Molecular bases for circadian clocks

How plants tell the time

The components of the circadian system that have recently been discovered in plants share some characteristics with those from cyanobacterial, fungal and animal circadian clocks. Light input signals to the clock are contributed by multiple photoreceptors: some of these have now been shown to function specifically in response to light of defined wavelength and fluence rate. New reports of clock-controlled processes and genes are highlighting the importance of time management for plant development.

Transplanted Drosophila excretory tubules maintain circadian clock cycling out of phase with the host

Circadian rhythms in behaviors and physiological processes are driven by conserved molecular mechanisms involving the rhythmic expression of clock genes in the brains of animals [1]. The persistence of similar molecular rhythms in peripheral tissues in vitro [2] [3] suggests that these tissues contain self-sustained circadian clocks that may be linked to rhythmic physiological functions. It is not known how brain and peripheral clocks are organized into a synchronized timing system; however, it has been assumed that peripheral clocks submit to a master clock in the brain. To address this matter we examined the expression of two clock genes, period (per) and timeless (tim), in host and transplanted abdominal organs of Drosophila. We found that excretory organs in tissue culture display free-running, light-sensitive oscillations in per and tim gene activity indicating that they house self-sustained circadian clocks. To test for humoral factors, we monitored cycling of the TIM protein in excretory tubules transplanted into host flies entrained to an opposite light-dark cycle. We show that the clock protein in the donor tubules cycled out of phase with that in the host tubules, indicating that different organs may cycle independently, despite sharing the same hormonal milieu. We suggest that one way to achieve circadian coordination of physiological sub-systems in higher animals may be through the direct entrainment of light-sensitive clocks by environmental signals.

A synthetic oscillatory network of transcriptional regulators

Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks.

Distribution and circadian expression of dbp in SCN and extra-SCN areas in the mouse brain

The expression of dbp, a putative clock-controlled transcription factor, was investigated in the mouse brain by in situ hybridization using antisense cRNA probe. Positive dbp mRNA signals were detected in various parts of the brain, with the highest expression in the suprachiasmatic nucleus (SCN). The circadian expression profile was investigated in SCN and extra-SCN areas. In the SCN, dbp mRNA signals showed a peak at early daytime (ZT/CT4) and a trough at early nighttime (ZT/CT16) in both light-dark and constant dark conditions. In the cerebral cortex and the caudate-putamen, dbp mRNA was also expressed in a circadian manner, but the phase of dbp mRNA expression in these structures showed a 4-8 hr delay compared to that in the SCN. These findings indicate that the circadian expression profile of dbp in the extra-SCN brain areas is different from that in the SCN.

Forskolin induces circadian gene expression of rPer1, rPer2 and dbp in mammalian rat-1 fibroblasts

Mammalian culture cells have the potential for periodicity, since high concentrations of serum can elicit the circadian expression of clock genes in rat-1 fibroblasts. However, the mechanism by which serum affects circadian gene expression remains unclear. In the present study, we incubated rat-1 cells with forskolin and successfully induced the rhythmic expression of Per1, Per2 and dbp. In the initial step of the circadian gene expression, a marked transient induction of Per1 was observed accompanied with CREB phosphorylation. Thus the present study strongly suggests that CREB activation through the cAMP/PKA pathway is involved in the generation of circadian rhythm in rat-1 cells

Circadian rhythms in Neurospora crassa: lipid deficiencies restore robust rhythmicity to null frequency and white-collar mutants

