Reactome | Circadian clock

Circadian clock

Stable Identifier

R-HSA-9909396

Type

Pathway

Species

Homo sapiens

ReviewStatus

5/5

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Circadian clock (Homo sapiens)

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At the center of the mammalian circadian clock is a negative transcription-translation feedback loop (TTFL) (reviewed in Albrecht 2012, Gustafson and Partch 2015, Cox and Takahashi 2019). In the morning, the BMAL1:CLOCK/NPAS2 heterodimer activates transcription of CRY1, CRY2, PER1, PER2, PER3 and many other circadian-regulated genes. Levels of PER and CRY proteins rise during the day and inhibit their own expression and the expression of other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening (inferred from mouse homologs in Cao et al. 2021). During the night, CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning (reviewed in Abdalla et al. 2022).
A secondary loop also exists in the mammalian clock: transcription of the BMAL1, CLOCK, and NPAS2 genes is activated by Retinoid-related orphan receptor-alpha (RORA) and RORC (ROR-gamma) paralogs and repressed by NR1D1 (REV-ERBA), all of which are targets of regulation by BMAL1:CLOCK/NPAS2 and all of which compete for the same ROR regulated elements (RREs, ROREs) in the BMAL1 and CLOCK promoters and in the promoters of many other genes (reviewed in Duez and Staels 2008). This mutual control forms a reinforcing loop of the circadian clock (reviewed in Kim et al. 2022).
BMAL1 can form heterodimers with either CLOCK or NPAS2, which appear to act redundantly but may show different tissue specificity (inferred from mouse homologs in Landgraf et al. 2016, Reick et al. 2001, Peng et al. 2021). After translation in the cytosol, BMAL1 and CLOCK (and probably NPAS2) are phosphorylated, heterodimerize and enter the nucleus (reviewed in Lee et al. 2001, Hirano et al. 2016). The phosphorylated BMAL1:CLOCK heterodimers bind E-box elements (consensus CANNTG) in the promoters of target genes (inferred from mouse homologs in Gekakis et al. 1998) and recruit coactivators to enhance transcription of the target genes. Genes activated by BMAL1:CLOCK are expressed diurnally. DBP is among the genes activated by phosphorylated BMAL1:CLOCK/NPAS2 and binds D-box elements in the promoters of many circadian-regulated genes to increase the amplitude of rhythmic expression (inferred from mouse homologs in Yamaguchi et al. 2000).
The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are also among those activated by BMAL1:CLOCK and BMAL1:NPAS2 (reviewed in Cox and Takahashi 2019). PER gene and CRY gene mRNAs accumulate during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by kinases CSNK1D or CSNK1E, which phosphorylate PER and CRY proteins (reviewed in Narasimamurthy and Virshup 2021). Phosphorylation of the PER:CRY:kinase complex is required for its translocation into the nucleus. CDK5 phosphorylates PER2 at serine residue 396 (serine-394 of the mouse orthologue) in a diurnal fashion. This phosphorylation facilitates interaction with CRY1 and nuclear entry of the PER2-CRY1 complex (Brenna et al. 2019). Within the nucleus the phosphorylated PER:CRY:kinase complexes bind BMAL1:CLOCK heterodimers, inhibiting their transactivation activity and causing dissociation of BMAL1:CLOCK from DNA (inferred from mouse homologs Cao et al. 2021). This reduces transcription of the target genes of BMAL1:CLOCK during the afternoon and evening.
During the night PER:CRY complexes are polyubiquitinated and degraded by the 26S proteasome, allowing the cycle to begin again (reviewed in Abdalla et al. 2022). PER:CRY complexes traffic out of the nucleus into the cytosol due to the nuclear export signal of PER proteins (inferred from mouse homologs in Vielhaber et al. 2001). In the cytosol, phosphorylated PER proteins are bound by Beta-TrCP1, a F-box component of a cytosolic SCF E3 ubiquitin ligase complex that polyubiquitinylates the PER proteins (Shirogane et al. 2005). Also in the cytosol, CRY proteins are bound by FBXL21, another F-box component of a SCF E3 ubiquitin ligase complex that polyubiquitinylates the CRY proteins (inferred from mouse homologs in Hirano et al. 2013, Yoo et al. 2013). In the nucleoplasm, CRY proteins are bound by FBXL3, a F-box component of a SCF E3 ubiquitin ligase complex that polyubiquitinylates CRY proteins (inferred from mouse homologs in Busino et al. 2007). FBXL21 appears to antagonize FBXL3, though the mechanism is not clear.
The core circadian clock both regulates metabolism and receives inputs from metabolism (reviewed in Bass and Takahashi 2010, Laothamatas et al. 2023). BMAL1:CLOCK,NPAS2 transcriptionally activate thousands of genes, including PPARA, which regulates lipid metabolism (inferred from mouse homologs in Oishi et al. 2005), and NAMPT (inferred from mouse homologs in Nakahata et al. 2009), which is involved in NAD+ metabolism. Retinoid-related orphan receptors (RORs) and NR1D1 also regulate numerous genes, including CPT1A (inferred from mouse homologs in Lau et al. 2004) involved in fatty acid catabolism and SREBF1 (inferred from mouse homologs in Lau et al. 2008) involved in cholesterol biosynthesis. Metabolic inputs include NAD+, which is a substrate in the deacetylation of BMAL1 by SIRT1 (inferred from mouse homologs in Ramsey et al. 2009), and AMP, which regulates the phosphorylation of CRY1 by AMPK, causing enhanced degradation of CRY1 (inferred from mouse homologs in Lamia et al. 2009). Additional metabolic inputs are provided through CLOCK acetylase activity, GSK3beta kinase activity, and casein kinase II (CK2) kinase activity (reviewed in Laothamatas et al. 2023).
The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, gene transcription (reviewed in Albrecht et al. 2012), and cell division (reviewed in Farshadi et al. 2020). The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake (reviewed in Bechtel 2024). The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients.
Relationships between the circadian clock and metabolism, disease, and drug efficacy are extensive and are the subject of active investigation (reviewed in Cederroth et al. 2019, Battaglin et al. 2021, Laothamatas et al. 2023, Zhuang et al. 2024).
Mice are often used as model organisms for studying the mammalian circadian clock, however some differences exist between mouse clocks and human clocks. For example, peak expression of core circadian genes such as CRY1, CRY2, PER1, PER2, PER3, and NR1D1 occurs about 6 hours earlier in humans than in mice (Li et al. 2013).

