Team:Peking R/Project

From 2011.igem.org

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   <p class="notbookmaintitle" align=center>Softcoding of Genetic Program<a name="start" id="start"></a></p>
   <p class="notbookmaintitle" align=center>Softcoding of Genetic Program<a name="start" id="start"></a></p>
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   <p class="mainbody"><strong>Background of softcoding</strong><br />
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    There are basically two design principles  in computer programming: hardcoding and softcoding. Hardcoding1  refers to the practice of embedding parameters and functions into the source  code of a program, whereas softcoding2 obtains values and functions  from external source. Hardcoding would be convenient when no dynamic parameters  are required in the program, but the source code should be rewritten anytime  the input data or functions change. On the contrary, softcoding enables users  to customize the software to their needs by altering external input, without  having to edit the program&rsquo;s source code time after time. </p>
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  <p class="mainbody">In the exciting field of synthetic biology,  various genetic programs have been developed to perform certain functions in  living organismswhich are similar to computer programs. For instance, a genetic  toggle switch <em>in vivo</em> was developed  that could be switched between two states by chemical or thermal induction.Another  example is that an oscillatory network was constructed in which the synthesis  of green fluorescent protein was periodically induced.Yet  genetic programs need optimization to achieve ideal performance, especially  when several genetic modules are coupled. Similarly, optimization of metabolic  pathways is also a key issue in the field of metabolic engineering. </p>
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  <p>Traditional methods to optimize genetic  programs or metabolic pathways generally involve construction of libraries that  contain large amounts of mutants, and multi-round screening is usually  required. Apart from the obvious drawback that the constructing and screening  procedures are laborious and time-consuming, these methods could only generate  mutants with a fixed configuration, and to fine-tune their performance would  require another round of mutagenesis and selection, which resembles &ldquo;hardcoding&rdquo;.  Therefore, a platform for &ldquo;softcoding&rdquo; of genetic programs is urgently needed. </p>
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  <p>&nbsp;</p>
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  <p class="mainbody"><strong>Softcoding Approach</strong><br />
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  Based on the principle of softcoding, this  year our team established an extensible and versatile platform for softcoding  of genetic program, which is composed of anRNA toolkit and a methodology-- The RNA  toolkit consists of interoperable and truly modular ligand-responsive  riboswitches/ribozymes, while the methodology is automated design of synthetic  ribosomal binding sites (RBS) with customized translation rate. When combining  them together, a quantitative correlation between the concentration of specific  ligand and synthetic RBS&rsquo; translation strength can be established. Therefore,  when tuning genetic program, customized RBS&rsquo; translation strength at multiple  sites can be high-throughputly achieved without having to conduct laborious  mutagenesis and characterization, followed by easily determining the  configuration of RBS(s)&rsquo;translation strength. Then RBS sequences that meet this  configuration will be automatically designed via computer  algorithms. </p>
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  <p class="mainbody"><strong>Background of softcoding</strong><br />
 +
    There are basically two design principles  in computer programming: hardcoding and softcoding. Hardcoding1  refers to the practice of embedding parameters and functions into the source  code of a program, whereas softcoding2 obtains values and functions  from external source. Hardcoding would be convenient when no dynamic parameters  are required in the program, but the source code should be rewritten anytime  the input data or functions change. On the contrary, softcoding enables users  to customize the software to their needs by altering external input, without  having to edit the program&rsquo;s source code time after time. </p>
 +
  <p class="mainbody">In the exciting field of synthetic biology,  various genetic programs have been developed to perform certain functions in  living organismswhich are similar to computer programs. For instance, a genetic  toggle switch <em>in vivo</em> was developed  that could be switched between two states by chemical or thermal induction.Another  example is that an oscillatory network was constructed in which the synthesis  of green fluorescent protein was periodically induced.Yet  genetic programs need optimization to achieve ideal performance, especially  when several genetic modules are coupled. Similarly, optimization of metabolic  pathways is also a key issue in the field of metabolic engineering. </p>
 +
  <p>Traditional methods to optimize genetic  programs or metabolic pathways generally involve construction of libraries that  contain large amounts of mutants, and multi-round screening is usually  required. Apart from the obvious drawback that the constructing and screening  procedures are laborious and time-consuming, these methods could only generate  mutants with a fixed configuration, and to fine-tune their performance would  require another round of mutagenesis and selection, which resembles &ldquo;hardcoding&rdquo;.  Therefore, a platform for &ldquo;softcoding&rdquo; of genetic programs is urgently needed. </p>