The conidiation rhythm in the fungus Neurospora crassa is a model system for investigating the genetics of circadian clocks. Null mutants at the frq (frequency) locus (frq(9) and frq(10)) make no functional frq gene products and are arrhythmic under standard conditions. The white-collar strains (wc-1 and wc-2) are insensitive to most effects of light, and are also arrhythmic. All three genes are proposed to be central components of the circadian oscillator. We have been investigating two mutants, cel (chain-elongation) and chol-1 (choline-requirer), which are defective in lipid synthesis and affect the period and temperature compensation of the rhythm. We have constructed the double mutant strains chol-1 frq(9), chol-1 frq(10), chol-1 wc-1, chol-1 wc-2, cel frq(9), cel frq(10), and cel wc-2. We find that these double mutant strains are robustly rhythmic when assayed under lipid-deficient conditions, indicating that free-running rhythmicity does not require the frq, wc-1, or wc-2 gene products. The rhythms in the double mutant strains are similar to the cel and chol-1 parents, except that they are less sensitive to light. This suggests that the frq, wc-1, and wc-2 gene products may be components of a pathway that normally supplies input to a core oscillator to transduce light signals and sustain rhythmicity. This pathway can be bypassed when lipid metabolism is altered.

Phosphorylation of the Neurospora clock protein FREQUENCY determines its degradation rate and strongly influences the period length of the circadian clock

Under free running conditions, FREQUENCY (FRQ) protein, a central component of the Neurospora circadian clock, is progressively phosphorylated, becoming highly phosphorylated before its degradation late in the circadian day. To understand the biological function of FRQ phosphorylation, kinase inhibitors were used to block FRQ phosphorylation in vivo and the effects on FRQ and the clock observed. 6-dimethylaminopurine (a general kinase inhibitor) is able to block FRQ phosphorylation in vivo, reducing the rate of phosphorylation and the degradation of FRQ and lengthening the period of the clock in a dose-dependent manner. To confirm the role of FRQ phosphorylation in this clock effect, phosphorylation sites in FRQ were identified by systematic mutagenesis of the FRQ ORF. The mutation of one phosphorylation site at Ser-513 leads to a dramatic reduction of the rate of FRQ degradation and a very long period (>30 hr) of the clock. Taken together, these data strongly suggest that FRQ phosphorylation triggers its degradation, and the degradation rate of FRQ is a major determining factor for the period length of the Neurospora circadian clock.

Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria

A negative feedback control of kaiC expression by KaiC protein has been proposed to generate a basic oscillation of the circadian clock in the cyanobacterium Synechococcus sp. PCC 7942. KaiC has two P loops or Walker's motif As, that are potential ATP-/GTP-binding motifs and DXXG motifs conserved in various GTP-binding proteins. Herein, we demonstrate that in vitro KaiC binds ATP and, with lower affinity, GTP. Point mutation by site-directed mutagenesis of P loop 1 completely nullified the circadian rhythm of kaiBC expression and markedly reduced ATP-binding activity. Moreover, KaiC can be autophosphorylated in vitro. These results suggest that the nucleotide-binding activity of KaiC plays important roles in the generation of circadian oscillation in cyanobacteria.

The clocks controlling the tide-associated rhythms of intertidal animals

The living clock that governs tide-associated organismic rhythms has previously been assumed to have a fundamental period of approximately 12.4 h, an interval that reflects the average period of the ebb and flow of the tide. But, in 1986, marine chronobiologists began to accumulate laboratory results that could not be explained by the action of such a clock. Prime among these findings was the discovery that, occasionally, one of the two daily peaks in an organism's rhythm assumed a different period from its partner. Similar results have since been observed in a host of different organisms. These data led to the circalunidian-clock hypothesis that envisions two basic 24.8 h clocks, coupled together in antiphase, as the driving force for these rhythms. There is, however, only a slight difference (50 minutes) in running times between a solar-day clock with a period of approximately 24 h and a lunar-day clock with a period of approximately 24.8 h, both of which display "circa" periods that overlap. Here, I postulate that the two clocks are fundamentally one and the same. BioEssays 22:32-37, 2000.

