Systems-level characterization of the kernel mechanism of the cyanobacterial circadian oscillator

Lan Ma, Rama Ranganathan

Research output: Contribution to journalArticle

Abstract

Circadian clock is an essential molecular regulatory mechanism that coordinates daily biological processes. Toward understanding the design principles of the circadian mechanism in cyanobacteria, the only prokaryotes reported to possess circadian rhythmicity, mathematical models have been used as important tools to help elucidate the complicated biochemical processes. In this study, we focus on elucidating the underlying systems properties that drive the oscillation of the cyanobacterial clockwork. We apply combined methods of time scale separation, phase space analysis, bifurcation analysis and sensitivity analysis to a model of the in vitro cyanobacterial circadian clock proposed by us recently. The original model is reduced to a three-dimensional slow subsystem by time scale separation. Phase space analysis of the reduced subsystem shows that the null-surface of the Serine-phosphorylated state (S-state) of KaiC is a bistable surface, and that the characteristic of the phase portrait indicates that the kernel mechanism of the clockwork behaves as a relaxation oscillator induced by interlinked positive and negative feedback loops. Phase space analysis together with perturbation analysis supports our previous viewpoint that the S-state of KaiC is plausibly a key component for the protein regulatory network of the cyanobacterial circadian clock.

Original languageEnglish (US)
Pages (from-to)30-39
Number of pages10
JournalBioSystems
Volume117
Issue number1
DOIs
StatePublished - Mar 2014

Fingerprint

Circadian Clocks
Clocks
Phase Space
kernel
Serine
Subsystem
Time Scales
Biochemical Phenomena
Relaxation oscillators
Feedback
Biological Phenomena
Cyanobacteria
Positive Feedback
Negative Feedback
Bifurcation (mathematics)
Phase Portrait
Regulatory Networks
Perturbation Analysis
Combined Method
Feedback Loop

Keywords

  • Circadian clock
  • Mathematical model
  • Phase space
  • Relaxation oscillator

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Applied Mathematics
  • Modeling and Simulation
  • Statistics and Probability

Cite this

Systems-level characterization of the kernel mechanism of the cyanobacterial circadian oscillator. / Ma, Lan; Ranganathan, Rama.

In: BioSystems, Vol. 117, No. 1, 03.2014, p. 30-39.

Research output: Contribution to journalArticle

Ma, Lan ; Ranganathan, Rama. / Systems-level characterization of the kernel mechanism of the cyanobacterial circadian oscillator. In: BioSystems. 2014 ; Vol. 117, No. 1. pp. 30-39.
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