Team:KAIST Korea/Home Intro

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<a href="https://2012.igem.org/Team:KAIST_Korea/Home_iGEM"><img src="https://static.igem.org/mediawiki/2012/c/c0/Igem_ico.png"/></a>
<a href="https://2012.igem.org/Team:KAIST_Korea/Home_iGEM"><img src="https://static.igem.org/mediawiki/2012/c/c0/Igem_ico.png"/></a>
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<div id="top-img-description-box"><span id="top-img-description">KAIST, KI Building</span></div>
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<div id="top-img-description-box"><span id="top-img-description">Home : Introduction</span></div>
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        <h1> Abstract</h1>
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<span id="sub-title">Reguli</span></br></br>
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<span id="little"></span><span id="starter">B</span>iological engineering has brought us handy tools to produce desired products. However, we have to induce genes to properly express them on correct cell phase. We, KAIST 2012 iGEM team, suggest a module that automatically turns the transcription of gene on or off using dual-phase switching module. In our model, promoter orientation is designed to be reversed when sufficient quorum molecule is detected. Then, genes on the other side, indigo synthesizing enzyme bFMO, lactonase, and excisionase are expressed. Indigo is meaningful in that it is the end-product of its metabolic pathway and, its color can be easily detected. Lactonase quenches quorum molecule(lactone), which will generate an oscillating pattern. Excisionase acts on the recombination site to set promoter to its initial orientation.  In this way, we can regulate metabolic pathways. So we call it regulative E.coli, Reguli.
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         <h1> Introduction</h1>
         <h1> Introduction</h1>
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<span id="sub-title">"There have been attempts to reduce atmospheric level of carbon dioxide in various approaches."</span></br></br>
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<span id="sub-title">"We suggest an auto-regulation module free from induction which utilizes dual-phase switching system."</span></br></br>
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<span id="starter">S</span>ince the Industrial Revolution, fossil fuels have been used to power industries and machines. As the world gets more industrialized in accordance with population growth, the demand for fossil fuels has grown more than ever. Due to drastic increase of fossil fuel consumption, massive amount of carbon dioxide (CO<sub>2</sub>) has been emitted into the atmosphere and the amount is still growing. As carbon dioxide (CO<sub>2</sub>) is considered to be a significant factor accelerating global warming, there have been numerous attempts to reduce the atmospheric level of carbon dioxide (CO<sub>2</sub>). Administrators have ratified protocols to regulate the emission of carbon dioxide (CO<sub>2</sub>). Scientists have endeavored to figure out ways to reduce this greenhouse gas despite several limitations.
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<span id="little"></span><span id="starter">T</span>hroughout past iGEM competitions, many kinds of bio-modules were proposed and tested. They were great and some were brilliant, but it doesn’t seem many of them are universally available. Of course the goal of iGEM is to enrich the database, but we view the beauty of this registry is to contain as many modules which can be readily applied to actual research as possible. Thus, here now, we suggest an auto-regulation module free from induction which utilizes dual-phase switching system and quorum sensing.
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<span id="starter">W</span>e, Team KAIST, Korea, suggest an idea of carbon dioxide (CO<sub>2</sub>) fixation with specially engineered bacterial strain which converts atmospheric carbon dioxide (CO<sub>2</sub>) into meaningful biomass as well as consuming it.
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<span id="little2"></span>We may think of many meanings for this module; bio-computing, in-cell signal processing, and auto-control of cell metabolism. For example, since we use dual-phase switching system, we may consider each direction of gene expression as a signal; signal 0 or 1 of binary code. Thereby we can use this module to generate in vivo logic gates or computational system.  
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        <h1> Project Overview</h1>
 
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<span id="sub-title">CO<sub>2</sub> Fixation Pathway and Pathway Switching Module</span></br></br>
 
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<span id="sub-sub-title"> 1. CO<sub>2</sub> Fixation Pathway</span></br></br>
 
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<span id="starter">R</span>eductive acetyl-CoA pathway is a pathway for carbon dioxide (CO<sub>2</sub>) fixation in many anaerobes. Acetogenic bacteria, or acetogens, use this pathway to synthesize acetic acid from carbon dioxide. This pathway allows acetogens to grow autotrophically using hydrogen(H<sub>2</sub>) and carbon monooxide(CO) as electron donor and carbon dioxide (CO<sub>2</sub>) as electron acceptor.[1]
 
