The origin of biological clocks


The Earth has rhythm. Every 24 hours, the planet pirouettes on its axis, bathing its surface alternately in sunlight and darkness.

Organisms from algae to people have evolved to keep time with the planet’s light/dark beat. They do so using the world’s most important timekeepers: daily, or circadian, clocks that allow organisms to schedule their days so as not to be caught off guard by sunrise and sunset.

A master clock in the human brain appears to synchronize sleep and wake with light. But there are more. Circadian clocks tick in nearly every cell in the body. “There’s a clock in the liver. There’s a clock in the adipose [fat] tissue. There’s a clock in the spleen,” says Barbara Helm, a chronobiologist at the University of Glasgow in Scotland. Those clocks set sleep patterns and meal times. They govern the flow of hormones and regulate the body’s response to sugar and many other important biological processes (SN: 4/10/10, p. 22).

Having timekeepers offers such an evolutionary advantage that species have developed them again and again throughout history, many scientists say. But as common and important as circadian clocks have become, exactly why such timepieces arose in the first place has been a deep and abiding mystery.

Many scientists favor the view that multiple organisms independently evolved their own circadian clocks, each reinventing its own wheel. Creatures probably did this to protect their fragile DNA from the sun’s damaging ultraviolet rays. But a small group of researchers think otherwise. They say there had to be one mother clock from which all others came. That clock evolved to shield the cell from oxygen damage or perhaps provide other, unknown advantages.

The original biological timepiece may not have resembled the precision body clocks that scientists study today. The ancestral clock may have started out as simple as a sundial, researchers say, but it provided a foundation for building the more elaborate mechanisms that now control everything from blood pressure to bedtime.

Circadian clocks don’t have gears and hands. They’re composed of RNA molecules and proteins that oscillate in abundance. At particular times of day, certain clock proteins switch on production of messenger RNA, used by the cell to bake fresh batches of other clock proteins. Eventually levels of those proteins reach a certain threshold; they then shut off creation of the messenger RNA that produces them. The self-suppressing proteins disintegrate or get nibbled away by other proteins until their levels fall below a threshold, signaling the need for another batch, and the cycle starts again.

Just as Rolex, Timex, Swatch and Seiko make their own versions of a wristwatch, organisms including cyanobacteria, fungi, plants and insects have all invented their own varieties of circadian clocks. The cycling proteins are as different among these organisms as digital watches are from precision quartz clockworks. But all of them mark days with the predictable ebb and flow of messenger RNA and protein production.

There’s no doubt that today’s circadian clocks are must-have accessories for most organisms living on Earth’s surface. But does the run-away-from-the-light origin story make sense?

A main piece of evidence in favor of the “flight from light” idea is that cells tend to replicate their DNA at night safely under cover of darkness and repair it during the day as damage from UV light accumulates. Some of the same protein cogs that drive the circadian clocks are also involved in DNA repair, further solidifying the connection.

“That’s a nice idea,” says circadian cell biologist John O’Neill of the MRC Laboratory of Molecular Biology in Cambridge, England, “but it doesn’t fit with modern data.”

Going way back

Several lines of evidence argue against flight from light as the common force propelling the evolution of circadian clocks, says O’Neill, one of the scientists rewriting the circadian clock origin story.

If the cycle arose to protect DNA, one would expect cycling to happen only if there was DNA to protect. But circadian rhythms can happen in a test tube without DNA.

A type of cyanobacteria, or blue-green algae, known as Synechococcus elongatus has one of the simplest known circadian clocks. It consists of three proteins called KaiA, KaiB and KaiC. Those three gears, along with two accessory proteins, help the algae prepare for sunrise by stockpiling proteins needed for photosynthesis and other important daily activities.

Plop the three clock proteins into a test tube. Add energy from adenosine triphosphate (better known as ATP), and the clock will rhythmically add and subtract phosphate molecules from KaiC, Takao Kondo of Nagoya University in Japan and colleagues reported in Science in 2005. The finding shook up circadian researchers because it showed that clocks can operate without DNA. It also revealed that they don’t need to switch messenger RNA and protein production on and off to keep time.

Those blue-green algae and the mysterious, unnamed ancestor of insects and animals formed different branches on the evolutionary tree more than 1 billion years ago. Clock proteins of S. elongatus are nothing like the central timekeeping proteins of mammals. So some researchers doubted that DNA-free clocks existed in organisms more complex than algae.

O’Neill and his collaborator Akhilesh Reddy of the University of Cambridge thought that they could find DNA-free clocks elsewhere. They decided to look for circadian clocks in human red blood cells, which lack a nucleus where DNA is stored. Without DNA, there is also no messenger RNA production, which is essential for the classic circadian clocks to work. Nevertheless, the cells still have circadian rhythms, O’Neill and Reddy reported in Nature in 2011.

The red blood cell clock is entirely different from the protein and messenger RNA cycle that synchronizes nucleus-containing cells with the sun. In the red blood cells, antioxidant proteins called peroxiredoxins accept or give up oxygen molecules in a persistent circadian rhythm. Their action helps mop up hydrogen peroxide, a by-product of a cell’s normal energy-manufacturing activities. Hydrogen peroxide and other oxidants can damage many components of a cell, so keeping them in check is essential for survival.

Peroxiredoxins are found in a wide variety of organisms, including marine algae called Ostreococcus tauri. Working with other collaborators, O’Neill and Reddy examined the peroxiredoxins in the algae. “Just like the red blood cells, there was a rhythm,” O’Neill says. The amount of oxygen molecules clinging to the peroxiredoxins rose and fell in a persistent 24-hour cycle. The team reported that finding in the same 2011 issue of Nature.

A year later, the researchers reported in Nature that they had found peroxiredoxin cycles in fruit flies, the plant Arabidopsis thaliana, a fungus called Neurospora crassa, S. elongatus cyanobacteria and an archaean called Halobacterium salinarum. Together, the organisms represent all of the major domains of life. If every domain has peroxiredoxin clocks, the antioxidants are most likely ancient, probably dating back billions of years.

The oxygen menace

No one knows for sure how far back those antioxidant clocks go, but O’Neill has a time frame in mind: 2.5 billion years. That’s when cyanobacteria, which had recently begun using photosynthesis to fuel their activities, started releasing vast amounts of oxygen in the Great Oxidation Event. While photosynthesis and an oxygen-rich atmosphere are now considered necessities, oxygen was poison for Precambrian life-forms. Organisms that could not tolerate free oxygen either died or ended up in the anaerobic deep sea. “If they didn’t die off, they had to cope,” O’Neill says.

Oxygen would have been a problem mainly during the day, when photosynthesis was taking place. Organisms that geared up their antioxidant defenses — stripping peroxiredoxin of oxygen molecules so that it could sponge up hydrogen peroxide when the sun peeked over the horizon — would get a jump on survival. A timing mechanism that could anticipate oxygen’s arrival instead of just reacting to it would be “such an enormous advantage,” says O’Neill, “that it just became hardwired.”