Team:Groningen/Brainstorm/Glucose Sensing

From 2009.igem.org

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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.
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{{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:
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* The PTS system, which is already present in ... {{todo|Which organisms?}}
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* [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:
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** Constitutively active, but repressed by ccpa(?).
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** Constitutively active, but repressed by CcpA.
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** Activated by ccpa(?).
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** Activated by CcpA.
* Product behind promoter as response.
* Product behind promoter as response.
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* Degradation-tag(?) for product to increase response time.
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* 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]].
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* 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#Hoefnagel2004|Hoefnagel2004]].
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* 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.
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{{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]

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.