 +
  <hr />
 +
  <p>&nbsp;</p>
 +
  <p class="mainbody"><strong>Softcoding Approach</strong><br />
 +
  Based on the principle of softcoding, this  year our team established an extensible and versatile platform for softcoding  of genetic program, which is composed of anRNA toolkit and a methodology-- The RNA  toolkit consists of interoperable and truly modular ligand-responsive  riboswitches/ribozymes, while the methodology is automated design of synthetic  ribosomal binding sites (RBS) with customized translation rate. When combining  them together, a quantitative correlation between the concentration of specific  ligand and synthetic RBS&rsquo; translation strength can be established. Therefore,  when tuning genetic program, customized RBS&rsquo; translation strength at multiple  sites can be high-throughputly achieved without having to conduct laborious  mutagenesis and characterization, followed by easily determining the  configuration of RBS(s)&rsquo;translation strength. Then RBS sequences that meet this  configuration will be automatically designed via computer  algorithms. </p>
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     <em>RNA toolkit</em>()<br />
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     <em>RNA toolkit</em><a href="https://2011.igem.org/Team:Peking_R/Project/RNAToolkit">(Learn more...)</a><br />
     Recently, RNA devices have emerged as powerful  tools to regulate gene expression <em>in vivo</em>,  and particularly, ligand-responsive riboswitches/ribozymes enable us to  manipulate translation strength of specific genes upon different concentrations  of ligands.<a href="#_edn3" name="_ednref3" title="" id="_ednref3"> </a>Ligand-responsive  riboswitches/ribozymes regulate the translation rate of downstream gene by changing  conformations, cleaving or splicing upon external addition of ligand. Compared  with transcriptional and post-translational regulation, riboswitches/ribozymes  function through allostery of RNA structure, which requires little or no  assistance from proteins, so the regulation mechanism is relatively simpler and  their functions are more decoupled from native biological activities.</p>
     Recently, RNA devices have emerged as powerful  tools to regulate gene expression <em>in vivo</em>,  and particularly, ligand-responsive riboswitches/ribozymes enable us to  manipulate translation strength of specific genes upon different concentrations  of ligands.<a href="#_edn3" name="_ednref3" title="" id="_ednref3"> </a>Ligand-responsive  riboswitches/ribozymes regulate the translation rate of downstream gene by changing  conformations, cleaving or splicing upon external addition of ligand. Compared  with transcriptional and post-translational regulation, riboswitches/ribozymes  function through allostery of RNA structure, which requires little or no  assistance from proteins, so the regulation mechanism is relatively simpler and  their functions are more decoupled from native biological activities.</p>
<p class="mainbody">We characterized some existing  riboswitches/ribozymes, namely thiamine pyrophosphate (TPP)-responsive hammerhead  ribozymes and theophylline riboswitches. By altering the upstream promoter and  downstream coding sequence of the RNA controllers, we demonstrated that their  performance was independent from sequence context, which proved the modularity  of these RNA devices.</p>
<p class="mainbody">We characterized some existing  riboswitches/ribozymes, namely thiamine pyrophosphate (TPP)-responsive hammerhead  ribozymes and theophylline riboswitches. By altering the upstream promoter and  downstream coding sequence of the RNA controllers, we demonstrated that their  performance was independent from sequence context, which proved the modularity  of these RNA devices.</p>
   <p class="mainbody">To further extend the range of application  of our RNA toolkit, we created a ribozyme that functions with a different  mechanism, which has an extreme low level of backgrounds. We substituted the  aptamer domain of c-di-GMP group Intron to theophylline-responsive aptamer, thus  invented a group I intron that senses theophylline to perform splicing function.  Moreover, we introduced a general method to evolve hammerhead ribozyme that  senses a new ligand. By coupling an adenine aptamer with hammerhead ribozyme  and randomizing nucleotides in the linker domain, we evolved new hammerhead  ribozymes through dual selection, whose self-cleavage could be regulated by  adenine. Our project provided a new design principle for rational or  semi-rational design of riboswitches/ribozymes. </p>
   <p class="mainbody">To further extend the range of application  of our RNA toolkit, we created a ribozyme that functions with a different  mechanism, which has an extreme low level of backgrounds. We substituted the  aptamer domain of c-di-GMP group Intron to theophylline-responsive aptamer, thus  invented a group I intron that senses theophylline to perform splicing function.  Moreover, we introduced a general method to evolve hammerhead ribozyme that  senses a new ligand. By coupling an adenine aptamer with hammerhead ribozyme  and randomizing nucleotides in the linker domain, we evolved new hammerhead  ribozymes through dual selection, whose self-cleavage could be regulated by  adenine. Our project provided a new design principle for rational or  semi-rational design of riboswitches/ribozymes. </p>
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   <p class="mainbody"><em>RBS automated design</em><br />
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  <hr />
 +
   <p class="mainbody"><em>RBS automated design</em><a href="https://2011.igem.org/Team:Peking_R/Project/RBSAutomatedDesign">(Learn more...)</a><br />
