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Plants use an entrained circadian clock to change their sensitivity to stimuli, while also responding directly to the current light and temperature environment. The same external stimulus can therefore have different effects at different internal phases. This circadian gating must be distinguished from a daily rhythm caused solely by daily variation in the stimulus itself.

The plant circadian clock contains interlocking regulation of gene expression, protein accumulation and protein activity. Morning-associated regulators such as CCA1 and LHY interact with later-acting components, including TOC1, to generate a sequence of phases rather than a single daily on–off switch. Light information, including inputs involving phytochromes and cryptochromes, and temperature cues adjust the clock through entrainment of circadian rhythm. Under suitably constant conditions, a free-running circadian rhythm persists. Anticipation of dawn or dusk is therefore possible before the corresponding environmental transition occurs.

Clock outputs can modify several points in a stimulus-response pathway. A receptor or transport protein may accumulate at a particular phase; signaling inhibitors may be removed at another. The clock can regulate hormone production, hormone inactivation, transport and sensitivity of downstream transcription factors. Post-translational regulation allows a phase-specific transcript to produce an output only under a second permissive condition. Consequently, a rhythmic hormone concentration and rhythmic responsiveness to that hormone are distinct explanations and may coexist.

Auxin provides direct experimental evidence for sensitivity gating. Timed auxin treatments and transcriptional reporters in Arabidopsis showed that an externally supplied hormone stimulus produces phase-dependent responses; growth responses were also gated. Because the stimulus was supplied experimentally, the result cannot be explained merely by assuming that the plant normally makes more auxin at one time of day. Reporter dynamics and pretreatment baselines still require appropriate controls, and a reporter is not a direct measurement of free hormone.^[ref]

An illustrative local description iswhere $S$ is a small standardized stimulus, $\varphi$ is circadian phase and $\Delta R$ is the response above the matched untreated baseline. A phase-dependent gain $g$ represents gating. In contrast, if $g$ is constant but the baseline response oscillates, observing different absolute values after treatment does not establish gating. Real pathways can saturate or change sign, so this equation illustrates the experimental distinction rather than defining a universal linear law.

Photoperiodism shows how internal time can be combined with an external cue to produce a developmental decision. In Arabidopsis, timed expression of CONSTANS interacts with light-dependent regulation of the protein. In long days, a permissive expression phase overlaps light sufficiently to support FLOWERING LOCUS T activation. The external coincidence model therefore responds to when light occurs relative to the clock, rather than merely adding up photons. Photoreceptor-dependent protein regulation provides a molecular connection between timing and the external environment.^[ref] FT protein can then communicate from leaves to the shoot apex. Phloem-specific expression and grafting experiments support FT protein movement as part of this long-distance floral signal.^[ref]

A convincing demonstration of circadian gating compares matched stimuli at several internal phases under constant external conditions, with untreated controls at every phase. Plants entrained to opposite schedules can help distinguish internal phase from laboratory clock time. Clock perturbations and restoration of clock function strengthen causal interpretation, provided effects on general health and growth are considered. A phase-shifted response in constant conditions supports clock control; disappearance immediately when the environmental cycle is removed suggests direct environmental control, although weak rhythms and altered physiology can complicate that inference. Masking of circadian rhythm, in which an environmental cue directly changes a measured output, can coexist with clock control.

Timing is useful because demands and risks recur. Coordinating stomatal conductance, photosynthetic preparation and growth with expected light availability can improve resource use. Yet the optimum phase depends on temperature, water availability and day length, and a strong acute stress can override a normal daily preference. Plants combine an internal estimate of time with current conditions, changing pathway sensitivity as well as the abundance of signals and response machinery.