A clock-work somite

Somites are transient structures which represent the most overt segmental feature of the vertebrate embryo. The strict temporal regulation of somitogenesis is of critical developmental importance since many segmental structures adopt a periodicity based on that of the somites. Until recently, the mechanisms underlying the periodicity of somitogenesis were largely unknown. Based on the oscillations of c-hairy1 and lunatic fringe RNA, we now have evidence for an intrinsic segmentation clock in presomitic cells. Translation of this temporal periodicity into a spatial periodicity, through somite formation, requires Notch signaling. While the Hox genes are certainly involved, it remains unknown how the metameric vertebrate axis becomes regionalized along the antero-posterior (AP) dimension into the occipital, cervical, thoracic, lumbar, and sacral domains. We discuss the implications of cell division as a clock mechanism underlying the regionalization of somites and their derivatives along the AP axis. Possible links between the segmentation clock and axial regionalization are also discussed. BioEssays 22:72-83, 2000.

From biological clock to biological rhythms

The genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output pathways that control diverse rhythmic phenomena.

Ultradian clocks in eukaryotic microbes: from behavioural observation to functional genomics

Period homeostasis is the defining characteristic of a biological clock. Strict period homeostasis is found for the ultradian clocks of eukaryotic microbes. In addition to being temperature-compensated, the period of these rhythms is unaffected by differences in nutrient composition or changes in other environmental variables. The best-studied examples of ultradian clocks are those of the ciliates Paramecium tetraurelia and Tetrahymena sp. and of the fission yeast, Schizosaccharomyces pombe. In these single cell eukaryotes, up to seven different parameters display ultradian rhythmicity with the same, species- and strain-specific period. In fission yeast, the molecular genetic analysis of ultradian clock mechanisms has begun with the systematic analysis of mutants in identified candidate genes. More than 40 "clock mutants" have already been identified, most of them affected in components of major regulatory and signalling pathways. These results indicate a high degree of complexity for a eukaryotic clock mechanism. BioEssays 22:16-22, 2000.

Circadian clocks in the mammalian brain

Daily cycles in physiology and behaviour are probably a universal feature of multicellular organisms. These rhythms are predominantly driven by endogenous clocks with a periodicity approximating to one day, i.e. circadian. In mammals, the circadian clock governing activity/ rest, neuroendocrine and autonomic rhythms lies in the hypothalamus, in the suprachiasmatic nuclei (SCN). Intrinsic circadian oscillators are also present in the retina. The SCN "clockwork" is based on a cell autonomous, genetically determined mechanism. Mammalian homologues of a number of Drosophila genes which encode elements of the fly circadian mechanism have recently been identified. In Drosophila, the protein products of these genes interact in a negative feedback loop, establishing a circadian cycle in gene expression. Characterisation of the roles played by putative mammalian clock genes in the SCN, and how the emergent cellular signal imposes order over the entire neuraxis, will provide a fundamental contribution to our understanding of the molecular basis of behaviour. BioEssays 22:23-31, 2000.

A cell-intrinsic timer that operates during oligodendrocyte development

Multicellular organisms develop on a predictable schedule that depends on both cell-intrinsic timers and sequential cell-cell interactions mediated by extracellular signals. The interplay between intracellular timers and extracellular signals is well illustrated by the development of oligodendrocytes, the cells that make the myelin in the vertebrate central nervous system. An intrinsic timing mechanism operates in each oligodendrocyte precursor cell to limit the length of time the cell divides before terminally differentiating. This mechanism consists of two components, a timing component, which depends on the mitogen platelet-derived growth factor (PDGF) and measures elapsed time, and an effector component, which depends on thyroid hormone and stops cell division and initiates differentiation at the appropriate time. The cell-cycle inhibitor p27/Kip1 accumulates in the precursor cells as they proliferate and is part of both components of the timer. It seems likely that similar timing mechanisms operate in other cell lineages. BioEssays 22:64-71, 2000.

