Team:KULeuven/Biobricks

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<h3>Biobricks</h3>
<h3>Biobricks</h3>
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<b><u><i> still under construction: Clarifying pictures will be added soon, all biobricks will be clickable and lead towards the biobrick register </b></u></i><br><br>
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The list of all the biobricks that we used are on the iGEM registry which can be found<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2011&group=KULeuven" target="blank"> here</a>. <br><br>
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Our system consists of 4 components which are outlined underneath: a regulation plasmid; an antifreeze component; a freeze component and a cell death mechanism.<br><br>
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Below you can see two short videos in which we added different kinds of <i>E.D Frosti</i> to supercooled (-6°C)
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ultrapure “milli-Q” water (Millipore Corporation). The first video (GFP-control), is a control: when <i>E.D. Frosti</i> constitutively expressing a GFP construct is added to the supercooled water, it does not freeze.  
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<h2> 1: Regulation plasmid </h2>
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In the second video (INP), <i> E.D. Frosti</i> contains a constitutively active Ice-Nucleating Protein producing biobrick (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K584027" target="blank">  <b>BBa_K584027</b></a>).
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Transcription of this component will activate the AFP and repress the INP formation. Activation proceeds through the luxR protein (Bba_C0062) and repression through the luxI protein (Bba_C0061). LuxR is an activator of the Lux-CI promoter which is used in our antifreeze component. At the other hand luxI is a repressor of the Lac-lux promoter, which is used in our freeze component, so that both genes (<i>luxR</i> and<i>luxI</i>) are under the control of the pBAD promoter (Bba_I3453) which is induced when L-arabinose is present. [A picture of these biobricks will be uploaded]<br><br>
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When we added this to the supercooled water, it froze immediately.
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<br><br>
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<h2> 2: Antifreeze</h2>
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The purpose of this component is to synthesize an antifreeze protein after a given stimulus, in this case arabinose. Normally, the antifreeze protein is produced intracellularly to prevent a cell from freezing. We however, try to prevent the environment from freezing and therefore we design a system that couples the antifreeze protein to the extracellular membrane. To check if we really have transcribed the protein we couple melanin production to the promoter as well. Melanin is a black pigment and thus visualizes the antifreeze production.<br><br>
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The most important biobrick in the antifreeze system is the extracellular antifreeze protein. It is a new biobrick we want to synthesize. In order to couple the antifreeze protein to the extracellular membrane, we fuse it to an extracellular anchor (Bba_K103006) and a flexible linker (BBa_K105012 ). Also the antifreeze protein (AFP) itself  is a new biobrick.[A picture of this new biobrick will be added] <br><br>
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The second protein that we will use in the antifreeze system, is the enzyme tyrosinase (EC 1.14.18.1) (BBa_K193600). This enzyme converts tyrosine to dopaquinone. Dopaquinone is an intermediate product of melanin biosynthesis pathway. After production of Dopaquinone, Melanin is generated by non-enzymatical chain reaction, so overexpression of tyrosinase in <i>E.coli</i> causes accumulation of Melanin. (reference: https://2009.igem.org/Team:Tokyo_Tech/DarkercoloredEcoli) The Tokyo tech team of 2009 showed that the color of the strain expressing tyrosinase became 10-fold darker than that of the control.<br><br>
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The promoter we use for both proteins is the plux-CI promotor (BBa_R0065). It is a hybrid promoter responding to cI repressor and LuxR. CI repressor negatively regulates this promoter and LuxR activates its transcription. The effect of cI is dominant over LuxR.<br><br>
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<h2>3: Freeze</h2>
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This component induces water to freeze through the use of Ice Nucleating Proteins (INPs). INPs are already anchored in the outer membrane through its N-terminal and C-terminal region. In order to check if we really have transcribed the protein, we couple the production of luminescent pigment to the promoter as well. This bright pigment, lets us visualize the freezing system.<br><br>
