Molecular Mechanisms in the Circadian Rhythm

Abstract

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.
close

References

Allada R, White NE, So WV, et al. (1998) A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell 93: 791–804.

Bargiello TA and Young MW (1984) Molecular genetics of a biological clock in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 81: 2142–2146.

Bargiello TA, Jackson FR and Young MW (1984) Restoration of circadian behavioural rhythms by gene transfer in Drosophila. Nature 312: 752–754.

Ceriani MF, Darlington TK, Staknis D, et al. (1999) Light‐dependent sequestration of TIMELESS by CRYTOCHROME. Science 285: 553–556.

Darlington TK, Wager‐Smith K, Ceriani MF, et al. (1998) Closing the circadian feedback loop: CLOCK‐induced transcription of its own inhibitors, period and timeless. Science 280: 1599–1603.

Dibner C, Schibler U and Albrecht U (2010) The mammalian circadian timing system: Orgainization and coordination of central and peripheral clocks. Annual Review of Physiology 72: 517–549.

Do MT and Yau KW (2010) Intrinsically photosensitive retinal ganglion cells. Physiological Reviews 90: 1547–1581.

Fang Y, Sathyanarayanan S and Sehgal A (2007) Post‐translational regulation of the Drosophila circadian clock requires protein phosphatase 1 (PP1). Genes & Development 21: 1506–1518.

Gallego M, Kang H and Virshup DM (2006) Protein phosphatase 1 regulates the stability of the circadian protein PER2. Biochemical Journal 399: 169–175.

Gekakis N, Staknis D, Nguyen HB, et al. (1998) Role of the CLOCK protein in the mammalian circadian mechanism. Science 280: 1564–1969.

Green DJ and Gillette R (1982) Circadian rhythm of firing rate recorded from single cells in the rat suprachiasmatic brain slice. Brain Research 245: 198–200.

Grima B, Lamouroux A, Chelot E, et al. (2002) The F‐box protein slimb controls the levels of clock proteins period and timeless. Nature 420: 178–182.

Golombek DA and Rosenstein RE (2010) Physiology of circadian entrainment. Physiological Reviews 90: 1063–1102.

Groos GA and Hendriks J (1982) Circadian rhythms in electrical discharge of rat suprachiasmatic neurones recorded in vitro. Neurosci Letters 34: 283–288.

Hamada T, Antle MC and Silver R (2004) The role of Period1 in non‐photic resetting of the hamster circadian pacemaker in the suprachiasmatic nucleus. Neurosci Letters 362: 87–90.

Hardin PE (2011) Molecular genetic analysis of circadian timekeeping in Drosophila. Advances in Genetics 74: 141–173.

Hastings MH, Duffield GE, Ebling FJP, et al. (1997) Non‐photic signalling in the suprachiasmatic nucleus. Biology of the Cell 89: 495–503.

Hirano A, Yumimoto K, Tsunematsu R, et al. (2013) FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. Cell 152: 1106–1118.

Huang RC (2018) The discoveries of molecular mechanisms for the circadian rhythm: The 2017 Nobel Prize in Physiology or Medicine. Biomedical Journal 41: 5–8.

Inouye SIT and Kawamura H (1979) Persistence of circadian rhythmicity in a mammalian hypothalamic ‘island’ containing the suprachiasmatic nucleus. Proceedings of the National Academy of Sciences of the United States of America 76: 5962–5966.

Kalsbeek A, Palm IF, La Fleur SE, et al. (2006) SCN outputs and the hypothalamic balance of life. Journal of Biological Rhythms 21: 458–469.

Kloss B, Price JL, Saez L, et al. (1998) The Drosophila clock gene double‐time encodes a protein closely related to human casein kinase Iϵ. Cell 94: 97–107.

Konopka RJ and Benzer S (1971) Clock mutants of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America 68: 2112–2116.

Kume K, Zylka MJ, Sriram S, et al. (1999) mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98: 193–205.

Leak RK and Moore RY (2001) Topographic organization of suprachiasmatic nucleus projection neurons. Journal of Comparative Neurology 433: 312–334.

Lee C, Etchegaray JP, Cagampang FR, et al. (2001) Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107: 855–867.

Lear BC and Allada R (January 2012) Circadian rhythms. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0000040.pub2.

Lin JM, Kilman VL, Keegan K, et al. (2002) A role for casein kinase 2alpha in the Drosophila circadian clock. Nature 420: 816–820.

Lowrey PL, Shimomura K, Antoch MP, et al. (2000) Positional syntenic cloning and functional characterization of the mammalian circadian mutation tau. Science 288: 483–492.

Lyer R, Wang TA and Gillette MU (2014) Circadian gating of neuronal functionality: a basis for iterative metaplasticity. Frontiers in Systems Neuroscience 8: 164.

Martinek S, Inonog S, Manoukian AS, et al. (2001) A Role for the segment polarity gene shaggy/GSK‐3 in the Drosophila circadian clock. Cell 105: 769–779.

Maywood ES, Chesham JE, O'Brien JA, et al. (2011) A diversity of paracrine signals sustains molecular circadian cycling in suprachiasmatic nucleus circuits. Proceedings of the National Academy of Sciences of the United States of America 108: 14306–14311.