   In bacteria, ribosomal binding site (RBS) sequence  is one of the most important determinants of translational initiation/translation  strength. Therefore manipulating RBS sequence would significantly affect the  translation strength of downstream gene. Salis <em>et.al</em>. used Gibbs energy (∆G) of the &ldquo;docked&rdquo; state of the mRNA-30S ribosomal subunit complex to  predict the translation strength of RBS sequence. Based on their pioneering  work, we developed a methodology that correlated the performance of the RNA  controllers under certain concentration of ligand to translation strength met  by corresponding RBS sequence. Combining this methodology with our RNA toolkit,  we can generate an RBS sequence through automated design once we achieved an  ideal configuration of genetic programs through RNA controllers.</p>
   In bacteria, ribosomal binding site (RBS) sequence  is one of the most important determinants of translational initiation/translation  strength. Therefore manipulating RBS sequence would significantly affect the  translation strength of downstream gene. Salis <em>et.al</em>. used Gibbs energy (∆G) of the &ldquo;docked&rdquo; state of the mRNA-30S ribosomal subunit complex to  predict the translation strength of RBS sequence. Based on their pioneering  work, we developed a methodology that correlated the performance of the RNA  controllers under certain concentration of ligand to translation strength met  by corresponding RBS sequence. Combining this methodology with our RNA toolkit,  we can generate an RBS sequence through automated design once we achieved an  ideal configuration of genetic programs through RNA controllers.</p>
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  <hr />
   <p class="mainbody"><strong>Application</strong><br />
   <p class="mainbody"><strong>Application</strong><br />
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   we utilized the  platform to improve performance of two modular genetic devices, <u>AND gate</u> and<u> bistable switch</u>. </p>
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   we utilized the  platform to improve performance of two modular genetic devices,<a href="https://2011.igem.org/Team:Peking_R/Project/Application/AG"> <u>AND gate</u></a> and<u> <a href="https://2011.igem.org/Team:Peking_R/Project/Application/BS">bistable switch</a></u><a href="https://2011.igem.org/Team:Peking_R/Project/Application/">.</a></p>
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  <p class="mainbody">&nbsp;</p>
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  <p class="mainbody"><a href="https://2011.igem.org/Team:Peking_R/Project/Application/AG">AND gate</a></p>
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  <p><a href="https://2011.igem.org/Team:Peking_R/Project/Application/BS">Bistable switch</a></p>
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   <p class="mainbody">We further applied this platform to  optimize a segment of <u>violacein biosynthetic pathway</u>, and achieved  producing purer desired products. </p>
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  <p class="mainbody"> <u><a href="https://2011.igem.org/Team:Peking_R/Project/Application/VIO">violacein biosynthetic pathway</a></u></p>
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   <p class="mainbody">We further applied this platform to  optimize a segment of<u><a href="https://2011.igem.org/Team:Peking_R/Project/Application/VIO">violacein biosynthetic pathway</a></u>, and achieved  producing purer desired products. </p>
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<p class="mainbody"><span class="Reference">Reference:</span><a name="r101" id="r101"></a><a name="r102" id="r102"></a><a name="r103" id="r103"></a><a name="r201" id="r201"></a><a name="r202" id="r202"></a><a name="r203" id="r203"></a><a name="r204" id="r204"></a><a name="r301" id="r301"></a><a name="r302" id="r302"></a><a name="r303" id="r303"></a><a name="r304" id="r304"></a></p>
<p class="mainbody"><span class="Reference">Reference:</span><a name="r101" id="r101"></a><a name="r102" id="r102"></a><a name="r103" id="r103"></a><a name="r201" id="r201"></a><a name="r202" id="r202"></a><a name="r203" id="r203"></a><a name="r204" id="r204"></a><a name="r301" id="r301"></a><a name="r302" id="r302"></a><a name="r303" id="r303"></a><a name="r304" id="r304"></a></p>
<p>[1]  <a href="http://en.wikipedia.org/wiki/Hard_coding">http://en.wikipedia.org/wiki/Hard_coding</a><br />
<p>[1]  <a href="http://en.wikipedia.org/wiki/Hard_coding">http://en.wikipedia.org/wiki/Hard_coding</a><br />
-
   [] <a href="http://en.wikipedia.org/wiki/Softcoding">http://en.wikipedia.org/wiki/Softcoding</a></p>
+
   [2] <a href="http://en.wikipedia.org/wiki/Softcoding">http://en.wikipedia.org/wiki/Softcoding</a></p>
<p><span class="mainbody">[3].Gardner, Timothy S. <em>et. al.</em> (2000). Construction of a genetic toggleswitch in <em>Escherichia coli</em>. Nature 403, 339-342</span> [4].Elowitz, Michael B. and  Leibler, Stanislas (2000). A synthetic oscillatory network of transcriptional  regulators. Nature 403, 335-338  [5].Breaker, Ronald R (2004).Natural and engineered nucleicacids as  tools to explore biology. Nature 432, 838-845<br />
<p><span class="mainbody">[3].Gardner, Timothy S. <em>et. al.</em> (2000). Construction of a genetic toggleswitch in <em>Escherichia coli</em>. Nature 403, 339-342</span> [4].Elowitz, Michael B. and  Leibler, Stanislas (2000). A synthetic oscillatory network of transcriptional  regulators. Nature 403, 335-338  [5].Breaker, Ronald R (2004).Natural and engineered nucleicacids as  tools to explore biology. Nature 432, 838-845<br />
   [6].Salis, Howard M <em>et.al.</em> (2009). Automated design of synthetic ribosome binding sitesto control protein  expression. Nat. Biotech. 27, 946-950</p>
   [6].Salis, Howard M <em>et.al.</em> (2009). Automated design of synthetic ribosome binding sitesto control protein  expression. Nat. Biotech. 27, 946-950</p>

