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Team:Dundee/Project
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Revision as of 14:32, 4 October 2014
Project
What we did
Initial planning and cloning strategy
Pseudomonas quinolone signal (2-heptyl-3-hydroxy-4-quinolone) is a quorum-sensing molecule produced by Pseudomonas aeruginosa, which regulates the expression of genes involved in biofilm development and virulence.1 Expression of these traits is mediated through the LysR-type transcriptional regulator, PqsR. Sequence analysis of PqsR predicts that it is a soluble protein but fractionation of P. aeruginosa has shown that the protein is primarily associated with the inner membrane. 2 It is not clear whether this is through the interaction with membrane lipids or with an unidentified integral inner membrane protein. In the presence of PQS, PqsR interacts with the promoter region of the pqsABCDE operon, allowing transcription of the downstream genes.3 We have engineered E. coli to express this signal transduction system for the detection of PQS, with a promoter-less mCherry fused to the pqsA promoter to give a fluorescent output.
Building the PQS sensor
Chromosomal DNA from Pseudomonas Aeruginosa PA01 strain was kindly gifted to us by Robert Ryan and Shi-Qi An from The Division of Molecular Microbiology in the College of Life sciences at the University of Dundee. This was used as a template for the amplification of the pqsA promoter. The pqsA promoter region was cloned into the pSB1C3 plasmid (to give Biobrick (BBa_K1315001), and was then subcloned into pBluescript. Promoterless mCherry was amplified using BBa K562011 as a template and was cloned into pBluescript downstream of the pqsABCDE promoter. The PpqsA-mCherry construct was then subcloned into pUniprom. The pqsR gene (present in BBa_K1157001) which was designed and cloned by Lin Ang Chieh from iGEM13-NTU-Taida was used as a template for the amplification of pqsR with an influenza virus haemagglutinin (HA) tag coding sequence, which can be detected with commercial antibodies. This tag was added to the C-terminus of the protein to facilitate immunohistochemistry.
The completed construct was transformed into E. coli strain MC1061 as a chassis for our biosensor.
Sigmoidal Expression of mCherry in PQS System
When the PQS system was induced with synthetic PQS, no mCherry was expressed and so the wet team sought the advice of the dry team to find out why and how the situation could be resolved.
After constructing a series of ordinary differential equations (full derivation can be found in the appendix) we established the following relationship between PQS (Se) and mCherry:
Equation (1) was then analysed in MAPLE for varying PQS concentrations using the parameters in table 1.
Figure 2 shows how the concentration of mCherry increases over time. The general trend is that at low concentrations the rate of production of mCherry is slow and at high concentrations the production is fast.
When the gradients of d[mcherry]/dt were plotted against PQS concentration, figure 3, the result was a sigmoidal curve. This implies that for PQS concentrations below 0.1𝜇M there should be low mCherry production and above 1𝜇M there should be high mCherry production.
We predict that the low expression could correlate to P.aeruginosa being in an acute planktonic state and the high expression to a chronic biofilm state.
Stochastic confirms “switch” behaviour
Once the PQS “switch” was found using the sigmoidal graphs for low and high production of mCherry, we were able to construct stochastic simulations in order to visualise this with regards to a single cell model. The simulations were able to show how varying the PQS signal would promote various level of mCherry expression over one cell cycle.
The stochastic mean in A seems low in comparison to the rest of the realisations which implies there were many reactions which didn’t express any mCherry. Figure 5 reveals that in 77% of the realisations for 0.02μM of PQS, no mCherry was produced. Increasing the PQS concentration by 10-fold, increases the number of reactions fired to 90%. For PQS concentrations greater than 2μM all the reactions fire in the given time frame.
What is interesting to note is that once the reactions have started they produce mCherry at the same rate, shown by the parallel realisations in figure 4. We can conclude that a rate limiting step in the system is the probability that the reaction for mCherry expression starts.