Moore RY and Eichler VB (1972) Loss of a circadian adrenal corticosterone rhythm following suprachiasmatic lesions in the rat. Brain Research 42: 201–206.

Myers MP, Wager‐Smith K, Wesley CS, et al. (1995) Positional cloning and sequence analysis of the Drosophila clock gene timeless. Science 270: 805–808.

Noguchi T and Watanabe K (2005) Tetrodotoxin resets the clock. European Journal of Neuroscience 21: 3361–3367.

Partch CL, Shields KF, Thompson CL, et al. (2006) Posttranslational regulation of the mammalian circadian clock by cryptochrome and protein phosphatase 5. Proceedings of the National Academy of Sciences of the United States of America 103: 10467–10472.

Price JL, Blau J, Rothenfluh A, et al. (1998) double‐time is a novel Drosophila clock gene that regulates PERIOD protein accumulation. Cell 94: 83–95.

Ralph MR, Foster RG, Davis FC, et al. (1990) Transplanted suprachiasmatic nucleus determines circadian period. Science 247: 975–978.

Reischl S, Vanselow K, Westermark PO, et al. (2007) Beta‐TrCP1‐mediated degradation of PERIOD2 is essential for circadian dynamics. Journal of Biological Rhythms 22: 375–386.

Reddy P, Zehring WA, Wheeler DA, et al. (1984) Molecular analysis of the period locus in Drosophila melanogaster and identification of a transcript involved in biological rhythms. Cell 38: 701–710.

Rutila JE, Suri V, Le M, et al. (1998) CYCLE is a second bHLH‐PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless. Cell 93: 805–814.

Sathyanarayanan S, Zheng X, Xiao R, et al. (2004) Posttranslational regulation of Drosophila PERIOD protein by protein phosphatase 2A. Cell 116: 603–615.

Schwartz WJ and Gainer H (1977) Suprachiasmatic nucleus: use of 14C‐labeled deoxyglucose uptake as a functional marker. Science 197: 1089–1091.

Sehgal A, Price J, Man B and Young M (1994) Loss of circadian behavioral rhythms and per RNA oscillations in the Drosophila mutant timeless. Science 263: 1603–1606.

Shearman LP, Sriram S, Weaver DR, et al. (2000) Interacting molecular loops in the mammalian circadian clock. Science 288: 1013–1019.

Shibata S, Oomura Y, Kita H, et al. (1982) Circadian rhythmic changes of neuronal activity in the suprachiasmatic nucleus of the rat hypothalamic slice. Brain Reserach 247: 154–158.

Siepka SM, Yoo SH, Park J, et al. (2007) Circadian mutant Overtime reveals F‐box protein FBXL3 regulation of cryptochrome and period gene expression. Cell 129: 1011–1023.

Silver R, LeSauter J, Tresco PA, et al. (1996) A diffusible coupling signal from the transplanted suprachiasmatic nucleus controlling circadian locomotor rhythms. Nature 382: 810–813.

Stephan FK and Zucker I (1972) Circadian rhythms in drinking and locomotor activity of rats are eliminated by hypothalamic lesions. Proceedings of National Academy of Science USA 69: 1583–1586.

Toh KL, Jones CR, He Y, et al. (2001) An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome. Science 291: 1040–1043.

Ueda HR, Chen W, Adachi A, et al. (2002) A transcription factor response element for gene expression during circadian night. Nature 418: 534–539.

Weaver DR (2016) Introduction to circadian rhythms and mechanisms of circadian oscillations. In: Gumz LM (ed.) Circadian Clocks: Role in Health and Disease, pp 1–55. Springer New York: New York.

Welsh DK, Logothetis DE, Meister M, et al. (1995) Individual neurons dissociated from rat suprachiasmatic nucleus express independently phased circadian firing rhythms. Neuron 14: 697–706.

Yamakawa GR, Basu P, Cortese F, et al. (2016) The cholinergic forebrain arousal system acts directly on the circadian pacemaker. Proceedings of the National Academy of Sciences of the United States of America 113: 13498–13503.

Yan L, Karatsoreos I, Lesauter J, et al. (2007) Exploring spatiotemporal organization of SCN circuits. Cold Spring Harbor Symposium on Quantitative Biology 72: 527–541.

Xu Y, Padiath QS, Shapiro RE, et al. (2005) Functional consequences of a CKIdelta mutation causing familial advanced sleep phase syndrome. Nature 434: 640–644.

Zehring WA, Wheeler DA, Reddy P, et al. (1984) P‐element transformation with period locus DNA restores rhythmicity to mutant, arrhythmic Drosophila melanogaster. Cell 39: 369–376.

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.

Ibäñez C (2017) The 2017 Nobel prize in physiology or medicine ‐ advanced information: discoveries of molecular mechanisms controlling the circadian rhythm. Nobelprize.org. Nobel Media AB 2020. https://www.nobelprize.org/prizes/medicine/2017/advanced‐information/ (accessed 14 January 2020).

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.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

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