Revision as of 22:58, 5 October 2011

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Softcoding of Genetic Program


Background of softcoding
There are basically two design principles in computer programming: hardcoding and softcoding. Hardcoding1 refers to the practice of embedding parameters and functions into the source code of a program, whereas softcoding2 obtains values and functions from external source. Hardcoding would be convenient when no dynamic parameters are required in the program, but the source code should be rewritten anytime the input data or functions change. On the contrary, softcoding enables users to customize the software to their needs by altering external input, without having to edit the program’s source code time after time.

In the exciting field of synthetic biology, various genetic programs have been developed to perform certain functions in living organismswhich are similar to computer programs. For instance, a genetic toggle switch in vivo was developed that could be switched between two states by chemical or thermal induction.Another example is that an oscillatory network was constructed in which the synthesis of green fluorescent protein was periodically induced.Yet genetic programs need optimization to achieve ideal performance, especially when several genetic modules are coupled. Similarly, optimization of metabolic pathways is also a key issue in the field of metabolic engineering.

Traditional methods to optimize genetic programs or metabolic pathways generally involve construction of libraries that contain large amounts of mutants, and multi-round screening is usually required. Apart from the obvious drawback that the constructing and screening procedures are laborious and time-consuming, these methods could only generate mutants with a fixed configuration, and to fine-tune their performance would require another round of mutagenesis and selection, which resembles “hardcoding”. Therefore, a platform for “softcoding” of genetic programs is urgently needed.


 

Softcoding Approach
Based on the principle of softcoding, this year our team established an extensible and versatile platform for softcoding of genetic program, which is composed of anRNA toolkit and a methodology-- The RNA toolkit consists of interoperable and truly modular ligand-responsive riboswitches/ribozymes, while the methodology is automated design of synthetic ribosomal binding sites (RBS) with customized translation rate. When combining them together, a quantitative correlation between the concentration of specific ligand and synthetic RBS’ translation strength can be established. Therefore, when tuning genetic program, customized RBS’ translation strength at multiple sites can be high-throughputly achieved without having to conduct laborious mutagenesis and characterization, followed by easily determining the configuration of RBS(s)’translation strength. Then RBS sequences that meet this configuration will be automatically designed via computer algorithms.

