title: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.
abstract: Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene Pseudo-Response Regulator 9 was repressed by an evening gene, previously identified with Timing Of CAB Expression1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure.
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Pokhilko
authors.forename: Aurora Piñas
authors.initials: AP
authors.lastname: Fernández
authors.forename: Kieron D
authors.initials: KD
authors.lastname: Edwards
authors.forename: Megan M
authors.initials: MM
authors.lastname: Southern
authors.forename: Karen J
authors.initials: KJ
authors.lastname: Halliday
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Millar
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000502:physiology; D056926:CLOCK Proteins / Q000235:genetics* / Q000502:physiology; D002940:Circadian Rhythm / Q000235:genetics; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000235:genetics; D025461:Feedback, Physiological / Q000502:physiology*; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D053263:Gene Regulatory Networks / Q000502:physiology*; D008027:Light; D008954:Models, Biological; D017440:Photoperiod; D030821:Plants, Genetically Modified; D012097:Repressor Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology; D044767:Ubiquitin-Protein Ligases
chemical_list: D029681:Arabidopsis Proteins; C114425:CCA1 protein, Arabidopsis; D004268:DNA-Binding Proteins; C121183:GI protein, Arabidopsis; C113192:LHY protein, Arabidopsis; D012097:Repressor Proteins; D014157:Transcription Factors; D056926:CLOCK Proteins; C471983:AT2G32950 protein, Arabidopsis; D044767:Ubiquitin-Protein Ligases