It's About Time: Biological Clock Research Keeps Ticking

Release Date:
12/23/1998
Contact:
Alison Davis, NIGMS

It all started nearly 30 years ago, when scientists first stumbled upon mutant fruit flies with a permanent case of jet lag. Since then, NIGMS-sponsored basic research has fueled the fire for a recent explosion of discoveries in the field of circadian rhythms.

So-called clock researchers now appreciate a striking evolutionary parsimony in the molecules and pathways used by seemingly every organism on the planet--including bacteria, fungi, plants, silk moths, mice, and humans--to establish a 24-hour physiologic day. Many of the protein parts of biological clocks in such widely diverse life forms appear remarkably alike.

Such conservation of function has clock scientists excited that they will be able to use fruit flies and other genetically tractable model organisms to dissect the mammalian biological clock, a feat that would lead to a better understanding of a host of human afflictions, including not only jet lag but also a variety of sleep disorders and mental illnesses.

"You can't ask a fly to read, add, or operate heavy machinery," says Dr. Michael Young of Rockefeller University. But you can rely on Drosophila (fruit flies) to help fit all the pieces of the clock together, he notes. Dr. Young and other scientists think that, in flies and mammals, those pieces are a set of probably a dozen or so proteins.

By way of Drosophila genetics, predicts Dr. Jeffrey Hall of Brandeis University, "We will find every single one of the clock genes." At last count, six Drosophila clock genes had been discovered, four within the past year. Many similar genes have been identified in mammals; already, three versions of one of the fly genes have been found in the mouse genome, which is very similar to that of humans.

In humans and other mammals, the body's "master clock" resides in a small sliver of brain tissue called the suprachiasmatic nucleus, or SCN. Light streaming into the eye of an animal sends a signal to the SCN, where 10,000 individual cellular pacemakers are housed. Within each of these SCN neurons, levels of a cast of protein characters--with names such as Period, Timeless, and Clock--rise and fall throughout the course of the day. Each protein helps keep cellular time by acting in a feedback loop in which the other proteins' production is shut off during certain parts of the day.

Tiny, Brainless Fungus Sheds Light on How All Clocks Work
Despite the fact that decades of research have pointed to the brain as the organ that houses the body's "master clock," another treasure trove of knowledge has come from studies on a tiny brainless fungus called Neurospora crassa. Over the years, Neurospora work pioneered by Dr. Jerry Feldman (then at the State University of New York at Albany), and continued to the present by Dr. Jay Dunlap, Dr. Jennifer Loros, and colleagues at Dartmouth University, has revealed the extraordinary utility of this simple organism, more commonly known as bread mold. Recent work from these scientists is beginning to reveal the ways that temperature--not light--resets the Neurospora clock and synchronizes it to the outside world. Those findings, as with much of the Neurospora circadian rhythm research, will likely hold true in higher organisms.

Dr. Dunlap and Dr. Loros' work has pointed to the essential role of clock protein partnering, a phenomenon that scientists are discovering in all biological clock systems, including those of humans. Clock proteins in Neurospora, Drosophila, mice, and most likely, humans contain a recognizable molecular motif, a string of amino acids called a "PAS" domain, the structure of which was published in the November 25, 1998 issue of the journal Cell. This motif instructs a protein to attach itself to another PAS domain-containing protein. It is only after the two proteins fit together like pieces of a jigsaw puzzle that they can enter the cell's nucleus and perform their regulatory role in helping set the clock's time.

Cryptic Role of Proteins Revealed in Plants, Animals
Along with Neurospora, flies, and mice, another--albeit unlikely--species is offering new insight into how biological clocks work: the mustard plant Arabidopsis thaliana. Recent research using this plant (which is a popular model system for genetic research) has yielded a valuable clue toward solving a long-standing circadian mystery: how light is first detected by, and then triggers the activities of, clock genes and proteins.

One unanswered question in the field of circadian rhythm research has been the identity of the mystery proteins that serve as links between the inner workings of a biological clock and the outside world. Recently, several independent groups of scientists have begun to come to grips with this problem.

They have found one such mystery protein, called cryptochrome, a pigment found in abundance in the eyes and brains of mice and humans, that has--in evolutionary terms--been around for a while. Cryptochrome proteins were first identified in plants many years ago, but only relatively recently did Dr. Anthony Cashmore and his colleagues at the University of Pennsylvania obtain the gene sequence for the cryptochrome protein in Arabidopsis, permitting more thorough study of its properties and functions.