 



RNA toolkit(Learn more...)
Recently, RNA devices have emerged as powerful tools to regulate gene expression in vivo, and particularly, ligand-responsive riboswitches/ribozymes enable us to manipulate translation strength of specific genes upon different concentrations of ligands. Ligand-responsive riboswitches/ribozymes regulate the translation rate of downstream gene by changing conformations, cleaving or splicing upon external addition of ligand. Compared with transcriptional and post-translational regulation, riboswitches/ribozymes function through allostery of RNA structure, which requires little or no assistance from proteins, so the regulation mechanism is relatively simpler and their functions are more decoupled from native biological activities.

We characterized some existing riboswitches/ribozymes, namely thiamine pyrophosphate (TPP)-responsive hammerhead ribozymes and theophylline riboswitches. By altering the upstream promoter and downstream coding sequence of the RNA controllers, we demonstrated that their performance was independent from sequence context, which proved the modularity of these RNA devices.

To further extend the range of application of our RNA toolkit, we created a ribozyme that functions with a different mechanism, which has an extreme low level of backgrounds. We substituted the aptamer domain of c-di-GMP group Intron to theophylline-responsive aptamer, thus invented a group I intron that senses theophylline to perform splicing function. Moreover, we introduced a general method to evolve hammerhead ribozyme that senses a new ligand. By coupling an adenine aptamer with hammerhead ribozyme and randomizing nucleotides in the linker domain, we evolved new hammerhead ribozymes through dual selection, whose self-cleavage could be regulated by adenine. Our project provided a new design principle for rational or semi-rational design of riboswitches/ribozymes.


RBS automated design(Learn more...)
In bacteria, ribosomal binding site (RBS) sequence is one of the most important determinants of translational initiation/translation strength. Therefore manipulating RBS sequence would significantly affect the translation strength of downstream gene. Salis et.al. used Gibbs energy (∆G) of the “docked” state of the mRNA-30S ribosomal subunit complex to predict the translation strength of RBS sequence. Based on their pioneering work, we developed a methodology that correlated the performance of the RNA controllers under certain concentration of ligand to translation strength met by corresponding RBS sequence. Combining this methodology with our RNA toolkit, we can generate an RBS sequence through automated design once we achieved an ideal configuration of genetic programs through RNA controllers.


Application
we utilized the platform to improve performance of two modular genetic devices, AND gate and bistable switch.

 

AND gate

   
 

Figure 1. AND gate performance regulated by different concentration of thiamine pyrophosphate (TPP). The on/off ratio of AND gate increases with ligand concentration, while the single induction of arabinose is diminished, resulting in a well performed AND gate.

 

 

Bistable switch

   
 

Figure 2.  Fluorescence images of E.coli DH5α strain populations with different plasmids from bistable switch mutant library. Each plasmid contains different ribosome binding sites (RBSs) which control the expression of cI434 gene, demonstrating that the ratiometric of green cells to red cells is correlated with translation strength.

 

violacein biosynthetic pathway

We further applied this platform to optimize a segment ofviolacein biosynthetic pathway, and achieved producing purer desired products.

   
 

Figure 3.  E. coli producing pigments. When induced by arabinose, the engineered E. coli produced dark-green pigments. Upon addition of different concentration of thiamine pyrophosphate (TPP), the color of the bacteria gradually shifted from dark-green to dark-brown.

 

 

 


Reference:

[1]  http://en.wikipedia.org/wiki/Hard_coding
[2] http://en.wikipedia.org/wiki/Softcoding

[3].Gardner, Timothy S. et. al. (2000). Construction of a genetic toggleswitch in Escherichia coli. Nature 403, 339-342 [4].Elowitz, Michael B. and Leibler, Stanislas (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 [5].Breaker, Ronald R (2004).Natural and engineered nucleicacids as tools to explore biology. Nature 432, 838-845
[6].Salis, Howard M et.al. (2009). Automated design of synthetic ribosome binding sitesto control protein expression. Nat. Biotech. 27, 946-950

 

 

 

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