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<span id="starter">B</span>ecause the pathway is non-regenerative, reductive acetyl CoA pathway is a appropriate target pathway to consume atmospheric carbon dioxide (CO<sub>2</sub>). Nowadays, full genome sequences of bunch of acetogens are available. Also, the enzymes consisting the pathway are elucidated allowing us to reconstruct the pathway in Escherichia coli.
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<span id="little2"></span>Dual-phase switching system adopts DNA recombination system of bacteriophage origin. In this system, DNA integrase recognizes specific sequences called attB and attP and then invert the sequence between them. Exisionase revert this sequence into its original state by recognizing the recombination site. We can thereby use this system to turn the pathway on or off.
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<i>[1] Environ Microbiol. 2008 October ; 10(10): 2550-2573.</i>
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<span id="little2"></span>Products of LuxI and LuxR are used to generate signals in our quorum sensing model. They initiate the operation of auto-regulation module. Lactonase will regulate the signal to yield an oscillating pattern.
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<span id="little2"></span>As our end product, we selected bio-indigo which comes from indole. This widespread pigment is produced by bFMO, bacterial Flavin-containing MonoOxygenase. Successful production of bio-indigo verifies that our module can be embodied well in metabolic pathway and also proposes its potential usage.
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<span id="sub-sub-title"> 2. Pathway Switching Module</span></br></br>
 
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<span id="starter">T</span>hroughout past iGEM competitions, many kinds of bio-modules were proposed and tested. In our project, we are suggesting dual-phase switching module using DNA recombination system that is new to iGEM part registry. With this module we will be able to control metabolic pathway we are targeting.
 
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<span id="starter">C</span>oupling of suggested module with cell growth and metabolic pathway, we expect our module enable our cells to control their metabolisms according to cell growth.
 
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<h1>Synthetic Biology</h1>
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Latest revision as of 15:19, 26 October 2012

KAIST Korea 2012 iGEM

Home : Introduction

Abstract

Reguli

Biological engineering has brought us handy tools to produce desired products. However, we have to induce genes to properly express them on correct cell phase. We, KAIST 2012 iGEM team, suggest a module that automatically turns the transcription of gene on or off using dual-phase switching module. In our model, promoter orientation is designed to be reversed when sufficient quorum molecule is detected. Then, genes on the other side, indigo synthesizing enzyme bFMO, lactonase, and excisionase are expressed. Indigo is meaningful in that it is the end-product of its metabolic pathway and, its color can be easily detected. Lactonase quenches quorum molecule(lactone), which will generate an oscillating pattern. Excisionase acts on the recombination site to set promoter to its initial orientation. In this way, we can regulate metabolic pathways. So we call it regulative E.coli, Reguli.


Introduction

"We suggest an auto-regulation module free from induction which utilizes dual-phase switching system."

Throughout past iGEM competitions, many kinds of bio-modules were proposed and tested. They were great and some were brilliant, but it doesn’t seem many of them are universally available. Of course the goal of iGEM is to enrich the database, but we view the beauty of this registry is to contain as many modules which can be readily applied to actual research as possible. Thus, here now, we suggest an auto-regulation module free from induction which utilizes dual-phase switching system and quorum sensing.

We may think of many meanings for this module; bio-computing, in-cell signal processing, and auto-control of cell metabolism. For example, since we use dual-phase switching system, we may consider each direction of gene expression as a signal; signal 0 or 1 of binary code. Thereby we can use this module to generate in vivo logic gates or computational system.

Dual-phase switching system adopts DNA recombination system of bacteriophage origin. In this system, DNA integrase recognizes specific sequences called attB and attP and then invert the sequence between them. Exisionase revert this sequence into its original state by recognizing the recombination site. We can thereby use this system to turn the pathway on or off.

Products of LuxI and LuxR are used to generate signals in our quorum sensing model. They initiate the operation of auto-regulation module. Lactonase will regulate the signal to yield an oscillating pattern.

As our end product, we selected bio-indigo which comes from indole. This widespread pigment is produced by bFMO, bacterial Flavin-containing MonoOxygenase. Successful production of bio-indigo verifies that our module can be embodied well in metabolic pathway and also proposes its potential usage.

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