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Team:University College London/Module 1/Design
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== Design == | == Design == | ||
| - | + | <html><div align="center"><img src="https://static.igem.org/mediawiki/2012/e/ef/UcligemDetection_BioBrick.png" alt="Detection" /></div></html> | |
| - | + | We identified certain requirements from this system, and have designed the module to meet each requirement. | |
| - | + | '''Requirement 1: The detection of OPs should proportionally and reliably indicate the presence of plastic''' | |
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| + | 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. Similarly to plastics, they run-off into the oceans, and accumulate in gyres. | ||
| + | OPs have low water solubility, and adsorb onto hydrophobic surfaces – like the surfaces of <span class="footnote" title="OrganicPollutants">plastics</span>. As plastics are the main material in the polluted gyres, a bacterium colliding with a OP 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 OP as an indicator of plastic would appear to be reliable. | ||
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| + | '''Requirement 2: The bacteria should carry a system capable of binding a distinguishing feature of OPs''' | ||
| - | + | Organic Pollutants have domains homologous to the molecule salicylate – an organic acid found in a number of plants. Using the similarity of OPs to salicylate, it is possible to use a natural salicylate detection system as a means to detect the presence of OPs. 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 <span class="footnote" title="NahR">NahR</span>. 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. | ||
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| + | '''Requirement 3: The OP detection system should reliably trigger the production of Curli.''' | ||
| - | + | The NahR protein binds a promoter called pSal which upregulates the transcription of an enzyme operon required to metabolise <span class="footnote" title="NahR">salicylate</span>. 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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{{:Team:University_College_London/templates/foot}} | {{:Team:University_College_London/templates/foot}} | ||
Latest revision as of 17:11, 26 September 2012
Module 1: Detection
Description | Design | Construction | Characterisation | Modelling | Conclusions
Design
We identified certain requirements from this system, and have designed the module to meet each requirement.
Requirement 1: The detection of OPs should proportionally and reliably indicate the presence of plastic
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. Similarly to plastics, they run-off into the oceans, and accumulate in gyres. OPs 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 OP 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 OP 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 OPs
Organic Pollutants have domains homologous to the molecule salicylate – an organic acid found in a number of plants. Using the similarity of OPs to salicylate, it is possible to use a natural salicylate detection system as a means to detect the presence of OPs. 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 OP detection system should reliably trigger the production of Curli.
The NahR protein binds a promoter called pSal 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.
