The circadian coordination of cell biology

Abstract

Circadian clocks are cell-autonomous timing mechanisms that organize cell functions in a 24-h periodicity. In mammals, the main circadian oscillator consists of transcription-translation feedback loops composed of transcriptional regulators, enzymes, and scaffolds that generate and sustain daily oscillations of their own transcript and protein levels. The clock components and their targets impart rhythmic functions to many gene products through transcriptional, posttranscriptional, translational, and posttranslational mechanisms. This, in turn, temporally coordinates many signaling pathways, metabolic activity, organelles' structure and functions, as well as the cell cycle and the tissue-specific functions of differentiated cells. When the functions of these circadian oscillators are disrupted by age, environment, or genetic mutation, the temporal coordination of cellular functions is lost, reducing organismal health and fitness.

Figure 1.

Molecular oscillators that generate circadian rhythms in multiple organisms. Circadian rhythms are generated by autonomous molecular oscillators that cycle between different activation states within a period of ∼24 h. (A) In cyanobacteria, the KaiABC complex, made of KaiA, KaiB, and a hexamer of KaiC (green), constitute the molecular oscillator. The complex transitions between a phosphorylated and unphosphorylated state within a period of 24 h. (B) In fungi, plants, and animals, the circadian oscillator is based on a TTFL. In mammals, the TTFL involves the activation of Per, Cry, Rev-Erb, and Ror transcription by the CLOCK/BMAL1 heterodimer. Upon translation, PER and CRY proteins form a complex that is imported in the nucleus and suppresses CLOCK/BMAL transcriptional activity. ROR and REV-ERB proteins can activate or repress the transcription of BMAL1, respectively. ROR/REV-ERB also act on the transcription of other clock components and refine their phase of expression. The alternating waves of activation and repression, coupled with the short t_1/2 of their respective mRNA and proteins, generate circadian oscillations of clock components. These circadian transcriptional regulators also act on other genes to produce transcriptional oscillation. (C) In bacteria, archaea, and eukaryotes, antioxidant enzymes called PRX cycle between the oxidized (S-S disulfide bond) and reduced (SH thiol bond) state; this cycle can function as a circadian oscillator (see main text for details). CCG, clock-controlled gene.

Figure 2.

Many steps of gene expression have a circadian rhythm of activity. “Omics” technologies, primarily in mouse hepatocytes, show that circadian rhythms are involved in almost all of the steps of gene expression, from transcription to posttranslational modifications of proteins. Between 3 and 16% of the transcriptome displays circadian rhythms. Several mechanisms have been involved in this regulation. The recruitment of clock transcription factors (TFs) associated with tissue-specific transcription factors is circadian. As a result, the activity of the RNA polymerase II (RNA Pol II) is circadian. The architecture of the chromatin as well as histone modifications also show circadian rhythms. The sirtuin family of deacetylases is involved in this regulation. Even in absence of rhythmic transcription, some mRNA oscillate daily owing to general circadian rhythms in mRNA processing. Splicing factor expression and splicing activity varies with the time of day. PolyA tail editing (as by nocturnin) or binding to RBPs affecting mRNA stability as well as modifications by noncoding RNAs also are circadian. Translation also peaks at a certain time of the day. In hepatocytes, this happens in sync with feeding, when the cellular energy level is high. Cyclical changes in both the activation of the translation initiation complex and biogenesis of ribosome contributes to circadian translation. Finally, at the proteome level, posttranslational modifications like phosphorylation (P), poly-ADP-ribosylation (R), and glucose-N-acetylation (O-GlcNAc) oscillate daily. In hepatocytes, they are tuned to cellular energetics because the donors for these posttranslational modifications are directly affected by metabolic activity. asRNA, antisense RNA; lincRNA, long intergenic noncoding RNA.

Figure 3.

Circadian oscillations in intracellular organelle’s structure and function. Intracellular organelles play critical cellular functions. Recently, their structure and function have been shown to be time-of-day dependent. In the nucleus (blue), the NE protein Man1 binds to Bmal1 promoter, and disruption of NE proteins affects CLOCK oscillations. DNA damage responses (NER and double-strand breaks [DSBs]) also show circadian rhythms because of the circadian oscillations in the level of xeroderma pigmentosum A (XPA) and the interaction of ataxia telangiectasia mutated (ATM) with PER1. In the mitochondria (green), mitochondria biogenesis is circadian owing to the reciprocal interaction between Pgc1α and Bmal1. Furthermore, Bmal1 controls the expression of Fis1, which plays a major role in mitochondrial dynamics (fission and fusion). Oxidative and hypoxia stress responses have a circadian component. Reciprocally, hypoxia affects the clock via hypoxia-inducible factor 1α (HIF1α)–mediated transcriptional control of Per1. The circadian clock is required for oscillation of mitochondrial metabolic activity, in particular FAO. CLOCK/BMAL1 entrains cyclical mitochondrial function and gene expression. Furthermore, they control the expression of nicotinamide phosphoribosyltransferase (Nampt), which drives a circadian rhythm in the level of NAD⁺. Sirt3 activity depends on the level of the cofactor NAD⁺. Because they are targets of Sirt3, the activity of the FAO enzymes long-chain acyl coenzyme A dehydrogenase (LCAD) and electron-transferring flavoprotein (ETF) oscillates. Additional mechanisms likely contribute as well. In the lysosomes (purple), upon nutrient deprivation, the kinase AMPK activates the ULK1 complex, which induces autophagy to recycle cellular energy. AMPK also controls the circadian clock by phosphorylating CRY1. The clock also drives rhythmic expression of CCAAT enhancer–binding protein β (C/EBPβ), a master regulator of transcriptional activation of autophagy. In the ER (red), the expression of components of the secretory pathway is circadian. In hepatocytes, this happens in sync with feeding, when liver exocrine and endocrine functions are at a maximum. The activity of ER-resident PRX, which is essential for protein folding and maintaining the redox state in the ER, also is circadian. The strength of UPR activation in the ER is time-of-day dependent. Clock-mediated transcription of ATF4 and the circadian oscillation in Xbp1 pre-mRNA splicing are contributing mechanisms. Reciprocally, the UPR modulates the clock via feedback from IRE1-mediated splicing of Per1 mRNA and ATF4-driven transcription of Per2.