Team:University College London/Module 1/Design

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== Design ==
== Design ==
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<html><div align="center"><img src="http://2012.igem.org/wiki/images/e/ef/UcligemDetection_BioBrick.png" alt="Detection" /></div></html>
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We identified certain requirements from this system, and have designed the module to meet each requirement.  
We identified certain requirements from this system, and have designed the module to meet each requirement.  
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The NahR protein binds a promoter called P(sal) which upregulates the transcription of an enzyme operon required to metabolise salicylate. In place of the enzyme operon, we aim to place the Curli cluster of genes, which should therefore lead to upreguation of Curli proteins in the presence of plastic.
The NahR protein binds a promoter called P(sal) which upregulates the transcription of an enzyme operon required to metabolise salicylate. In place of the enzyme operon, we aim to place the Curli cluster of genes, which should therefore lead to upreguation of Curli proteins in the presence of plastic.
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<html><div align="center"><img src="http://2012.igem.org/wiki/images/e/ef/UcligemDetection_BioBrick.png" alt="Detection" /></div></html>
 
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Revision as of 17:10, 15 August 2012


Module 1: Detection

Description | Design | Construction | Characterisation | Modelling | Conclusions

Design

Detection


We identified certain requirements from this system, and have designed the module to meet each requirement.


Requirement 1: The detection of POPs should proportionally and reliably indicate the presence of plastic


Persistent Organic Pollutants are organic compounds that accumulate and persist in the environment. They have numerous uses, and have been employed as pesticides, in industrial processes and in pharmaceuticals. Just like plastics, they run-off into the oceans, and accumulate in gyres. POPs have low water solubility, and adsorb onto hydrophobic surfaces – like the surfaces of plastics. As plastics are the main material in the polluted gyres, a bacterium colliding with a POP has a high likelihood of being in the proximity to plastic. Therefore our system is likely only to be triggered in the presence of plastic. For this reason, the use of POP as an indicator of plastic would appear to be reliable.


Requirement 2: The bacteria should carry a system capable of binding a distinguishing feature of POPs


Persistant Organic Pollutants have domains homologous to the molecule salicylate – an organic acid found in a number of plants. Using the similarity of POPs to salicylate, it is possible to use a natural salicylate detection system as a means to detect the presence of POPs. Our research identified such a system, originating from the NAH7 plasmid of Pseudomonas putida . P.putida uses this system to detect salicylate, and upregulate enzymes (20 fold) that enable the bacterium to metabolise it.


How does this system work? The regulator of this system is a protein called NahR. The NahR protein belongs to the most abundant class of transcriptional regulators found in prokaryotes – the LysR transcriptional regulators. At the C-terminal end of the protein, there is a co-factor binding domain, which binds salicylate, and activates the transcriptional activity of the N-terminal domain of NahR. This enables the salicylate-activated NahR to bind DNA and upregulate the transcription of the enzyme operon.


Requirement 3: The POP detection system should reliably trigger the production of Curli.


The NahR protein binds a promoter called P(sal) which upregulates the transcription of an enzyme operon required to metabolise salicylate. In place of the enzyme operon, we aim to place the Curli cluster of genes, which should therefore lead to upreguation of Curli proteins in the presence of plastic.