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Two other biobricks used in Freeze component are crtB coding sequence encoding phytoene synthase and crtI coding sequence encoding phytoene dehydrogenase. The first one is the coding sequence of crtI from <i>Pantoea ananatis</i> (formerly <i>Erwinia uredovora</i>) (Accession number D90087). It encodes phytoene dehydrogenase, part of the carotenoid biosynthesis pathway, which converts Phytoene to Lycopene (Misawa, et al., 1990).<br><br>
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The second one is the coding sequence of crtI from <i>Pantoea ananatis</i> (formerly <i>Erwinia uredovora</i>) (Accession number D90087). It encodes phytoene dehydrogenase, part of the carotenoid biosynthesis pathway, which converts Phytoene to Lycopene (Misawa, et al., 1990).  <br><br>
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The promoter we use is the pLac-lux hybrid promoter, BBa_K091100. This promoter is repressed by the lacI repressor and induced by IPTG. It is repressed by the luxR repressor bound to the corepressor CO6HSL. It contains a lux box and a lacI binding site. Besides, The cI regulated promoter is based on the pR promoter from bacteriophage <i>lambda</i>. The promoter has two DNA binding sites for lambda cI repressor BBa_C0051. <br><br>
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<h2>4: cell death mechanism</h2>
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The cell death mechanism we use will be induced when stimulus 1 (L-arabinose) or stimulus 2 (lactose) is given and at the same time a cold temperature is sensed by the bacterium. <br><br>
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For this we created the following procedure: we grow the bacteria at the optimal temperature of 37°C. Then we produce the protein we wish by applying the correct stimulus (e.g., L-arabinose to produce AFP). After synthesizing the desired amount of protein, we lower the temperature to induce the cell death mechanism.<br><br>
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<iframe src="http://player.vimeo.com/video/29380418?title=0&amp;byline=0&amp;portrait=0" width="590" height="315" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe><br><br>
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The most essential protein for inducing cell death is the colicin activity gene, CeaB (Bba_K131009). CeaB is part of the Colicin E2 operon. The operon comprises the colicin activity gene, ceaB, the colicin immunity gene, ceiB, and the lysis gene, celB, which is essential for colicin release from producing cells. We only use CeaB , because we only have to kill the inner system of the cell and not the membrane with its useful proteins (AFP or INP). Via this way we also try to prevent horizontal exchange of DNA between <i>E.D. Frosti</i> and other bacteria.<br><br>
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To obtain the desired regulation of the cell death mechanism, a key-lock mechanism is implemented. A ribokey is under regulation of a cold sensing promoter, either CspA promoter (Bba_K328001) or HybB promoter (Bba_K410000). This ribokey is the key to unlock the ribolock, which happens when cold conditions are applied. The ribolock prevents the CeaB protein to be transcribed under normal conditions (37°C). Only cold temperatures are not sufficient to induce cell death, also a stimulus associated with INP- or AFP generation is needed. This prevents cells from being killed when stored in the fridge before generation of INP or AFP. To become dependent on a second stimulus we put the same promoters as for generation of INP or AFP in front of the ribolock. These promoters are the Lux-CI promoter (Bba_R0065) (the same promoter as for generation of AFP) and Lac-Lux promoter (Bba_K091100) (the same promoter as for generation of INP).<br><br>
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<iframe src="http://player.vimeo.com/video/29380483?title=0&amp;byline=0&amp;portrait=0" width="590" height="315" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe><br><br>
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Latest revision as of 12:47, 27 October 2011

KULeuven iGEM 2011

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Biobricks


The list of all the biobricks that we used are on the iGEM registry which can be found here.

Below you can see two short videos in which we added different kinds of E.D Frosti to supercooled (-6°C) ultrapure “milli-Q” water (Millipore Corporation). The first video (GFP-control), is a control: when E.D. Frosti constitutively expressing a GFP construct is added to the supercooled water, it does not freeze. In the second video (INP), E.D. Frosti contains a constitutively active Ice-Nucleating Protein producing biobrick ( BBa_K584027). When we added this to the supercooled water, it froze immediately.












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