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Tick tock circadian clock

Plants and us - we’re not so different, especially when it comes to the daily rituals of life - and circadian clocks show we’re all creatures of habit.

July 08, 2019

Plants and us - we’re not so different, especially when it comes to the daily rhythms of life - and circadian clocks prove that we’re all creatures of habit. Work at the Earlham Institute is helping us to understand the importance of plant circadian rhythms, so that we might fine tune them to make better crops in the future.

Hannah Rees and the Anthony Hall group are passionate about plants (as we all should be), and one of the topics that most interests them is the daily (and nightly) cycle of different plant species. We know quite a lot about human circadian rhythms, and even those of model species such as Arabidopsis, but what about plants that are important for food security such as wheat?

Before we fill you in completely, let’s explore the tick tock of the molecular clock for a moment!

Circadian rhythms don't just occur in humans, they also affect plants, including those that are important for food security.

Circadian rhythms don't just occur in humans, they also affect plants, including those that are important for food security.
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We know quite a lot about human circadian rhythms, and even those of model species such as Arabidopsis, but what about plants that are important for food security such as wheat?

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Circadian clock

It’s 6am. The sun is shining through the curtains and wakes you from your slumber an hour and a half before the alarm was even supposed to go off.

Summertime has truly kicked in and you curse your laziness for forgetting to order the light-blocking blinds, as now there’s absolutely no chance you can go back to sleep or you’ll risk snoozing through the time you’ve allowed for your morning routine.

At least it’s easier in summertime - the body not ripped unkindly from its slumber due to winter darkness, forcing itself up and out of bed for the dismal, dark journey into work.

We are all trained to a daily cycle, constrained by the periods of light and dark that accompany the rising and setting of the sun. We know that we get knocked out of kilter when the clocks change, or we travel backwards or forwards in time and suffer the effects of jetlag.

However, this daily rhythm isn’t purely a reaction to day and night: it is genetically hard-wired. That’s why persistent night shift workers can expect to suffer a higher early mortality due to heart disease and other issues, including cancer. We’ve evolved in a seasonally variable climate of days and nights, and the rhythms imposed by our genes persist, confusing our bodies if we deny them.

This is as true for plants as it is for us, and it’s our green cousins that form the focus of this article.

Plants, just like us humans, are affected by the daily rhythms which aren't just a reaction to day and night, but instead are hard-wired within our genes.

Tick tock alarm clock summertime circadian rhythms
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We’ve evolved in a seasonally variable climate of days and nights, and the rhythms imposed by our genes persist, confusing our bodies if we deny them. This is as true for plants as it is for us.

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Wakey wakey!

Did you know, circadian rhythms were actually first discovered in plants? (Read the more sciency history in the Plant Cell by C. Robertson McClung - it’s great.)

It’s been a topic of fascination for quite some time. Charles Darwin, the man attributed with giving us a rounded view of evolution, was a keen botanist - and his interest inspired his son to study circadian rhythms in mimosa. If you want to go back further, even Androsthenes was at it back when Alexander the Great was marauding through the Persian Gulf.

Mimosa was a source of fascination for several eighteenth century scientists who came long before Darwin’s son, however. French astronomer de Mairan noticed that the daily leaf movements of the plant continued even when subjected to constant darkness, meaning that they are indeed under circadian control.

One point in favour of the gene-driven circadian clock aspect of the cycle is indeed that it doesn’t match a 24 hour clock precisely, so in a way it rules out the actions of the plant being dictated by some pull of a rotating earth. It was the heritability of these circadian rhythms that the aforementioned Darwins pointed out, as was their style.

All this was long before anyone had shown anything of similar note in animals, which first happened in 1894!

It took a long time thereafter to actually clone the first gene involved in circadian rhythms in plants, though, with TOC1 (a core gene involved in daily cycles in plants) being unearthed in 2000. Yes, there is also a TIC gene - which stands for Time for Coffee - which was discovered by our very own Professor Anthony Hall.

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One point in favour of the gene-driven circadian clock aspect of the cycle is indeed that it doesn’t match a 24 hour clock precisely, so in a way it rules out the actions of the plant being dictated by some pull of a rotating earth.

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How the circadian clock works

Much of what we know about plant clocks today comes from experiments on the plant model Arabidopsis.

Genetically, the circadian clock works on a system mediated by a “central oscillator” and a series of interconnected feedback loops - with TOC1 at the core dictating the events of an evening, and a combination of genes CCA1/LHY coordinating what happens through dawn and day via some light receptors called phytochromes and cryptochromes, which “let in” the light signals that then set the clock, so to speak.

