h3> | <h3>Regulation of lactate production in E.coli 1</h3> | ||
<img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/c/cb/Lego_description-regulation_E1.png" /> | <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/c/cb/Lego_description-regulation_E1.png" /> | ||
| − | + | ||
<div class="division"> | <div class="division"> | ||
<div class="two_third"> | <div class="two_third"> | ||
| Line 272: | Line 272: | ||
</div> | </div> | ||
<div class="one_third last"> | <div class="one_third last"> | ||
| − | When being outside the cells, lactate acidifies the medium, which is dangerous for the bacteria. That’s why a pH-sensing module has been built to detect pH levels and produce the TetR protein when the pH is lower than 5 | + | When being outside the cells, lactate acidifies the medium, which is dangerous for the bacteria. That’s why a pH-sensing module has been built to detect pH levels and produce the TetR protein when the pH is lower than 5.5. |
</div> | </div> | ||
</div> | </div> | ||
| Line 287: | Line 287: | ||
<h3>Communication between E.coli 1 and E.coli 2</h3> | <h3>Communication between E.coli 1 and E.coli 2</h3> | ||
<img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/a/af/Lego_description-communication.png" /> | <img class="" alt="Regulation E1" src="https://static.igem.org/mediawiki/2015/a/af/Lego_description-communication.png" /> | ||
| − | <p>In fact, the module that produces lactate not only produces it but is also responsible for the synthesis of a small molecule called HSL (HomoSeryl-Lactone) . This molecule is exported into the medium and is able to enter the second | + | <p>In fact, the module that produces lactate not only produces it but is also responsible for the synthesis of a small molecule called HSL (HomoSeryl-Lactone) . This molecule is exported into the medium and is able to enter the second bacterium, being responsible for communication between E.coli 1 and 2.</p> |
<div class="division"> | <div class="division"> | ||
<div class="two_third"> | <div class="two_third"> | ||
Revision as of 15:42, 14 November 2015
General Concepts
A genetic module is constituted of 4 elements, called parts, that are DNA sequences which possess a specific function: the promotor, the RBS, the coding sequence and the terminator.
The role of a genetic module is to produce certain quantity of a protein under some specific conditions. The fabrication process, from DNA to protein, consists in two steps: transcription and translation.
If the DNA is a book of recipes, the transcription process consists in photocopying one page, in which are written the instructions for one specific food; and the translation process corresponds to the cooking phase, in which the "cooker" is the ribosome. The ribosome reads the instructions and at the same time builds the protein. This is called the Central Dogma of Biology.
General Concepts
The transcription can be regulated by different factors (repressors, pH, light, etc) which are detected by the promotor. These signals induce or inhibit the activation of the module.
If the module is activated then the transcription process begins, in which several copies of the message are made.
The RBS (Ribosomal Bonding Site) intervenes in the translation process: if it is strong, many proteins will be synthesised. If it is weak, few proteins will be synthetized. So the function of RBS is regulate the quantity of produced proteins.
The coding sequence is the message, the recipe that shall be translated to protein.
The terminator is a DNA sequence that puts an end to the transcription process.
Why Legos are a friendly way to explain SB?
The team decided to used legos to explain the pla project due to different reasons.
First Reason
They make tangible microscopic things
Second Reason
They allow a strong analogy with the DNA parts called « bio-bricks»
They are standard and modular like a biobricks
Third Reason
Finally, they are a funny way to explain complex concepts... for the students...and the teachers!
E. Coli 1 Population: “Lactadora”
In our project we used two bacterias « Escherichia coli »: name and first name of the bacteria.
This population are responsible for lactate production.
E. Coli 2 Population: “PLAdora”
« Escherichia coli »: name and first name of the bacteria. « 1 » y « 2 » only mean that these bacteria, in this process, are responsible for different functions (but they belong the same bacteria strain).
This population are responsible for process the lactate into PLA.
Transformation of glucose into pyruvate is a bacterial natural process, it doesn’t need human intervention.
LDH uses pyruvate and transforms it into lactate, the intermediate compound that allows PLA synthesis.
Finally, lactate can be obtained from glucose thanks to LDH, which gene we insert into the bacterium.
The lactate produced by the E.coli 1 Population is secreted into the medium and enters in the bacteria of the E.coli 2 Population
Lactate enters into the E.coli 2 Population to be processed into PLA by the presented module.
The P-CoA-T unites lactate with a cofactor called « Coenzyme A », transforming lactate into « Lactyl-CoA ».
PhaC1 gathers all the lactyl-CoA that are present in the cell and unites them together. . .
This reaction is called « polymerization ». The product of this polymerization is the PLA.
To sum up, this module processes lactate to transform it into PLA.
The produced PLA is processed by a second module, which produces a hybrid protein constituted of a first protein called phasyn and of a much smaller protein having affinity for PLA. The role of this hybrid protein is to make the cell know that PLA is ready for exportation.
The hybrid protein sticks with PLA and the cell exports it into the extra-cellular medium, ready to be extracted and purified.
Important Modules of the process
E.coli 1 Population
E.coli 2 Population
Regulation of lactate production in E.coli 1
Communication between E.coli 1 and E.coli 2
In fact, the module that produces lactate not only produces it but is also responsible for the synthesis of a small molecule called HSL (HomoSeryl-Lactone) . This molecule is exported into the medium and is able to enter the second bacterium, being responsible for communication between E.coli 1 and 2.
Communication between E.coli 1 and E.coli 2
The concerted action of LuxR with HSL activates the PLA production and makes possible its exportation. This activation is possible only if there is enough lactate in the medium (since it is the same module that produces lactate and HSL). This way, E.coli 1 leads the production, telling to E.coli 2 when the PLA synthesis can begin). That’s why it is said that HSL is a communication molecule.
The concerted action of LuxR with HSL activates the PLA production and makes possible its exportation. This activation is possible only if there is enough lactate in the medium (since it is the same module that produces lactate and HSL). This way, E.coli 1 leads the production, telling to E.coli 2 when the PLA synthesis can begin). That’s why it is said that HSL is a communication molecule.