Difference between revisions of "Team:IIT-Madras/Description"

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<li>The original idea was to study the degradation of lignin to produce vanillin which has higher economic value.
 
<li>The original idea was to study the degradation of lignin to produce vanillin which has higher economic value.
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We looked up literature regarding the degradation of the aromatic rings of lignin. We needed an organism that could degrade such aromatics.</li>
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We conducted a literature survey regarding the degradation of the aromatic rings of lignin and organisms capable of degrading such aromatics.</li>
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<li>For popular organisms like <em>E. coli</em> and <em>L. lactis.</em>, we need to make competent cells for transformation. We looked up the surrounding literature and found several ‘naturally competent’ microorganisms. However, most of them were pathogenic and are known to cause harm to humans. Hence, they cannot be worked with in a biosafety level 1 lab. <em>Streptococcus pneumoniae</em> (Griffith's "pneumococcus"), <em>Neisseria gonorrhoeae</em>, <em>Bacillus subtilis</em> and <em>Haemophilus influenzae</em> are some examples.</li>
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<li>For popular organisms like <em>E. coli</em> and <em>L. lactis.</em> competent cells are required for transformation. From a brief literature survey we found several ‘naturally competent’ microorganisms. However, most of them were pathogenic and are known to harm humans. Hence, we cannot work with them in a biosafety level 1 laboratory.
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The organism that best fits both these requirements is <em>Acinetobacter baylyi</em> ADP1 strain. This organism is naturally competent, non-pathogenic, and has the amazing property of degrading aromatics. The strain can be purchased from DSMZ.
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An organism that best fits both these requirements is <em>Acinetobacter baylyi</em>. The ADP1 strain of this organism is naturally competent, non-pathogenic, and has the property of degrading aromatics. This strain can be purchased from DSMZ.
  
 
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<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
 
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
  
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While perusing literature for <em>Acinetobacter baylyi</em> ADP1 we couldn't find substantial material, as information was sparse and not many tools were available to undertake synthetic biology experiments with this organism. This motivated us to build a toolbox for <em>Acinetobacter baylyi</em> that was generic and hence could effectively be used by research groups working with other organisms as well.
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We looked up the literature for <em>Acinetobacter baylyi</em> ADP1 but could not find substantial material. The literature was too sparse and not many tools were available to undertake synthetic biology experiments with this organism. This was the motivation to generate a toolbox for <em>Acinetobacter baylyi</em> and to try and make the tools as generic as possible such that any teams or research groups wishing to work with other organisms could still use them.
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<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
 
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
  
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A primary requirement for experimentation in synthetic biology is a fluorescent reporter protein. Hence we planned to codon-optimize two reporter proteins, GFP and mCherry, for <em>A. baylyi</em>. </p>
  
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The first thing that is required for any synthetic biology experiments is a fluorescent reporter protein. We wished to codon-optimize GFP and mCherry for <em>A. baylyi</em>. However,  when we asked the companies to codon-optimize the fluorescent proteins, the companies did not have the codon bias table for <em>A. baylyi</em>.<br><br>
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<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
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When we approached companies for codon-optimized reporter proteins they did not have a codon bias table available for <em>A. baylyi</em>.Thus we made a freely available online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking the protein coding annotation into consideration. This tool can be used for all organisms whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex website.</a><br> We generated the codon usage table from the protein annotation of <em>A. baylyi</em> available on the  <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this codon table, we codon optimized reporter proteins and the characterization can be found here. <br><br>
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<strong>Solution 1:</strong> We made a free-to-use online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking into consideration the protein coding annotation. This tool can be used for any other organism whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex website.</a><br>We generated the codon usage table from the protein annotation of <em>A. baylyi</em> available on the  <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this codon table, we codon optimized reporter proteins and the characterization can be found here. <br><br>
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<strong>Solution 2:</strong> Next we moved on to building a synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1. But we wanted to make the promoter library as generic as possible. So, we made a T5 promoter-based library which exhibits varying expression strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.<br>
 
<strong>Solution 2:</strong> Next we moved on to building a synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1. But we wanted to make the promoter library as generic as possible. So, we made a T5 promoter-based library which exhibits varying expression strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.<br>
  

Revision as of 15:16, 17 October 2018

iGEM Collaborations Page

☰

Team: IIT-Madras/ADaPtat1on

Description

ADaPtat1on

Motivations:

  1. The original idea was to study the degradation of lignin to produce vanillin which has higher economic value. We conducted a literature survey regarding the degradation of the aromatic rings of lignin and organisms capable of degrading such aromatics.
  2. For popular organisms like E. coli and L. lactis. competent cells are required for transformation. From a brief literature survey we found several ‘naturally competent’ microorganisms. However, most of them were pathogenic and are known to harm humans. Hence, we cannot work with them in a biosafety level 1 laboratory.

Solution:

An organism that best fits both these requirements is Acinetobacter baylyi. The ADP1 strain of this organism is naturally competent, non-pathogenic, and has the property of degrading aromatics. This strain can be purchased from DSMZ.

Motivations:

While perusing literature for Acinetobacter baylyi ADP1 we couldn't find substantial material, as information was sparse and not many tools were available to undertake synthetic biology experiments with this organism. This motivated us to build a toolbox for Acinetobacter baylyi that was generic and hence could effectively be used by research groups working with other organisms as well.

Project:

A primary requirement for experimentation in synthetic biology is a fluorescent reporter protein. Hence we planned to codon-optimize two reporter proteins, GFP and mCherry, for A. baylyi.

When we approached companies for codon-optimized reporter proteins they did not have a codon bias table available for A. baylyi.Thus we made a freely available online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking the protein coding annotation into consideration. This tool can be used for all organisms whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the CUTE ChassiDex website.
We generated the codon usage table from the protein annotation of A. baylyi available on the NCBIwebsite. Using this codon table, we codon optimized reporter proteins and the characterization can be found here.

Solution 2: Next we moved on to building a synthetic promoter library for Acinetobacter baylyi ADP1. But we wanted to make the promoter library as generic as possible. So, we made a T5 promoter-based library which exhibits varying expression strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.