Genetics of circadian rhythms in Mammalian model organisms

The mammalian circadian system is a complex hierarchical temporal network which is organized around an ensemble of uniquely coupled cells comprising the principal circadian pacemaker in the suprachiasmatic nucleus of the hypothalamus. This central pacemaker is entrained each day by the environmental light/dark cycle and transmits synchronizing cues to cell-autonomous oscillators in tissues throughout the body. Within cells of the central pacemaker and the peripheral tissues, the underlying molecular mechanism by which oscillations in gene expression occur involves interconnected feedback loops of transcription and translation. Over the past 10 years, we have learned much regarding the genetics of this system, including how it is particularly resilient when challenged by single-gene mutations, how accessory transcriptional loops enhance the robustness of oscillations, how epigenetic mechanisms contribute to the control of circadian gene expression, and how, from coupled neuronal networks, emergent clock properties arise. Here, we will explore the genetics of the mammalian circadian system from cell-autonomous molecular oscillations, to interactions among central and peripheral oscillators and ultimately, to the daily rhythms of behavior observed in the animal.

The crosstalk between physiology and circadian clock proteins

In mammals, many physiological processes present diurnal variations, and most of these rhythms persist even in absence of environmental timing cues. These endogenous circadian rhythms are generated by intracellular timing mechanisms termed circadian clocks. In mammals, the master clock is located in the suprachiasmatic nuclei (SCN), but other brain regions and most peripheral tissues contain circadian clocks. These clocks are responsive to environmental cues, in particular light/dark and feeding/fasting cycles. In the last few years, tissue-specific knock-out and transgenic mouse models have helped to define the physiological roles of specific clocks. Recent reports indicate that the clock-physiology connection is bi-directional, and physiological cues, in particular the energetic status of the cell, can feed into the clockwork. This effect was discovered unexpectedly in molecular analyses of clock protein modifications. Beyond the positive and negative transcription/translation feedback loops of the molecular oscillator lies another level of complexity. Post-translational modifications of clock proteins are both critical for the timing of the clock feedback mechanism and to provide regulatory fine-tuning. This review summarizes recent advances in our understanding of the roles of peripheral clocks and of post-translational modifications occurring on clock proteins. These two matters are at the intersection of physiology, metabolism, and the circadian system.

Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2

PERIOD proteins are central components of the Drosophila and mammalian circadian clocks. The crystal structure of a Drosophila PERIOD (dPER) fragment comprising two PER-ARNT-SIM (PAS) domains (PAS-A and PAS-B) and two additional C-terminal α-helices (αE and αF) has revealed a homodimer mediated by intermolecular interactions of PAS-A with tryptophane 482 in PAS-B and helix αF. Here we present the crystal structure of a monomeric PAS domain fragment of dPER lacking the αF helix. Moreover, we have solved the crystal structure of a PAS domain fragment of the mouse PERIOD homologue mPER2. The mPER2 structure shows a different dimer interface than dPER, which is stabilized by interactions of the PAS-B β-sheet surface including tryptophane 419 (equivalent to Trp482_dPER). We have validated and quantitatively analysed the homodimer interactions of dPER and mPER2 by site-directed mutagenesis using analytical gel filtration, analytical ultracentrifugation, and co-immunoprecipitation experiments. Furthermore we show, by yeast-two-hybrid experiments, that the PAS-B β-sheet surface of dPER mediates interactions with TIMELESS (dTIM). Our study reveals quantitative and qualitative differences between the homodimeric PAS domain interactions of dPER and its mammalian homologue mPER2. In addition, we identify the PAS-B β-sheet surface as a versatile interaction site mediating mPER2 homodimerization in the mammalian system and dPER-dTIM heterodimer formation in the Drosophila system.

Most organisms have daily activity cycles (circadian rhythms), which are generated by circadian clocks. Circadian periodicity is produced by specific clock protein interactions and posttranslational modifications as well as changes in their cellular localization, expression, and stability. To learn more about the molecular processes underlying circadian clock operation in fruit flies and mouse, we analysed the homo- and heterodimeric interactions of the clock proteins Drosophila PERIOD (dPER) and mouse PERIOD2 (mPER2). We show that dPER and mPER2 use different interaction surfaces for homodimer formation, which are associated with different dimerization affinities. In addition, we present a structure-based biochemical analysis of the heterodimeric interaction of dPER with its partner Drosophila TIMELESS (dTIM). We identify a versatile molecular surface of the PERIOD proteins, which mediates homodimer formation of mPER2 but is used for dPER-dTIM heterodimer formation in Drosophila. Our results reveal quantitative and qualitative differences in the molecular interactions of PERIOD clock proteins in flies and mammals, allowing them to adjust to their different binding partners and regulatory functions in these different organisms.

Crystal structures and structure-based biochemical studies ofDrosophila PERIOD and mouse PERIOD2 circadian clock proteins reveal different homodimer interactions and identify a versatile molecular surface that mediates homodimerization of mouse PERIOD2 but is involved in heterodimeric interactions ofDrosophila PERIOD with TIMELESS.

The 2008 Pittendrigh/Aschoff Lecture: Peripheral Phase Coordination in the Mammalian Circadian Timing System

The mammalian timing system is composed of a bodywide web of cell-autonomous and self-sustained oscillators. A master clock in the SCN synchronizes peripheral clocks through yet poorly understood molecular signaling pathways. In this lecture I shall present some of the experimental approaches we are employing to elucidate signaling routes through which the SCN may phase entrain peripheral clocks. These attempts unveiled several candidate pathways worth pursuing in future studies, including signaling through nuclear receptors, cytoskeleton components, Ca2+, fibroblast growth factors, ubiquitin ligases, Sirtuin 1 (a redox-sensing histone deacetylase), RNA binding proteins, and body temperature.