SUMMARY: The Circadian System in 920 Words

Circadian rhythms are biological rhythms cycling once every 24 hours, expressing a wide array of individual shapes and peak times with respect to day and night.  A true circadian rhythm persists in an environment free of any recurring external timing cues (“constant conditions,” usually requiring a laboratory) with a near 24-hour cycle length that remains relatively stable even under ambient temperatures that may vary within the natural range (“temperature compensation”).  Such features point to the existence of an innate, self-sustained oscillatory mechanism (“circadian clock”) underlying the rhythms, a mechanism that both recognizes the local time of day and measures the passage of time.  Under natural conditions, the clock’s near 24-hour cycle length is reset (entrained) to match the Earth’s 24-hour axial rotation, establishing a stable relationship between them.  A key, but not exclusive, timing cue for this process is the 24-hour alternation of light and darkness.  The selective advantages of such a timekeeping system are myriad – including the regulation of the temporal organization of biological processes, anticipation of periodic daily events, adaptation to the seasons, and spatial orientation and navigation by the sun.

The mechanisms responsible for generating overt circadian rhythms bridge multiple levels of biological organization.  The core oscillatory mechanism lies within individual cells, utilizing a common design principle that involves a suite of clock genes functioning within transcription-translation negative feedback loops, with delayed repression of their mRNAs by their own protein products.  In eukaryotes, this regulatory mechanism is largely conserved, although the identities of the genes may differ between organisms (however, in a prokaryote [a cyanobacterium] the core mechanism instead involves three interacting proteins and rhythmic phosphorylation).  In the mammalian case, the positive (activator) limb of the loop is represented by the binding of the transcription factors BMAL1 and CLOCK as a heterodimeric complex to E (enhancer) box response elements on the DNA of clock-controlled, genome-wide target genes.  Among the genes activated by BMAL1/CLOCK are period (per1, per2, per3) and cryptochrome (cry1, cry2), which represent the negative (repressor) limb of the loop, as PER and CRY protein products are translocated to the nucleus and assemble as parts of large complexes that inhibit BMAL1/CLOCK activity and thus their own transcription.  Cycle length is set by the repressors; by their post-translational accumulation and phosphorylation via kinases such as casein kinases 1𝛿 and 1𝜀 and by their degradation through the ubiquitin-proteosome pathway.  Also identified are two additional loops that feedback on BMAL1/CLOCK transcriptional activity.  The first involves E-box mediated transcription of genes encoding nuclear hormone receptors REV-ERB𝛼/β and ROR𝛾 that bind to RORE (retinoic acid-related orphan receptor) response elements on the bmal1 and clock promoters; the second involves bZIP transcription factors DBP and NFIL3 that regulate the expression of ROR𝛼/β.  Beyond the loops, it is the combinatorial actions of these elements on clock-controlled output genes that contribute to the regulation of cellular-, tissue-, and time of day-specific transcriptional rhythms within organisms.

In metazoan animals, in addition to the presence of widespread intracellular clocks, the brain harbors specialized, heterogeneous populations of neurons and glia that function as centralized circadian pacemakers to coordinate rhythmicity at the supra-cellular level.  In mammals, there are about 20,000 neurons in the hypothalamic suprachiasmatic nucleus (SCN); and in Drosophila, about 150 neurons in the head.  Neurotransmitters and neuropeptides in the SCN – such as 𝛾-amino-butyric acid (GABA), vasoactive intestinal polypeptide (VIP), and arginine vasopressin (AVP) – and in Drosophila – such as pigment-dispersing factor (PDF) – play key roles in building dynamic neural circuits through synaptic and other signaling mechanisms.  Such circuitry enables multicellular pacemaker precision (from sloppy cellular oscillations), robustness (against incidental perturbations), plasticity (as with changes in daylength), and the capacity for multiphasic oscillatory outputs.  In mammals, entrainment of the circadian system to the light-dark cycle is via a monosynaptic retinal input to the SCN (“retino-hypothalamic tract”), involving the activity of melanopsin-expressing photoreceptive ganglion cells, which are especially sensitive to short wavelength light (blue, around 479 nm).  Light-induced neuronal depolarization in the SCN activates second-messenger signal transduction pathways and the induction of per1 and per2 to affect the phase of the molecular feedback loop.  If the circadian oscillation in the SCN is inactivated, either by physical lesion or genetic mutation, some downstream rhythms will be rendered arrhythmic (for example, resulting in continuous locomotor activity and absent pineal melatonin secretion) while others will persist but de-couple from the light-dark cycle (for example, in some but not all peripheral organs and tissues).  In Drosophila, in addition to circadian light input from the compound eye (and perhaps the ocelli), light resets the molecular loop by the rapid degradation of the clock protein TIM, mediated by the blue-light sensitive protein CRY in pacemaker neurons and other cells in the fly body (the Drosophila CRY is distinct from the mammalian CRYs that are part of the transcription-translation negative feedback loop and are not photoreceptive).

At the organismal level, the phase alignments of cell, tissue, and organ rhythms with each other and the day and night (the latter largely dependent on the SCN) is determined by the action of a panoply of coupling modes, including behavioral (such as feeding and sleeping), thermal, hormonal, autonomic, and metabolic.  Misalignments – between solar time, internal (circadian) time, sleep time, and/or social (societal) time – contribute to the symptoms of jet lag and the health risks of shiftwork and possibly of chronic or repeated stress.  Much current research is now focused on the significance and impact of circadian dysrhythmias in humans, such as mistimed food and medication intake, nighttime light pollution, aging, and vulnerability to diseases like metabolic syndrome, cancer, and neurodegeneration.