Open AccessA novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9
Author(s) -
Zeilinger Melanie N,
Farré Eva M,
Taylor Stephanie R,
Kay Steve A,
Doyle Francis J
Publication year - 2006
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb4100101
Subject(s) - arabidopsis , circadian clock , biology , computational biology , process (computing) , systems biology , identification (biology) , computational model , computer science , circadian rhythm , mutant , genetics , gene , artificial intelligence , neuroscience , botany , operating system
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.