Literature References

PubMed ID	Title	Journal	Year
19299583	Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis Ramsey, KM, Yoshino, J, Brace, CS, Abrassart, D, Kobayashi, Y, Marcheva, B, Hong, HK, Chong, JL, Buhr, ED, Lee, C, Takahashi, JS, Imai, S, Bass, J	Science	2009
36415204	Circadian stabilization loop: the regulatory hub and therapeutic target promoting circadian resilience and physiological health Kim, E, Yoo, SH, Chen, Z	F1000Res	2022
39519022	Interplay Between the Circadian Clock and Sirtuins Zhuang, Y, Zhang, Y, Liu, C, Zhong, Y	Int J Mol Sci	2024
27922612	The intricate dance of post-translational modifications in the rhythm of life Hirano, A, Fu, YH, Ptácek, LJ	Nat Struct Mol Biol	2016
26895328	NPAS2 Compensates for Loss of CLOCK in Peripheral Circadian Oscillators Landgraf, D, Wang, LL, Diemer, T, Welsh, DK	PLoS Genet	2016
36142478	Death of a Protein: The Role of E3 Ubiquitin Ligases in Circadian Rhythms of Mice and Flies Abdalla, OHMH, Mascarenhas, B, Cheng, HM	Int J Mol Sci	2022
11591712	Nuclear export of mammalian PERIOD proteins Vielhaber, EL, Duricka, D, Ullman, KS, Virshup, DM	J Biol Chem	2001
22542179	Timing to perfection: the biology of central and peripheral circadian clocks Albrecht, U	Neuron	2012
25303119	Emerging models for the molecular basis of mammalian circadian timing Gustafson, CL, Partch, CL	Biochemistry	2015
19833968	AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation Lamia, KA, Sachdeva, UM, DiTacchio, L, Williams, EC, Alvarez, JG, Egan, DF, Vasquez, DS, Juguilon, H, Panda, S, Shaw, RJ, Thompson, CB, Evans, RM	Science	2009
9616112	Role of the CLOCK protein in the mammalian circadian mechanism Gekakis, N, Staknis, D, Nguyen, HB, Davis, FC, Wilsbacher, LD, King, DP, Takahashi, JS, Weitz, CJ	Science	1998
34415290	Roles of NPAS2 in circadian rhythm and disease Peng, LU, Bai, G, Pang, Y	Acta Biochim Biophys Sin (Shanghai)	2021
11441147	NPAS2: an analog of clock operative in the mammalian forebrain Reick, M, Garcia, JA, Dudley, C, McKnight, SL	Science	2001
23452856	FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes Hirano, A, Yumimoto, K, Tsunematsu, R, Matsumoto, M, Oyama, M, Kozuka-Hata, H, Nakagawa, T, Lanjakornsiripan, D, Nakayama, KI, Fukada, Y	Cell	2013
21127246	Circadian integration of metabolism and energetics Bass, J, Takahashi, JS	Science	2010
15500444	CLOCK is involved in the circadian transactivation of peroxisome-proliferator-activated receptor alpha (PPARalpha) in mice Oishi, K, Shirai, H, Ishida, N	Biochem J	2005
31390550	Medicine in the Fourth Dimension Cederroth, CR, Albrecht, U, Bass, J, Brown, SA, Dyhrfjeld-Johnsen, J, Gachon, F, Green, CB, Hastings, MH, Helfrich-Förster, C, Hogenesch, JB, Lévi, F, Loudon, A, Lundkvist, GB, Meijer, JH, Rosbash, M, Takahashi, JS, Young, M, Canlon, B	Cell Metab	2019
