title: Transcription fluctuation effects on biochemical oscillations.
abstract: Some biochemical systems show oscillation. They often consist of feedback loops with repressive transcription regulation. Such biochemical systems have distinctive characteristics in comparison with ordinary chemical systems: i) numbers of molecules involved are small, ii) there are typically only a couple of genes in a cell with a finite regulation time. Due to the fluctuations caused by these features, the system behavior can be quite different from the one by deterministic rate equations, because the rate equations ignore molecular fluctuations and thus are exact only in the infinite molecular number limit. The molecular fluctuations on a free-running circadian system have been studied by Gonze et al. (2002) by introducing a scale parameter [Formula: see text] for the system size. They consider, however, only the first effect, assuming that the gene process is fast enough for the second effect to be ignored, but this has not been examined systematically yet. Here we study fluctuation effects due to the finite gene regulation time by introducing a new scale parameter [Formula: see text], which we take as the unbinding time of a nuclear protein from the gene. We focus on the case where the fluctuations due to small molecular numbers are negligible. In simulations on the same system studied by Gonze et al., we find the system is unexpectedly sensitive to the fluctuation in the transcription regulation; the period of oscillation fluctuates about 30 min even when the regulation time scale [Formula: see text] is around 30 s, that is even smaller than 1/1000 of its circadian period. We also demonstrate that the distribution width for the oscillation period and amplitude scales with [Formula: see text], and the correlation time scales with [Formula: see text] in the small [Formula: see text] regime. The relative fluctuations for the period are about half of that for the amplitude, namely, the periodicity is more stable than the amplitude.
authors.affiliation: Department of Physics, Kyushu University, Fukuoka, Japan.
authors.forename: Ryota
authors.initials: R
authors.lastname: Nishino
authors.forename: Takahiro
authors.initials: T
authors.lastname: Sakaue
authors.forename: Hiizu
authors.initials: H
authors.lastname: Nakanishi
mesh_terms: D001669:Biochemical Phenomena; D002940:Circadian Rhythm / Q000235:genetics; D003198:Computer Simulation; D003600:Cytosol / Q000378:metabolism; D008954:Models, Biological; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D011506:Proteins; D012333:RNA, Messenger