Team:UC Davis

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<div id="overview" class="textbg"><h1 class="title">PROJECT OVERVIEW</h1>
 
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<p>Transcription activator-like effectors (TALEs) are proteins secreted by the bacterial pathogen <i>Xanthomonas</i> that contain sequence specific DNA binding domains and can act as transcriptional repressors or activators (Mahfouz et al 2012). This binding occurs through hydrogen bonds and van der Waals interactions and is stabilized by the protein's secondary structure. The DNA binding domains are sequence specific due to consecutive protein repeats, the composition of each which corresponds to a certain base preference (Meckler et al). TAL repressors can therefore be engineered to bind to any DNA sequence of interest, following now well-understood rules for TAL-DNA binding (Boch J et al 2009, Moscou et al 2009).  TALEs are thus a powerful and modular tool for the control of gene expression in genetic circuits. Current efforts to quantify and predict TALE binding affinities and functionalities are being made in order to create libraries of TALE systems that will serve to streamline research and the development of genetic devices (Meckler et al).</p>
 
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<p><br />Riboswitches, on the other hand, are regulatory structures in the 5’-UTR of mRNA that undergo a conformational change in the presence of a specific ligand that binds to the aptamer domain of the structure (Caron et al 2012). This conformational change can regulate the initiation of translation by sequestering the ribosome binding site of the mRNA sequence, making it unavailable for binding (Caron et al 2012). Riboswitches have been shown to work in diverse bacterial species and many natural examples have been found for riboswitches that turn off translation in the presence of the target ligand as well (Topp et al 2010, Muranaka et al 2009). Riboswitches have also been well characterized, are dose-dependent and have been engineered to respond to non-natural ligands thus providing an orthogonal control system (Dixon et al 2009). These RNA-based devices, like the TALE proteins, are also modular and powerful tools for the control of gene expression.</p>
 
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<p><br/>The fusion of these two devices--placing the TAL repressors under the control of riboswitches--offers a means by which to control, in an inducible manner, the expression of any gene of interest. Our group’s goal is to develop a demonstrate the use of TAL repressors with different theophylline riboswitches and thus develop a library of fully characterized inducible repression devices, as well as a software application capable of predicting the functionality and dynamics of a riboswitch-TALE combination. Since our control device is RNA-based, a number of transcriptional and translational steps involved in usual genetic control constructs are eliminated, reducing noise. Furthermore, as our understanding of riboswitches develops it may be possible to develop a fully orthogonal, highly versatile system for control of gene expression. There is a potential for multiplexing, as riboswitches designed to respond to different molecules and fused to different TAL repressors can be used in parallel within a single chassis, or can be induced in a temporally sequential manner for many applications, such as developmental research.</p></br>  
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<h2>Our Sponsors</h2>
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<a class="twitter-timeline" width=250px height=300px href="https://twitter.com/UCDavisiGEM" data-widget-id="363400889542778880">Tweets by @UCDavisiGEM</a>
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<a href="http://engineering.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f6/UCD_CoE.png" width="200" height="40"></a>
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<a href="http://biosci.ucdavis.edu/index_js.html" target="_blank"><img src="https://static.igem.org/mediawiki/2011/b/b1/UCD_biosci_sponsor.jpg" width="200" height="90"></a>
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<a href="http://www.genomecenter.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/1/1b/UCD_Genome_center_sponsor.jpg" width="200" height="60"></a>
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<a href="http://www.bme.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/4/40/UCD_BME_logo_minimal_copy.png" width="200 height="70"></a>
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                    <div><a href="https://2013.igem.org/Team:UC_Davis/Project_Overview">
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                    <a href="https://2013.igem.org/Team:UC_Davis/Project_Overview"><h3>Project Overview</h3></a>
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                    <p>Learn about how we combine riboswitches and TALs into robust orthogonal mechanisms for    inducible repression.
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              <a href="https://2013.igem.org/Team:UC_Davis/Data"><img src="https://static.igem.org/mediawiki/2013/d/d5/Resultsicon_UCDavis.jpg" class="blur"></a>
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              <a href="https://2013.igem.org/Team:UC_Davis/Data"><h3>Results</h3></a>
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                    <p>Check out the cool results of our experiments with RiboTALs. <br />
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                            <a href="https://2013.igem.org/Team:UC_Davis/AndersonPromoters"><img src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png" class="checkmark"></a><p>We also made the Anderson promoter family controllable through induction with RiboTALs.</p>
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                    <a href="https://2013.igem.org/Team:UC_Davis/HumanPracticesOverview">
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                    <a href="https://2013.igem.org/Team:UC_Davis/HumanPracticesOverview"><h3>Human Practices</h3></a>
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                    <p>Take a look at how we promote sharing in iGEM through The Depot, an open BioBrick characterization database.<br />
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                        <a href="http://dilbert.cs.ucdavis.edu/Depot" class="bold">Visit the Depot!</a>
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              <a href="https://2013.igem.org/Team:UC_Davis/Criteria"><img src="https://static.igem.org/mediawiki/2013/f/f3/Judgingbutton_UCDavis.jpg" class="blur"</a>
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              <a href="https://2013.igem.org/Team:UC_Davis/Criteria"><h3>Judging Criteria</h3></a>
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                    <p>Here's the criteria that we met for this year's team.
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<h1>Welcome</h1>
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Welcome to the 2013 UC Davis iGEM Wiki!<br></br>We have created a novel class of transcription factors known as RiboTALs. We sought to address the constraints placed on circuit design by the limited number of well characterized promoters at our disposal, and their respective transcription factors. Our device is a hybrid system composed of two parts: Transcriptional Activator-Like (TAL) effectors which can be engineered to bind to and repress any sequence of interest and riboswitches that can respond to any inducer molecule due to their engineerable and modular aptamer binding domains. <br></br> We also designed and implemented a Biobrick characterization database called The Depot to promote sharing and openness in iGEM.</p>
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Tweets by @UCDavisiGEM</a>
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Latest revision as of 22:43, 5 December 2013

Our Sponsors

Project Overview

Learn about how we combine riboswitches and TALs into robust orthogonal mechanisms for inducible repression.

Results

Check out the cool results of our experiments with RiboTALs.

We also made the Anderson promoter family controllable through induction with RiboTALs.

Human Practices

Take a look at how we promote sharing in iGEM through The Depot, an open BioBrick characterization database.
Visit the Depot!

Judging Criteria

Here's the criteria that we met for this year's team.

Welcome

Welcome to the 2013 UC Davis iGEM Wiki!

We have created a novel class of transcription factors known as RiboTALs. We sought to address the constraints placed on circuit design by the limited number of well characterized promoters at our disposal, and their respective transcription factors. Our device is a hybrid system composed of two parts: Transcriptional Activator-Like (TAL) effectors which can be engineered to bind to and repress any sequence of interest and riboswitches that can respond to any inducer molecule due to their engineerable and modular aptamer binding domains.

We also designed and implemented a Biobrick characterization database called The Depot to promote sharing and openness in iGEM.

Retrieved from "http://2013.igem.org/Team:UC_Davis"