System identification of the Arabidopsis plant circadian system

Mathias Foo, David E. Somers, Pan-Jun Kim

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The circadian system generates an endogenous oscillatory rhythm that governs the daily activities of organisms in nature. It offers adaptive advantages to organisms through a coordination of their biological functions with the optimal time of day. In this paper, a model of the circadian system in the plant Arabidopsis (species thaliana) is built by using system identification techniques. Prior knowledge about the physical interactions of the genes and the proteins in the plant circadian system is incorporated in the model building exercise. The model is built by using primarily experimentally-verified direct interactions between the genes and the proteins with the available data on mRNA and protein abundances from the circadian system. Our analysis reveals a great performance of the model in predicting the dynamics of the plant circadian system through the effect of diverse internal and external perturbations (gene knockouts and day-length changes). Furthermore, we found that the circadian oscillatory rhythm is robust and does not vary much with the biochemical parameters except those of a light-sensitive protein P and a transcription factor TOC1. In other words, the circadian rhythmic profile is largely a consequence of the network's architecture rather than its particular parameters. Our work suggests that the current experimental knowledge of the gene-to-protein interactions in the plant Arabidopsis, without considering any additional hypothetical interactions, seems to suffice for system-level modeling of the circadian system of this plant and to present an exemplary platform for the control of network dynamics in complex living organisms.
Original languageEnglish
Pages (from-to)700-712
Number of pages13
JournalJournal of the Korean Physical Society
Volume66
Issue number4
DOIs
Publication statusPublished - 7 Feb 2015

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system identification
genes
proteins
organisms
rhythm
interactions
physical exercise
platforms
perturbation
profiles

Keywords

  • Complex systems
  • Biological networks
  • Nonlinear dynamics
  • Circadian systems

Cite this

System identification of the Arabidopsis plant circadian system. / Foo, Mathias; Somers, David E.; Kim, Pan-Jun.

In: Journal of the Korean Physical Society, Vol. 66, No. 4, 07.02.2015, p. 700-712.

Research output: Contribution to journalArticle

Foo, Mathias ; Somers, David E. ; Kim, Pan-Jun. / System identification of the Arabidopsis plant circadian system. In: Journal of the Korean Physical Society. 2015 ; Vol. 66, No. 4. pp. 700-712.
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