Stochasticity and Robustness in Bi-Stable Systems

The genetic bi-stable switch (toggle switch) consists of two genes which repress one another through their synthesised proteins. In the stochastic bi-stable case, the toggle switch exhibits noise induced flips. Using simulation based techniques, we identified three methods for reducing the random flipping probability, namely: (i) increasing the system size, (ii) increasing the synthesis rate, and (iii) increasing the Hill coefficient. Our heat-maps showed that for large parts of parameter space the toggle switch displays extremely low noise induced flipping probability, and consequently high robustness. We also analysed the noise analytically. The area of validity of the analytical approach was found to be constrained to low Hill coefficients and high synthesis rate (both conditions within biological realistic parameters). Most importantly, we observed that increasing the synthesis rate is more efficient in reducing the noise compared to the increase in system size, for systems affected by negative feedback.

[1]  Linda R. Petzold,et al.  Improved leap-size selection for accelerated stochastic simulation , 2003 .

[2]  P. R. ten Wolde,et al.  DNA looping provides stability and robustness to the bacteriophage λ switch , 2009, Proceedings of the National Academy of Sciences.

[3]  Ofer Biham,et al.  Stochastic simulations of genetic switch systems. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[4]  Johan Paulsson,et al.  Models of stochastic gene expression , 2005 .

[5]  P. R. ten Wolde,et al.  Reaction coordinates for the flipping of genetic switches. , 2007, Biophysical journal.

[6]  J. Paulsson Summing up the noise in gene networks , 2004, Nature.

[7]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[8]  Ofer Biham,et al.  Genetic toggle switch without cooperative binding. , 2006, Physical review letters.

[9]  Rui Zhu,et al.  A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics , 2006, J. Comput. Biol..

[10]  G. K. Ackers,et al.  Quantitative model for gene regulation by lambda phage repressor. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Oudenaarden,et al.  Enhancement of cellular memory by reducing stochastic transitions , 2005, Nature.

[12]  F R Adler,et al.  How to make a biological switch. , 2000, Journal of theoretical biology.

[13]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[14]  R. Allen,et al.  Publisher’s Note: “Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch” [J. Chem. Phys. 128, 045105 (2008)] , 2008 .

[15]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[16]  P. R. ten Wolde,et al.  Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch. , 2007, The Journal of chemical physics.

[17]  Andre S Ribeiro,et al.  Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. , 2007, Journal of theoretical biology.

[18]  Yang Cao,et al.  Sensitivity analysis of discrete stochastic systems. , 2005, Biophysical journal.

[19]  J. Collins,et al.  Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  P. R. ten Wolde,et al.  Chemical models of genetic toggle switches. , 2004, The journal of physical chemistry. B.

[21]  Dominique Chu,et al.  Models of transcription factor binding: sensitivity of activation functions to model assumptions. , 2009, Journal of theoretical biology.

[22]  Terence Hwa,et al.  Transcriptional regulation by the numbers: models. , 2005, Current opinion in genetics & development.

[23]  K. Burrage,et al.  Stochastic models for regulatory networks of the genetic toggle switch. , 2006, Proceedings of the National Academy of Sciences of the United States of America.