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Team:Groningen/Brainstorm/Glucose Sensing
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| - | Originally the [[Team:Groningen/Brainstorm/Rainbow Bacteria|Rainbow bacteria]] we now no longer plan to use the Cre/Lox system, but rather focus on glucose sensing. This choice was made because we have no good way to control the cre/lox recombination the way we would need for glucose sensing. | + | {{Team:Groningen/Header}} |
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| + | Originally the [[Team:Groningen/Brainstorm/Rainbow Bacteria|Rainbow bacteria]], we now no longer plan to use the Cre/Lox system, but rather focus on glucose sensing. This choice was made because we have no good way to control the cre/lox recombination the way we would need for glucose sensing. | ||
The idea now is to create a bacterium that senses the outside glucose concentration and produces an inversely proportional response. | The idea now is to create a bacterium that senses the outside glucose concentration and produces an inversely proportional response. | ||
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Our bacterium would have the following components: | Our bacterium would have the following components: | ||
| - | * The PTS system, which is already present in ... {{todo|Which organisms?}} | + | * [http://www.genome.jp/dbget-bin/www_bget?pathway:ko02060 The PTS system], which is already present in ... {{todo|Which organisms?}} |
* A promoter that hooks into the PTS system. Can be either: | * A promoter that hooks into the PTS system. Can be either: | ||
| - | ** Constitutively active, but repressed by | + | ** Constitutively active, but repressed by CcpA. |
| - | ** Activated by | + | ** Activated by CcpA. |
* Product behind promoter as response. | * Product behind promoter as response. | ||
| - | * Degradation-tag | + | * Degradation-tag attached to the product to increase turnover rate. |
==Modelling== | ==Modelling== | ||
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* A limited model consisting of only 9 substances and 7 reactions, as described in [[Team:Groningen/Literature#Neves1999|Neves1999]]. | * A limited model consisting of only 9 substances and 7 reactions, as described in [[Team:Groningen/Literature#Neves1999|Neves1999]]. | ||
| - | * A more complete model [http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=Lactococcus+lactis&category=metabolism by M.H.N. Hoefnagel, J. Hugenholtz and J.L. Snoep] (hoefnagel2), discussed in [[Team:Groningen/Literature# | + | * A more complete model [http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=Lactococcus+lactis&category=metabolism by M.H.N. Hoefnagel, J. Hugenholtz and J.L. Snoep] (hoefnagel2), discussed in [[Team:Groningen/Literature#Hoefnagel2002|Hoefnagel2002]]. |
Our attempts at using these models are available in [http://igemgroningen.googlecode.com/svn/trunk/glucose our SVN repository]. | Our attempts at using these models are available in [http://igemgroningen.googlecode.com/svn/trunk/glucose our SVN repository]. | ||
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| + | Once we have a model of the PTS system we will try adding one or more "reactions" for the HPr phosphorylation/dephosphorylation under the influence of FBP and ATP, as this leads to HPr-ser46, which lets Ccpa bind to a cre site more easily. For the moment it is assumed that HPr and Ccpa are available in abundance. | ||
| + | {{Team:Groningen/Footer}} | ||
Latest revision as of 10:57, 30 September 2009
[http://2009.igem.org/Team:Groningen http://2009.igem.org/wiki/images/f/f1/Igemhomelogo.png]
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Originally the Rainbow bacteria, we now no longer plan to use the Cre/Lox system, but rather focus on glucose sensing. This choice was made because we have no good way to control the cre/lox recombination the way we would need for glucose sensing.
The idea now is to create a bacterium that senses the outside glucose concentration and produces an inversely proportional response.
Requirements
We use the [http://en.wikipedia.org/wiki/MoSCoW_Method MoSCoW prioritization method]:
- Must have this:
- Response should be inversely proportional to the outside glucose concentration.
- It should be measurable on-line (visually for example).
- Should have this if at all possible:
- Response should be a gradient (not just on/off).
- Delay in the response should not exceed roughly 5-10 minutes.
- (Model) parameters should be known or obtainable.
- Could have this if it does not affect anything else:
- Response should reasonably accurately follow the concentration (after a delay).
- Won't have this now but would like in the future:
- Expand to other metabolisms.
- Produce something more useful than a colour.
Design
Our bacterium would have the following components:
- [http://www.genome.jp/dbget-bin/www_bget?pathway:ko02060 The PTS system], which is already present in ... Which organisms?
- A promoter that hooks into the PTS system. Can be either:
- Constitutively active, but repressed by CcpA.
- Activated by CcpA.
- Product behind promoter as response.
- Degradation-tag attached to the product to increase turnover rate.
Modelling
First of all we are trying to model the PTS system as is. We're looking at the following existing models:
- A limited model consisting of only 9 substances and 7 reactions, as described in Neves1999.
- A more complete model [http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=Lactococcus+lactis&category=metabolism by M.H.N. Hoefnagel, J. Hugenholtz and J.L. Snoep] (hoefnagel2), discussed in Hoefnagel2002.
Our attempts at using these models are available in [http://igemgroningen.googlecode.com/svn/trunk/glucose our SVN repository].
Once we have a model of the PTS system we will try adding one or more "reactions" for the HPr phosphorylation/dephosphorylation under the influence of FBP and ATP, as this leads to HPr-ser46, which lets Ccpa bind to a cre site more easily. For the moment it is assumed that HPr and Ccpa are available in abundance.
