3-D structure of biological clockwork revealedIn 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.
Egli and Johnson published the crystal structure-a kind of molecular "snapshot"-of KaiC in Molecular Cell in August and reported additional features of the protein in the Sept. 21 issue of the Proceedings of the National Academy of Sciences .
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."
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.
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