Molecular Mechanisms in the Circadian Rhythm


Circadian clocks evolved to allow organisms to anticipate and adjust their behaviours to the daily change in the external environment. The molecular mechanisms for generating the autonomous oscillation in the circadian clock with a period of ∼24 h, which is named as the transcriptional translational feedback loop (TTFL) model, have been established in the fruit fly Drosophila and are remarkably similar in mammals. The essence of the TTFL is a negative feedback loop with delay: transcription of the clock genes is inhibited by their own gene products (clock proteins). In mammals, circadian rhythms are orchestrated by the central circadian clock in the hypothalamic suprachiasmatic nucleus (SCN), which receives circadian light inputs from the retina. Light, as well as nonphotic inputs, can alter transcription of clock genes in the SCN and entrain the SCN to organise animal physiology and behaviours to be in sync with the environment.

Key Concepts

  • Circadian clocks allow organisms to anticipate the daily changing environment.
  • The free‐running period of circadian clocks in constant conditions is close to but not exactly 24 h.
  • The first clock gene was identified in 1984 by the three 2017 Nobel Laureates for Physiology or Medicine.
  • The autonomous oscillation in circadian clocks arises from ∼24 h oscillation of clock genes and clock proteins.
  • In circadian clocks transcription of the clock genes is inhibited by their own gene products (clock proteins).
  • The transcriptional translational feedback loop (TTFL) model is the dominant theory explaining the molecular mechanisms for the circadian clocks.
  • The molecular mechanisms for circadian clocks are very similar in fly and mammals.
  • The hypothalamic suprachiasmatic nucleus (SCN) is the central circadian clock in mammals.
  • Light at night alters expression of clock genes in the SCN and entrains the SCN to synchronise animal behaviours.
  • Circadian disruption in humans is associated with many diseases such as cardiovascular diseases and metabolic disorders.

Keywords: circadian; clock genes; Drosophila; entrainment; oscillator; pacemaker; rhythm; suprachiasmatic nucleus

Figure 1. Schematic illustration of a negative feedback with delay.
Figure 2. The transcriptional translational feedback loop (TTFL) clockwork mechanism in the fly Drosophila. The transcription factors CLK and CYC interact and bind to an E‐box in the promoter region of Per and Tim clock genes, leading to their transcription. In turn, the delayed formation of PER/TIM complex and its subsequent translocation to the nucleus then inhibit CLK/CYC‐induced gene transcription of Per and Tim mRNA. Protein kinases (DBT, CK2 and SGG) and phosphatases play a critical role in the delayed accumulation of PER/TIM by regulating their stability and localisation, thus setting the speed of the clock. Light activates CRY to bind TIM, which is then targeted for degradation by JET, and without TIM protection, PER is phosphorylated by DTB and then targeted for degradation by SLIMB. The degradation of PER/TIM allows CLK/CYC to start the cycle again. Two additional interlocked feedback loops involving CLK/CYC target genes vrille (vri) and Par domain protein 1 (Pdp1) as well as clockwork orange (cwo) that encode proteins to further regulate the core oscillator. Clock‐controlled genes (CCGs) regulate the expression of genes responsible for clock outputs such as sleep‐wake cycle, locomotor activity and pupal eclosion.
Figure 3. The circadian feedback loop in mammals. The transcription factors CLOCK and BMAL1 interact and bind to an E‐box in the promoter region of Per1, Per2, Cry1 and Cry2 clock genes, leading to their transcription. In turn, the delayed formation of PER/CRY complex and its subsequent translocation to the nucleus then inhibit CLOCK/BMAL1‐induced gene transcription of Per1, Per2, Cry1 and Cry2 mRNA. Protein kinases (CK1ϵ/δ and AMPK) and phosphatases set the speed of the clock by regulating the stability and localisation of PER and CRY proteins. PER proteins are phosphorylated by CK1ϵ/δ and targeted for degradation by β‐TrCP, and CRY proteins are phosphorylated by AMPK and targeted for degradation by FBXL21. The degradation of PER/CRY allows CLOCK/BMAL1 to start the cycle again. An additional interlocked feedback loop involves the CLOCK/BMAL1 target gene products REV‐ERBα and REV‐ERBβ, which suppress Bmal1 transcription by binding to the RORE region, as well as RORα and RORγ, which promotes Bmal1 transcription, adding additional layers of control. Broken‐lined box: Light activates a series of signalling pathways leading to an increase in intracellular [Ca2+] and/or [cAMP] and, in turn, the activated protein kinase phosphorylates transcription factor CREB, which then binds to CRE in the promoters of both Per1 and Per2 genes, leading to transcription of Per1 and Per2. Clock‐controlled genes (CCGs) regulate the expression of genes responsible for clock outputs such as sleep‐wake cycle, body temperature and blood pressure fluctuations, as well as metabolism.
Figure 4. SCN subdivisions, main inputs and outputs. The left SCN shows the core and shell subdivisions and the right, the selective distribution of arginine vasopressin (AVP) in the shell and gastrin‐releasing peptide (GRP) as well as vasoactive intestinal peptide (VIP) in the core. Photic and nonphotic cues converge to the core subdivision. The core (or ventrolateral) SCN receives direct photic input from the retina via the retinohypothalamic tract (RHT) which contains glutamate (Glu) as well as pituitary adenylate cyclase‐activating peptide (PACAP) as neurotransmitters, and indirect photic input from the intergeniculate leaflet (IGL) via the geniculohypothalamic tract (GHT) which contains neuropeptide Y (NPY) and γ‐aminobutyric acid (GABA) as neurotransmitters. Nonphotic cues are conveyed via the serotoninergic (5‐HT) projection from the median raphe nucleus (MRN) and the GABAergic and NPY‐ergic projections from the IGL. The SCN controls its targets by sending neural and diffusible humoral outputs.


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Further Reading

Foster RG and Kreitzman L (2005) Rhythms of Life. The Biological Clocks that Control the Daily Lives of Every Living Thing. Yale University Press: New Haven, CT.

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Peschel N and Helfrich‐Forster C (2011) Setting the clock –by nature: circadian rhythm in the fruitfly Drosophila melanogaster. FEBS Letters 585: 1435–1442.

Takahashi JS (2017) Transcriptional architecture of the mammalian circadian clock. Nature Reviews Genetics 18: 164–179.

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Huang, Rong‐Chi(Aug 2020) Molecular Mechanisms in the Circadian Rhythm. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0028836]