33846572	Clocking cancer: the circadian clock as a target in cancer therapy Battaglin, F, Chan, P, Pan, Y, Soni, S, Qu, M, Spiller, ER, Castanon, S, Roussos Torres, ET, Mumenthaler, SM, Kay, SA, Lenz, HJ	Oncogene	2021
17463251	SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of cryptochrome proteins Busino, L, Bassermann, F, Maiolica, A, Lee, C, Nolan, PM, Godinho, SI, Draetta, GF, Pagano, M	Science	2007
19286518	Circadian control of the NAD+ salvage pathway by CLOCK-SIRT1 Nakahata, Y, Sahar, S, Astarita, G, Kaluzova, M, Sassone-Corsi, P	Science	2009
33443219	Molecular mechanism of the repressive phase of the mammalian circadian clock Cao, X, Yang, Y, Selby, CP, Liu, Z, Sancar, A	Proc Natl Acad Sci U S A	2021
37708890	Metabolic and chemical architecture of the mammalian circadian clock Laothamatas, I, Rasmussen, ES, Green, CB, Takahashi, JS	Cell Chem Biol	2023
15917222	SCFbeta-TRCP controls clock-dependent transcription via casein kinase 1-dependent degradation of the mammalian period-1 (Per1) protein Shirogane, T, Jin, J, Ang, XL, Harper, JW	J Biol Chem	2005
18441015	The orphan nuclear receptor, RORalpha, regulates gene expression that controls lipid metabolism: staggerer (SG/SG) mice are resistant to diet-induced obesity Lau, P, Fitzsimmons, RL, Raichur, S, Wang, SC, Lechtken, A, Muscat, GE	J Biol Chem	2008
31557726	Circadian clock genes and the transcriptional architecture of the clock mechanism Cox, KH, Takahashi, JS	J Mol Endocrinol	2019
10848603	Role of DBP in the circadian oscillatory mechanism Yamaguchi, S, Mitsui, S, Yan, L, Yagita, K, Miyake, S, Okamura, H	Mol Cell Biol	2000
31687929	Cyclin-dependent kinase 5 (CDK5) regulates the circadian clock Brenna, A, Olejniczak, I, Chavan, R, Ripperger, JA, Langmesser, S, Cameroni, E, Hu, Z, De Virgilio, C, Dengjel, J, Albrecht, U	Elife	2019
23452855	Competing E3 ubiquitin ligases govern circadian periodicity by degradation of CRY in nucleus and cytoplasm Yoo, SH, Mohawk, JA, Siepka, SM, Shan, Y, Huh, SK, Hong, HK, Kornblum, I, Kumar, V, Koike, N, Xu, M, Nussbaum, J, Liu, X, Chen, Z, Chen, ZJ, Green, CB, Takahashi, JS	Cell	2013
11779462	Posttranslational mechanisms regulate the mammalian circadian clock Lee, C, Etchegaray, JP, Cagampang, FR, Loudon, AS, Reppert, SM	Cell	2001
18537094	The nuclear receptors Rev-erbs and RORs integrate circadian rhythms and metabolism Duez, H, Staels, B	Diab Vasc Dis Res	2008
23671070	Circadian patterns of gene expression in the human brain and disruption in major depressive disorder Li, JZ, Bunney, BG, Meng, F, Hagenauer, MH, Walsh, DM, Vawter, MP, Evans, SJ, Choudary, PV, Cartagena, P, Barchas, JD, Schatzberg, AF, Jones, EG, Myers, RM, Watson, SJ, Akil, H, Bunney, WE	Proc Natl Acad Sci U S A	2013