An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states

Ignasius Joanito,Jhih-Wei Chu,Shu-Hsing Wu,Chao-Ping Hsu

doi:10.1038/s41598-018-32030-z

Abstract

In higher plants (e.g., Arabidopsis thaliana), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the Arabidopsis clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY and PRR5/TOC1 generates a bistable, hysteretic behavior in the Arabidopsis circadian clock. We found that the IFFL involving PRR9/7 breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex (EC) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the Arabidopsis core oscillator.

Highlights

The circadian clock is an endogenous time-keeping mechanism in cells and organisms that anticipates daily changes in the environment[1,2,3,4]
This approach has been commonly used in many mathematical models such as in describing the expression of CCA1 and LATE ELONGATED HYPOCOTYL (LHY) (CCA1/LHY)[47,49,50,51], PRR9 and PRR7 (PRR9/7)[51,52], as well as EARLY FLOWERING 4 (ELF4) and LUX47,48,51
To increase the general applicability of the conclusions drawn from the modeling, we randomly generated all the parameter values in the model and selected parameter sets that generated sustained oscillations, with the lwd1/2 mutant correctly reproducing a shorter period (>3 hr) and lower amplitude (>50%) in both PRR9/7 and CCA1/LHY

Summary

Introduction

The circadian clock is an endogenous time-keeping mechanism in cells and organisms that anticipates daily changes in the environment[1,2,3,4]. LUX, ELF4, and ELF3 were found to form a complex in the middle of the night, defined as the evening complex (EC)[33] This EC has been proposed to play a crucial role in inhibiting PRR genes[34,35,36] and tracking seasonal change in both photoperiod and ambient temperature[37,38]. Among these dense repression processes, we can find another network motif called the incoherent feed-forward loop (IFFL), which has not been widely discussed in the clock systems. The roles of these IFFLs in the oscillating system, such as the circadian clock, are still elusive

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Conclusion