Clock Genes Keep Time to Daily Rhythm

By Jason Socrates Bardi

For a flowering plant, life is no bed of roses.

Burning sunlight during the day, freezing cold at night, and too much shade from the competition offer various threats that plants must overcome to stay alive and reproduce. A single blade in a field of grass has no other choice but to work round the clock to stay alive.

Plants have evolved the means to cope with the various challenges of their environment by reaching the point where they can alter or even predict their adaptive response to their niches day by day, as nature demands.

Plants survive by expressing certain genes and proteins at optimal times of the day—as they are needed to protect against the sun’s damaging UV radiation or the night’s cold air, for instance.

This so-called circadian rhythm follows the solar day, and a group of researchers at The Scripps Research Institute (TSRI) have been studying the rhythm in one small, leafy, weed-like relative of the mustard plant, Arabidopsis.

“When you can’t go indoors when it’s cold, or find some shade when it’s sunny,” says Cell Biology Professor Steve Kay, “you organize your stress responses on a daily basis. Plants need to anticipate changes in their environment, not just respond to them.” Kay says what they do is make their own equivalent of sunscreen in the morning and warm clothes at night.

Arabidopsis uses all the genetic tools at its disposal to do the daily work of adapting to the varying stresses of its environment in order to stay alive.

Timing on the Nano-Scale

Unlike chronometers, which keep the same time continuously, plant clocks have to change continuously. Plants must sense changes in their environment, such as length of the day, temperature, and the foliage around them that may be blocking the sun and entrain their clocks to adjust accordingly.

All such timing takes place on the level of individual cells, with molecules ebbing and flowing throughout the day and year as they are needed. Photoreceptors, for instance, need to be assembled in plant cells in the morning and afternoon, but not in the evening. Plant cells also need protection from freezing at night but not often during the day. Circadian rhythms can be identified, then, by observing this pendulum swing of molecular expression throughout the day.

But that’s only the beginning of the story—call it the loud ticking and turning hands that keeps the time on the face of the clock. The real mechanism that drives the circadian rhythm is the intricate and elegant genetic machinery that expresses the molecules that control the ticking of the ticking genes. The clockworks.

Clockworks comprise a number of complicated feedback switches involving the expression of sometimes large numbers of genes, mostly transcription factors, which regulate the ticking genes by binding to their promoter regions, their mRNA, and otherwise turning them on and off as needed.

Kay’s laboratory is particularly interested in these clockworks and has been tinkering with and studying them in Arabidopsis for some time. Members of the laboratory vary the plants’ environments—the amount of light these test plants receive, for instance—then ask how the plants adjust their own clocks to keep abreast of these changes, looking for which genes are turned on and off when and what other molecules are persistently present.

“We’ve begun to identify some of those transcription factors,” Kay says. His laboratory identified several genes that are under tight circadian control in a recent issue of the journal Science.

Next Page | The molecules are the message

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Professor Steve Kay has been studying the daily rhythms of one small, leafy, weed-like relative of the mustard plant, Arabidopsis.