BIOPHYSICAL THEORY AND MODELING |
Simulating the temporal modulation of inducible DNA damage
response in Escherichia coli
Ming Ni 1, Si-Yuan Wang 1, Ji-Kun Li 1 and Qi Ouyang 1*
1 Peking University
* To whom correspondence should be addressed. E-mail: qi{at}pku.edu.cn.
Submitted on June 13, 2006
Revised on July 21, 2006
Accepted on 28 February 2007
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Abstract |
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Living organisms make great efforts to maintain their genetic information integrity. However, DNA is vulnerable to many chemical or physical agents. In order to rescue the cell timely and effectively, the DNA damage response system must be well controlled. Recently, single cell experiments showing that after DNA damage, expression of the key DNA damage response regulatory protein oscillates with time. This phenomenon is observed both in eukaryotic (12) and bacterial cells (11). We establish a model to simulate the DNA damage response (SOS response) in bacterial cell Escherichia coli (E. Coli). The simulation results are compared to the experimental data. Our simulation results suggest that the modulation observed in the experiment is due to the fluctuation of inducing signal, which is coupled with DNA replication. The inducing signal increases when replication is blocked by DNA damage, and decreases when replication resumes.
Key Words:
DNA replication, SOS response, digital modulation, stochastic simulation
