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Conference publications

Abstracts

XX conference

Rule-based modelling of the bacterial transcription initiation

Sorokin A.A., Temlyakova E.A., Dzhelyadin T.R., Kamzolova S.G.

Institute of Cell Biophysics RAS, Russia, 142290, Pushchino, Institutskaya str.3, phone: (4967)739319, E-mail: lptolik@gmail.com

1 pp. (accepted)

E. coli chromosome believed to encode about five thousands promoters, so it contains about one promoter per 900 b.p. At the same time in dependence of the life cycle stage number of RNA-polymerase (RNAP) molecules that can bind to arbitrary DNA site, but initiate transcription from promoters only, vary between 1500 and 11000 per bacterial cell [1]. $\sigma$-subunit, small polypeptide required by RNAP for promoter recognition and transcription initiation even more rare: there are 500 $\sigma^{70}$, 95 $\sigma^{28}$ and 55 $\sigma^{54}$ molecules per cell [2]. The standard methods of kinetic modelling are not applicable in this case because of low molecule copy number and high competition between various promoters and non-promoter sites for the binding with limiting number of enzymes.

We have developed E. coli transcription initiation model with rule-based approach [3, 4]. Analysis of simulation results shows that various behaviour scenarios are possible. For example, one promoter could dominate the whole population and prevent synthesis from other promoters.

Work was supported by RFBR №11-04-01436-а.

References 1.Stefan Klumpp and Terence Hwa. Growth-rate-dependent partitioning of RNA polymerases in bacteria. // Proc Natl Acad Sci USA, 105(51):20245–20250, December 2008.

2.A Ishihama. Functional modulation of Escherichia coli RNA polymerase. // Annu Rev Microbiol, 54:499–518, 2000.

3.V Danos. Agile modelling of cellular signalling (invited paper). //Electronic Notes in Theoretical Computer Science, 229(4):3–10, 2009.

4.Joshua Colvinr, Michael I Monine, Ryan N Gutenkunst, William S Hlavacek, Daniel D Von Hoff, and Richard G Posner. RuleMonkey: software for stochastic simulation of rule- based models. //BMC Bioinformatics, 11(1):404, July 2010.



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