"Visualizing a Circadian Clock Protein: Crystal Structure of KaiC and Functional Insights;" Molecular Cell; 13 August 2004 ;"


Proceedings of the National Academies of Sciences; 21 September 2004

Melanie Bernard
Created by Sabuj Pattanayek
Illustration of the 3-D structure of the three blue-green algae clock proteins. KaiA subunits are colored yellow and purple; those of KaiB are colored aquamarine and salmon; and KaiC subunits are colored red, green, aquamarine, gold, blue and violet. The structure of KaiA was determined by researchers at Texas A&M; that of KaiB was done by a group of researchers at the University of Toronto; and the structue of KaiC was established by the Vanderbilt researchers.

3-D structure of biological clockwork revealed

In the last six months, scientists have taken an important step towards deciphering the inner workings of circadian clocks, an understanding that could ultimately lead to novel treatments for clock-related disorders, such as jet lag, sleep disorders and some types of depression. They have determined the three-dimensional structures of the three proteins that make up the simplest known biological clock, the one that operates in blue-green algae.

The structures of the two smaller biological clock molecules were determined by groups at Texas A&M, Nagoya University and the University of Toronto. Now two Vanderbilt researchers-—Martin Egli, associate professor of biochemistry, and Carl H. Johnson, professor of biological sciences—report that they have solved the structure of the third and largest of these biological clock proteins.

Blue-green algae are the simplest organism known to have biological clocks. As in higher organisms, like human beings, the clocks in these single-celled plants regulate gene expression, cyclically turning genes on and off. Three proteins-KaiA, KaiB, and KaiC, named after the Japanese word for cycle-are the key components of the algae's clock; without any one of them, the clock does not work.

Photo by Neil Brake
Martin Egli viewing image of clock protein

Egli and Johnson published the crystal structure-a kind of molecular "snapshot"-of KaiC in Molecular Cell Click to open/close footnote in August and reported additional features of the protein in the Sept. 21 issue of the Proceedings of the National Academy of Sciences . Click to open/close footnote

Though the proteins that make up the gears and springs of the circadian clock in these simple plants differ from those that form the human clock, it is quite likely that the fundamental biochemistry of clock function has remained unchanged, the investigators say.

"Hopefully, some of the basic principles that we uncover at the biochemical level [in blue-green algae] will guide the research in the mammalian systems," Johnson says.

With the structures of KaiA, KaiB and KaiC published in the last few months, the field is in a position to tackle complex questions of clock function, Egli says. "There's been this culmination of five years worth of work, all in a matter of months. It's a really exciting time."

Melanie Bernard
Photo by Neil Brake
Johnson inspecting a beaker of blue-green algae.

The KaiC structure is already providing hints to its biochemical operations, but the investigators stress that the work is still in an early stage.

"Even though we've learned things from the structure," Egli says, "the big question still is: what are the underlying biochemical mechanisms that allow organisms to control their rhythms so precisely?"

Six KaiC molecules appear to group together to form a ring-like structure that looks something like a mechanical gear-oddly appropriate, given its function as the core of the timepiece. KaiA and KaiB associate with the KaiC ring depending on a biochemical reaction called phosphorylation. Egli and Johnson's work has identified three phosphorylation sites on KaiC; mutation of any of these sites turns off the clock.

Courtesy of Martin Egli
View of the master clock of blue-green algae. The different colors illustrate that the clockwork protein is made up of six identical pieces joined together to give it the appearance of a double-donut.

The KaiC structure reveals unexpected evolutionary relationships to proteins that manufacture the energy molecule ATP and to DNA pumps. What these similarities mean is still anyone's best guess, Egli says, adding "I think there must be some unusual mechanism."

In addition to opening new avenues for the treatment of some sleep disorders and forms of depression, clock research raises questions about timing of medication dosing. There may be optimum times of day for hitting a particular target, depending on the cycling of genes on and off. Other groups are investigating whether the timing of chemotherapy, for example, can reduce side effects and enhance efficacy, Egli says.

According to the researchers, circadian clocks are increasingly being recognized as fundamental to biology.

"The emerging idea is that the organism is basically a clock shop-that everything is oscillating," Johnson says. "One function of the brain, particularly certain parts of the brain, is to keep all of that organized and synchronized. The brain acts as a pacemaker for all of the other clocks in all of the other cells in the body, even in your big toe."

The research was supported by the National Institutes of Health, the National Science Foundation and a Vanderbilt University Medical Center Intramural Discovery Grant.

-- Leigh MacMillan

Carl Johnson Laboratory website

Martin Egli's Laboratory website