U.S. flag

An official website of the United States government

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Dean L, McEntyre J, editors. Coffee Break: Tutorials for NCBI Tools [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 1999-.

Cover of Coffee Break

Coffee Break: Tutorials for NCBI Tools [Internet].

Show details

Dissecting the mechanism of our internal clock

how living organisms tune in to the time of day

Created: .

As any jet-setter knows, it takes time to adapt to the shifted day-night cycle of a foreign time zone. We have an internal circadian clock that times many physiological and behavioral events on a 24-hour cycle, according to day length. The clock can also reset itself, so we can cope with the seasonal variation in day light hours and the trappings of 20th century living such as shift work and air travel.

Not only humans have circadian rhythms. The eyes of marine molluscs, for example, show a correlation between perception of light and a circadian rhythm, as do the pineal glands of lizards and birds. The underlying clock that gives rise to these rhythms is dependent on feedback loops that regulate the expression of certain genes. Two animals in particular have given insight into the molecular mechanisms of internal clocks: the fungus Neurospora crassa and the fruit fly Drosophila melanogaster.

Control of circadian rhythms at the molecular level.


Control of circadian rhythms at the molecular level. We are just beginning to unravel the secrets of how circadian rhythms are controlled at the molecular level. Several components of what might be the 'core' molecular clock have now been cloned and (more...)

Several components of molecular clocks have now been cloned and sequenced. In Neurospora, the frq gene was the first found to be associated with period length; then two more genes, wc-1 and wc-2, were discovered in a strain of Neurospora that was blind to light. Both wc-1 and wc-2 are transcription factors that contain zinc fingers and transcriptional activation domains. Furthermore, these two proteins have PAS domains.

PAS domains were first identified in the Drosophila period clock protein PER, the vertebrate aryl hydrocarbon receptor nuclear translocator (ARNT), which is involved in a cell's response to lowered oxygen levels, and the Drosophila single-minded protein (SIM1), involved in the regulation of development. Many proteins have since been found to have PAS domains, which have now been shown to mediate protein-protein interactions.

A series of recent papers have confirmed that there is a common pattern to molecular clocks that has been conserved across evolution, from fungi to mammals. Part of the pattern is that PAS domains glue proteins such as wc-1 and wc-2 together to form a complex that switches on other clock components, such as frq, as a part of the organism's response to light. The frq protein then feeds back to inhibit the action of wc-1 and wc-2, thereby ultimately effecting its own expression. Signals from the environment, such as different light levels or temperature, could impact upon the loop to add more layers of regulation.

There are certain to be more feedback loops that are linked to this core component, because several observations have been made that do not quite fit this model, and it is not yet clear whether the clocks of plants or cyanobacteria will work in the same way. Perhaps these other cogs will be specific to different organisms, with only the "master clock", outlined here, being conserved across species.

Time will tell.

Search PubMed for day length and melatonin levels

Created: August 18, 1999

Click on the link below to start an html tutorial.

How might day length effect melatonin levels?

Search PubMed for new clock components

Created: August 18, 1999

Click on the link below to start an html tutorial.

What's the recent progress in identifying clock components?

Use BLAST to search for CLOCK protein

Created: August 18, 1999

Click on the link below to start an html tutorial.

CLOCK protein from the fruit fly is one of the most recently discovered clock components.