There are absolutely tonnes of genes involved, and if you want to get into the nitty-gritty, Hannah suggests that you read this review by Harmer et al. (2009) called “The Circadian System in Higher Plants”.

Essentially, though not always necessary in all plants, there exist some rhythmically coordinated genes, which then dictate the expression of other genes in a daily cycle. This daily pattern has knock-on effects, and is also very important in pretty much all of the most important functions of a plant.

The circadian clock is best described as a central oscillator, which is trained by inputs (such as light and temperature) that feed in information about what time of day it is, which leads to outputs that control about one third of all the genes in Arabidopsis.

Circadian clock genes prepare plants for dawn, by expressing those relevant for photosynthesis. They tell plants to close their stomata at night to conserve water. They can prime plants to make defensive chemicals to ward off hungry caterpillars in the morning. They help to regulate flowering time by understanding the changes in day length that indicate a change in the season. They affect starch metabolism (something perhaps true of humans, as well, though not with starch - as night shift workers tend to put on more weight): indeed, research at the John Innes Centre (JIC) has shown that plants predict how long night will be so that they can use starch most efficiently. The circadian genes protect plants from stresses such as freezing and heat or drought, and also regulates nitrogen fixation, carbon metabolism and uptake of essential minerals from the soil, making them the most efficient at particular times of day.

That was a non-exhaustive paragraph, and it’s clear that the circadian clock plays a vital role.

Thale cress (Arabidopsis thaliana) is a model plant often used for studying circadian clocks and rhythms

Arabidopsis Thaliana is model plant often used for studying circadian clocks and rhythms
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Much of what we know about plant clocks today comes from experiments on the plant model Arabidopsis.

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What about wheat?

What about in other plants, though?

The circadian clock is so important - and clearly has a huge role to play in the health of living things - so surely if we can better train it to suit certain conditions, we can help to make even better crops, for example?

One thing that throws a spanner in the circadian clogs might be that wheat, like many other domesticated crop plants, has a really confusing genome made up of three different ancestral genomes. What is the effect of this polyploidy in how the circadian clock works? Is there a difference? How might a wheat plant differ to Arabidopsis, or even to Brassica napus?

Hannah Rees of the Anthony Hall Group set out to explore just that, and came up with a nifty experimental method to help us find out. Hannah has developed a robust method of measuring daily patterns which has proven difficult previously as most methods have relied on using genetic modification - a technique that isn’t very easy to pull off in wheat.

Other techniques looking at leaf movement only work in dicots (plants with two seed leaves), whereas wheat is a monocot (a plant with one seed leaf, like grasses and lilies). Hannah’s technique works by measuring delayed fluorescence from photosystem II which, as the name implies, is crucial for photosynthesis. The activity of photosystem II oscillates in a 24-hour window, which is very useful in organisms which rely on the sun for energy.

She recently published the first piece of work using this method optimised for wheat and brassica to find differences between the two (the method itself has been used before in a study of Norwegian spruce), which suggested that plants can be night owls, too, and that - interestingly - Brassica napus plants had a more robustly rhythmic circadian clock when grown under 24 hour light, whereas wheat plants had better oscillations when grown under 24 hour darkness.

Even more interesting, in the process of optimising the method for wheat and brassica, Hannah discovered that the circadian clock in plants gets slower as they age - an effect that can even be seen in older leaves compared to younger leaves on the same plant!

Hannah Rees, PhD student in EI's Anthony Hall Group, showcasing her method to reliably measure plant circadian clock responses and rhythms in wheat

hannah rees
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Plants can be night owls, too, and interestingly - Brassica napus plants had a more robustly rhythmic circadian clock when grown under 24 hour light, whereas wheat plants had better oscillations when grown under 24 hour darkness.

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There was something in the air that night

This day-night training is interesting indeed, and is not the same everywhere, which is why Hannah has also been investigating Swedish Arabidopsis plants using her new method. The results from this have been similarly interesting - and we’ll fill you in on them when the article gets fully published, but in the meantime check out this preprint in BioRxiv.

It’s safe to say that circadian clocks are important indeed - and with each and every discovery comes an opportunity to probe what makes a plant tick (or tock). Now that we can measure these circadian effects in wheat, it’s only a matter of time before we can breed (or even train?) better plants for the future, or perhaps find plants that are best suited to grow under particular light conditions. We might even discover whether circadian rhythms have been inadvertently selected for in crops by the process of domestication.

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Now that we can measure these circadian effects in wheat, it’s only a matter of time before we can breed (or even train?) better plants for the future, or perhaps find plants that are best suited to grow under particular light conditions.

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Article author

Peter Bickerton

Scientific Communications & Outreach Manager