Working in flies, mice, and plants, several research teams now credit cryptochromes with playing important roles in clock functioning, although the precise ways cryptochromes go about decoding light signals appear to differ somewhat among the organisms studied to date. Nevertheless, all cryptochromes seem to work by soaking up particular wavelengths of light and then touching off a cascade of events that synchronizes the biological clock, thus enabling an organism to "know" what time of day--or even what season of the year--it is.

In the November 20, 1998 issue of Science, Dr. Steve Kay and his co-workers at the Scripps Research Institute reported that Arabidopsis relies upon cryptochrome and a similar light-sensitive pigment protein called phytochrome--responding to blue and red light, respectively--to synchronize its biological clock.

Of course, one might wonder: Why would a plant need a clock in the first place?

"It's to the plant's advantage to anticipate dusk and dawn," explains Dr. Paul Devlin, a postdoctoral fellow in Dr. Kay's laboratory. That way, Dr. Devlin says, the plant can gear up its photosynthetic machinery--the enzymes used to convert light into sugar for energy--just before the sun peeks over the horizon. Biological clocks in plants also appear to play a key role in timing pollination events, he adds.

From Flies to People: Clock Genes Offer Possible New Drug Targets
In recent years, fruit fly researchers have offered several important new chapters of the engaging story of circadian rhythms. Research from these scientists' labs has helped to flesh out the mechanics of the Drosophila clock, which, like the Neurospora and Arabidopsis clocks, hinges upon the coordinated functioning of a core set of "clock genes" whose protein products' abundance varies with the time of day.

Indeed, it might not be long before the fly data begins to bear pharmaceutical fruit.

In July 1998, Dr. Young and his co-workers discovered a clock protein called Double-time that, they believe, may be an easy target for drug developers. Double-time controls levels of the Period protein by adding a chemical tag called a phosphate group to it. By regulating amounts of Period, which itself regulates the abundance of other clock proteins, Double-time plays a major role in keeping the clock running smoothly.

Targeting such a master regulator of the biological clock, Dr. Young says, may make it possible to adjust levels of key clock components and re-wind the broken cellular timepieces that underlie a variety of human ailments.

Please mention support for this work from the National Institute of General Medical Sciences (NIGMS), a component of the National Institutes of Health that supports basic biomedical research. Please fax clips to (301) 402-0224.

REFERENCES

Ahmad M, Cashmore AD. HY4 gene of Arabidopsis thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 1993, 366:162-6.

Allada R, White NE, So WV, Hall JC, Rosbash M. A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell 1998, 93:791-804.

Cabral JHM, Lee A, Cohen SL, Chait BT, Li M, MacKinnon R. Crystal structure and functional analysis of the HERG potassium channel N terminus: A eukaryotic PAS domain. Cell 1998, 95:649-55.

Dunlap J. An end in the beginning. Science 1998, 280:1548-9.

Emery P, So WV, Kaneko M, Hall JC, Rosbash M. CRY, a Drosophila clock and light-regulated cryptochrome, is a major contributor to circadian rhythm resetting and photosensitivity. Cell 1998, 95:669-79.

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Miyamoto Y, Sancar A. Vitamin B 2-based blue-light photoreceptors in the retinohypothalamic tract as the photoactive pigments for setting the circadian clock in mammals. Proc. Natl. Acad. Sci. USA 1998, 95:6097-6102.

Price JL, Blau J, Rothenflu A, Abodeely M, Kloss B, Young MW. double-time is a new Drosophila clock gene that regulates PERIOD protein accumulation. Cell 1998, 94:83-95.

Rutila JE, Suri V, Le M, So, WV, Rosbash M, Hall, JC. CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless. Cell 1998, 93:805-14.

Somers DE, Devlin PF, Kay SA. Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 1998 282:1488-90.

Stanewsky R, Kaneko M, Emery P, Beretta B, Wager-Smith K, Kay SA, Rosbash M, Hall JC. The cry b mutation identifies cryptochrome as a circadian photoreceptor in Drosophila. Cell 1998, 95:681-92.

Thresher RJ, Vitaterna MH, Miyamoto Y, Kazantsev A, Hsu DS, Petit C, Selby CP, Dawut L, Smithies O, Takahashi JS, Sancar A. Role of mouse cryptochrome blue-light receptor in circadian photoresponses. Science 1998, 282:1490-4.

For scientific perspective on this research, call the NIGMS Office of Communications and Public Liaison at (301) 496-7301 to interview Dr. Michael Sesma, program director, Division of Genetics and Developmental Biology.