The molecular regulation of the Circadian Rhythm in plants

The circadian rhythm was first mentioned by Franz Halberg in the 1950s. The term is based on the words circa, meaning “around” and diem or dies, meaning “day”. It refers to the 24 hour rhythm of living beings, mainly animals and plants.

Its outstanding characteristic is that it retains a 24 h rhythm without any cues from the environment that indicate the daytime. This means the circadian rhythm is generated within the organism (generated endogenously). Generally speaking, if a person for instance is in a completely dark room for an extended period of time, he or she would still have a daily rhythm of 8 hours sleep and 16 hours waking state.

What is it good for to keep track of time you might ask. With the help of the circadian rhythm animals and plants can anticipate reoccurring events and adjust to them. As an example, plants anticipate dawn and activate their photosynthesis apparatus, so light gets used efficiently as soon as possible. But the time of dawn changes with the season of the year and the rhythm has to be adjusted. Here environmental cues called “Zeitgeber” (time giver) come into play. These are signals such as the change of light intensity or temperature and with them the circadian clock adjusts to the correct time.

Circadian Rhythm in Plants

As suspected the circadian rhythm plays a much more important role for plants than it does for animals, as they are sessile organisms and cannot escape stress. They just have to deal with it. And again, anticipating stress and preparing for it can make a big difference when it comes to survival.

On a molecular level, the plant circadian rhythm’s center is the central oscillator that consists of a few genes that interact in a feedback loop with each other. A hypothesis has been established that depicts its regulation in a circuit called repressilator. This is a network where genes are expressed, (meaning a protein is synthesised with a gene as blueprint) during a certain time of the day and suppress (expression is prevented) the temporally preceding genes in the loop. Its important to understand that gene products, proteins, convey the actual function and that genes are just the blueprint for them.

For a better understanding of the central oscillator regulation, let’s forget about time for a moment. In the figure below you can see three gene clusters that are connected (clear) and the same gene clusters shifted (faint). We will concentrate on the clear part first. Here, the genes CCA1 and LHY suppress the genes ELF3, ELF4 and LUX, indicated by the blunt arrow. As these three genes are prevented from being expressed (and therefore their acting proteins not being present), they on their part cannot suppress the genes TOC1 and PRR5/7/9. As a result these four genes get expressed and their proteins suppress CCA1 and LHY. This again leads to expression of ELF3/4 and LUX, due to cessation of suppression by CCA1 and LHY. So in fact, the whole cycle is based on suspension of suppression.

Sounds complicated, but is is not. This mechanism could be compared to a circulation of three buttons, whereof one is pressed in (suppressed) and two are out (expressed). Pushing button 1, after a while, leads to pushing in of the following button 2, and hence coming out of button 1. Now the circle continues as button 3 is pushed in after a while and button 2 comes out. The circle closes when button 1 is pushed again and button 3 comes out.

Lets bring in time at this point. Therefore you have to look at the faint parts of the figure that show you the time of day when the respective genes are expressed. In the morning, CCA1 and LHY are expressed for a few hours and as they suppress ELF3/4and LUX, these three genes are thereby suppressed in the morning. This results in suspension of suppression of TOC1PRR5/7/9 and these four genes are expressed during the day toward the evening/night. Their expression again leads to suppression of CCA1 and LHY during the day, which therefore results to a gradual suspension of ELF3/4– and LUX-suppression. The three genes are subsequently expressed at night, during which they suppress TOC1 and PRR5/7/9. The circle closes by suspension of CCA1 and LHY suppression towards dawn, when they are expressed again.


Repressilator new

Scheme for the repressilator consisting of genes expressed at dawn (CCA1 and LHY), during the day (PRR9, PRR7, PRR5 and TOC1) and at night (ELF3, ELF4 and LUX). Lines represent repression of one gene cluster by the preceding gene cluster.


In this way the nine genes of the central oscillator regulate themselves and generate the circadian rhythm endogenously.

What do these genes of the central oscillator do but just regulate each other? During the time of their expression they are involved in the regulation of a lot of processes in the plant. In fact, the circadian rhythm partially regulates the already mentioned photosynthesis, as well as flowering and fruit production, and even the plant immune system. It was estimated that up to one-third of all genes of plants are partially controlled by the circadian rhythm, showing the importance of this mechanism!



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Pokhilko, A. P. Fernández, K. D. Edwards, M. M. Southern, K. J. Halliday and A. J. Millar (2012): The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol. 8:574
Huang, P. Pérez-García, A. Pokhilko, A. J. Millar, I. Antoshechkin, J. L. Riechmann, P. Mas (2012): Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science.336:75-79G.
McWatters and P. F. Devlin (2011): Timing in plants – A rhythmic arrangement. FEBS Letters. 58:1474-84

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