title: A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9.
abstract: In plants, as in animals, the core mechanism to retain rhythmic gene expression relies on the interaction of multiple feedback loops. In recent years, molecular genetic techniques have revealed a complex network of clock components in Arabidopsis. To gain insight into the dynamics of these interactions, new components need to be integrated into the mathematical model of the plant clock. Our approach accelerates the iterative process of model identification, to incorporate new components, and to systematically test different proposed structural hypotheses. Recent studies indicate that the pseudo-response regulators PRR7 and PRR9 play a key role in the core clock of Arabidopsis. We incorporate PRR7 and PRR9 into an existing model involving the transcription factors TIMING OF CAB (TOC1), LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED (CCA1). We propose candidate models based on experimental hypotheses and identify the computational models with the application of an optimization routine. Validation is accomplished through systematic analysis of various mutant phenotypes. We introduce and apply sensitivity analysis as a novel tool for analyzing and distinguishing the characteristics of proposed architectures, which also allows for further validation of the hypothesized structures.
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.
authors.forename: Melanie N
authors.initials: MN
authors.lastname: Zeilinger
authors.forename: Eva M
authors.initials: EM
authors.lastname: Farré
authors.forename: Stephanie R
authors.initials: SR
authors.lastname: Taylor
authors.forename: Steve A
authors.initials: SA
authors.lastname: Kay
authors.forename: Francis J
authors.initials: FJ
authors.lastname: Doyle
mesh_terms: D017360:Arabidopsis / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000502:physiology*; D001683:Biological Clocks / Q000502:physiology*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000502:physiology; D008027:Light; D008954:Models, Biological; D012680:Sensitivity and Specificity; D015398:Signal Transduction; D014157:Transcription Factors / Q000502:physiology
chemical_list: C448161:APRR7 protein, Arabidopsis; C448159:APRR9 protein, Arabidopsis; D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; C113192:LHY protein, Arabidopsis; D014157:Transcription Factors