Many genes encoding enzymes of phenylpropanoid biosynthesis have peak RNA levels before dawn, perhaps because it is advantageous to accumulate photoprotective flavonoids before the sun rises ( Harmer et al., 2000). In several cases, genes that affect a common pathway or process are expressed at the same phase, suggesting that the phase might be important in the function of that process. This circadian gene expression produces the rhythms that pervade plant physiology, some of which are obvious (such as the “sleep movements” of legume leaves, noted since classical times), others less so. Microarray experiments indicate that at least 6% of Arabidopsis genes are rhythmically expressed, with expression peaks at all phases throughout the day and night ( Harmer et al., 2000 Schaffer et al., 2001). WHICH PLANT PROCESSES ARE CLOCK-REGULATED? The converse relationship does not necessarily hold: A rhythm with an early phase can arise without a change in period (for example, in the phyB mutant Hall et al., 2002). This relationship can be used experimentally to alter the phase of entrainment (see below in the discussion of photoperiodic regulation Yanovsky and Kay, 2002).
The period of the clock that we measure in constant conditions will nonetheless affect the phase of entrainment, all else being equal, so a rhythm with a longer period under constant conditions will have a later phase under entrainment. Therefore, the circadian clock contributes to plant physiology by regulating the phase of entrained rhythms, and natural selection acts primarily on phase, not on period. Plant circadian rhythms in nature are always entrained to 24 h by the day/night cycle the non-24 h period is expressed only in exceptional circumstances (or in the laboratory).
This process of “entrainment” is crucial to ensure that rhythmic processes occur at an appropriate time of day (circadian phase), particularly because the period of circadian clocks in the absence of entraining signals often differs from 24 h. The rhythms are all reset by light and/or temperature signals in a characteristic fashion that synchronizes the clock with the environment. The hallmarks of circadian regulation are very similar in all organisms, most obviously the persistence of biological rhythms even under constant environmental conditions. Plants, like other eukaryotes and some prokaryotes, have adapted to the day/night cycle by evolving the circadian system, which drives matching rhythms in very many aspects of metabolism, physiology, and behavior ( Harmer et al., 2001 Young and Kay, 2001). Locomotion would not alleviate the problem. Each day's solar energy propels their metabolism into a spate of carbon fixation, which must end at nightfall. Therefore, plants are stuck with a day/night cycle of light and temperature, with the possible exceptions of buried, germinating seedlings and polar inhabitants. Plants must be exposed to sunlight for photosynthesis, and sunlight is not available continuously.
The circadian clock is an intricate, even delicate, regulator of plant physiology, yet at least one of the selective pressures that drove its evolution is brutally simple.
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