Team:Imperial College/SingleCell

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Single Cell Modelling Overview

The first stage of our modelling process was to construct a single cell in silico model of our circuit. Our model was built using mass action kinetics in Simbiology (Matlab toolbox) and built up reaction by reaction.

We first separated the models into 3 modules: Quorum Communication, STAR-antiSTAR Comparator and Growth Regulation.



We constructed the four quorum systems that we considered viable choices for our system (cin, rhl, lux and las) to allow us to directly compare the expected behaviour and plan our growth module experiments accordingly. We designed the overall model for the Rhl and Cin systems (Chen et al., 2015) as they have been previously shown to operate with minimal crosstalk.

Assumptions We used numbers obtained from Chen et al for C4 and C14 production. This is a high level production term that ignores parts of the central dogma. We made this assumption due to the limited data on the enzymatic kinetics of the autoinducer synthases.

Rhl The Rhl system consists of an autoinducer synthase RhlI (that produces C4 AHL) and a transcriptional regulator RhlR that dimerises to activate a pRhl promoter which activates STAR transcription.

Cin The Cin system consists of an autoinducer synthase CinI (that produces C14 AHL) and a transcriptional regulator CinR that dimerises to activate a pCin promoter which induces Anti-STAR production.



Reactions



Communication module:

\[\varnothing\rightarrow C14\] \[\varnothing\rightarrow C4\] \[RNA_{pol} + g_{C4R} \rightarrow RNA_{pol} + g_{C4R} + mRNA_{C4R}]\ \[RNA_{pol} + g_{C14R} \rightarrow RNA_{pol} + g_{C14R} + mRNA_{C4R}]\ \[mRNA_{C4R}\rightarrow C4R\] \[mRNA_{C14R}\rightarrow C14R\] \[C14+C14R \rightarrow C14_{complex}\] \[C4+C4R \rightarrow C4_{complex}\] \[C4\rightarrow\varnothing\] \[mRNA_{C4R}\rightarrow\varnothing\] \[C4R\rightarrow\varnothing\] \[C4_{complex}\rightarrow\varnothing\] \[C4_{dimer}\rightarrow\varnothing\] \[C14\rightarrow\varnothing\] \[mRNA_{C14R}\rightarrow\varnothing\] \[C14R\rightarrow\varnothing\] \[C14_{complex}\rightarrow\varnothing\] \[C14_{dimer}\rightarrow\varnothing\]



Simulation Results



The results indicate that the species within this module reach steady states at time points unique to that species.



Figure 1: Production of C4 AHLs and C14 AHLs against time



Figure 2: Production of C4R and C14R regulatory proteins against time



Figure 3:C4:C4R and C14:C14R complex formation against time

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Works Cited

Chen, Y., Kim, J., Hirning, A., Josi, K. and Bennett, M. (2015). Emergent genetic oscillations in a synthetic microbial consortium. Science, 349(6251), pp.986-989.

Zhang, D. and Winfree, E. (2009). Control of DNA Strand Displacement Kinetics Using Toehold Exchange. J. Am. Chem. Soc., 131(47), pp.17303-17314.