Abstract
Negative feedback loops (NFLs) for circadian clocks include light-responsive reactions that allow the clocks to shift their phase depending on the timing of light signals. Phase response curves (PRCs) for light signals in various organisms include a time interval called a dead zone where light signals cause no phase shift during daytime. Although the importance of the dead zone for robust light entrainment is known, how the dead zone arises from the biochemical reactions in an NFL underlying circadian gene expression rhythms remains unclear. In addition, the observation that the light-responsive reactions in the NFL vary between organisms raises the question as to whether the mechanism for dead zone formation is common or distinct between different organisms. Here we reveal by mathematical modeling that the saturation of a biochemical reaction in repressor synthesis in an NFL is a common mechanism of daytime dead zone generation. If light signals increase the degradation of a repressor protein, as in Drosophila, the saturation of repressor mRNA transcription nullifies the effect of light signals, generating a dead zone. In contrast, if light signals induce the transcription of repressor mRNA, as in mammals, the saturation of repressor translation can generate a dead zone by cancelling the influence of excess amount of mRNA induced by light signals. Each of these saturated reactions is located next to the light-responsive reaction in the NFL, suggesting a design principle for daytime dead zone generation.
Highlights
Circadian clocks in various organisms are composed of cell autonomous gene expression rhythms with a nearly 24-hour period
The light-entrainment properties of these clocks have been studied by measuring phase shifts caused by light pulses administered at different times
The phase response curves of various organisms include a time window called the dead zone where the phase of the clock does not respond to light pulses
Summary
Circadian clocks in various organisms are composed of cell autonomous gene expression rhythms with a nearly 24-hour period. A light signal shifts the phase of the clocks by affecting the biochemical reactions in the TTFLs that regulate circadian gene expression. Such phase responses of circadian clocks to light signals allow their entrainment to the LD cycle. Most organisms maintain their behavioral rhythms under constant dark (DD) conditions, indicating that their circadian clocks set subjective day and night. The phase responses of the circadian clocks to light signals have been examined by exposing organisms to short light pulses under DD conditions. This time window during daytime, when the phase of the clock is insensitive to light pulses, is referred to as the dead zone
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