The circadian clock is an endogenous timekeeper that allows organisms to

The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. 2012 Each type of model has its own strengths and weaknesses and different methods can fulfill different functions in the study of the circadian clock. For example LTI systems have accurately predicted which clock gene senses a particular environmental transmission but do not offer information about the mechanism driving the oscillations. A more recent trend is the study and modeling of that retains the small quantity of components found in older models of the same type but incorporates many more recent discoveries into the wiring of the oscillator. Compared to the latest published models (Pokhilko et al. 2013 Fogelmark and Troein 2014 our minimal model is usually more qualitative. However its small size makes it more tractable. We show that the many connections between the model components Rabbit polyclonal to ACAD9. and the addition of multiple light inputs are sufficient to reproduce a big range of behaviors in various light conditions. We also demonstrate the ability of our model to describe clock-dependent processes by building a small output module that reproduces hypocotyl growth phenotypes. 2 Model 2.1 The model includes GSK-923295 four pairs of genes Given the large number of known clock components and the high degree of redundancy between some of them we chose to merge very similar genes into single variables which allowed us to include many well-characterized genes without needing several units of almost identical equations. This approach is not novel and has successfully been used with several clock genes in particular and were also combined into a single variable. Here we extended the same approach to two more pairs of genes. Our model structure shown in Physique ?Physique1 1 includes four groups of two genes each. Each pair of genes has comparable expression profiles regulators targets and defects in loss-of-function mutant lines. Physique 1 Clock model structure. CL represents the dawn genes and and and and and The dawn-phased genes and are transcription factors belonging to the GSK-923295 MYB superfamily (Schaffer et al. 1998 Wang and GSK-923295 Tobin 1998 They play largely although not completely redundant roles within the clock (Mizoguchi et al. 2002 They are negatively regulated by the family of genes (Nakamichi et al. 2010 and have been shown to inhibit the expression of many evening-phased genes including the clock components (Alabadí et al. 2001 (Kikis et al. 2005 and (Hazen et al. 2005 CCA1 and LHY also bind to the promoters of the morning genes and mRNA (Kim et al. 2003 In our model the expression of is usually transiently activated by light and inhibited by PRR9/PRR7 and PRR5/TOC1. The translation and mRNA degradation rates are increased by light. The protein inhibits the expression of the evening genes and and The Evening Complex (EC) is made up of three proteins and (Nusinow et al. 2011 Of the three LUX is the only proper transcription factor (Onai and Ishiura 2005 Helfer et GSK-923295 al. 2011 but the formation of the EC is necessary for LUX to become active (Mizuno et al. 2014 The EC acts as a transcriptional repressor that inhibits the expression of the morning genes and and (Mizuno et al. 2014 Two other clock genes and (Onai and Ishiura 2005 Dixon et al. 2011 Helfer et al. 2011 Mizuno et al. 2014 In light/dark cycles and have very similar expression profiles with a peak at dusk or around 12 h after dawn whichever is usually earlier (Doyle et al. 2002 Hazen et al. 2005 while the expression of extends much later into the night (Hicks et al. 2001 The expression of is only inhibited by CCA1/LHY while and are inhibited by CCA1/LHY TOC1 and the EC. Additionally is usually induced by light signaling-related proteins (Li et al. 2011 In the model we have assumed that ELF4 or LUX must be the limiting factor in the formation of the EC and have not included ELF3 explicitly. One equation represents the mRNA of is usually modeled as light dependent and inhibited by CCA1/LHY PRR5/TOC1 and the EC. The EC represses and but not is usually strong while the case for a similar regulation of and is slightly less obvious cut and nothing suggests an effect on (Mizuno et al. 2014 Therefore we based our decision mainly on for the pair and for the pair. 2.1 The PRR family: and and The family.