Time measurement and the control of flowering in plants

Many plants are adapted to flower at particular times of year, to ensure optimal pollination and seed maturation. In these plants flowering is controlled by environmental signals that reflect the changing seasons, particularly daylength and temperature. The response to daylength varies, so that plants isolated at higher latitudes tend to flower in response to long daylengths of spring and summer, while plants from lower latitudes avoid the extreme heat of summer by responding to short days. Such responses require a mechanism for measuring time, and the circadian clock that regulates daily rhythms in behaviour also acts as the timer in the measurement of daylength. Plants from high latitudes often also show an extreme response to temperature called vernalisation in which flowering is repressed until the plant is exposed to winter temperatures for an extended time. Genetic approaches in Arabidopsis have identified a number of genes that control vernalisation and daylength responses. These genes are described and models presented for how daylength might regulate flowering by controlling their expression by the circadian clock. BioEssays 22:38-47, 2000.

Rest in Drosophila is a sleep-like state

To facilitate the genetic study of sleep, we documented that rest behavior in Drosophila melanogaster is a sleep-like state. The animals choose a preferred location, become immobile for periods of up to 157 min at a particular time in the circadian day, and are relatively unresponsive to sensory stimuli. Rest is affected by both homeostatic and circadian influences: when rest is prevented, the flies increasingly tend to rest despite stimulation and then exhibit a rest rebound. Drugs acting on a mammalian adenosine receptor alter rest as they do sleep, suggesting conserved neural mechanisms. Finally, normal homeostatic regulation depends on the timeless but not the period central clock gene. Understanding the molecular features of Drosophila rest should shed new light on the mechanisms and function of sleep.

The circadian clock of cyanobacteria

A circadian clock, with physiological characteristics similar to those of eukaryotes, functions in the photosynthetic prokaryote, cyanobacteria. The molecular mechanism of this clock has been efficiently dissected using a luciferase reporter gene that reports the status of the clock. A circadian clock gene cluster, kaiABC, has been cloned via rhythm mutants of cyanobacterium, Synechococcus, and many clock mutations mapped to the three kai genes. Although kai genes do not share any homology with clock genes so far identified in eukaryotes, analysis of their expression suggests that a negative feedback control of kaiC expression by KaiC generates the circadian oscillation and that KaiA functions as a positive factor to sustain this oscillation. BioEssays 22:10-15, 2000.

Molecular mechanism and cellular distribution of insect circadian clocks

Circadian clocks are endogenous timing mechanisms that control molecular, cellular, physiological, and behavioral rhythms in all organisms from unicellulars to humans. Circadian rhythms influence many aspects of insect biology, finetuning life functions to the light and temperature cycles associated with the solar day. Genetic studies in the fruit fly Drosophila melanogaster have led to the cloning and characterization of several genes involved in the mechanism of the circadian clock. Periodic transcription and translation of these clock genes form the basis of a molecular feedback loop that has a "circa" 24-hour period. Rhythmic expression of clock genes in specific brain neurons appears to control behavioral rhythms in adult flies. However, clock genes are also expressed in other tissues, both within and outside of the nervous system. These observations prompted chronobiologists to investigate whether nonneural tissues possess intrinsic circadian clocks, what role they may be playing, and what the relationships are between clocks in the nervous system and those in peripheral tissues. Answers to those questions are providing important insights into the overall organization of the circadian system in insects.

Modeling the molecular regulatory mechanism of circadian rhythms in Drosophila

Thanks to genetic and biochemical advances on the molecular mechanism of circadian rhythms in Drosophila, theoretical models closely related to experimental observations can be considered for the regulatory mechanism of the circadian clock in this organism. Modeling is based on the autoregulatory negative feedback exerted by a complex between PER and TIM proteins on the expression of per and tim genes. The model predicts the occurrence of sustained circadian oscillations in continuous darkness. When incorporating light-induced TIM degradation, the model accounts for damping of oscillations in constant light, entrainment of the rhythm by light-dark cycles of varying period or photoperiod, and phase shifting by light pulses. The model further provides a molecular dynamical explanation for the permanent or transient suppression of circadian rhythmicity triggered in a variety of organisms by a critical pulse of light. Finally, the model shows that to produce a robust rhythm the various clock genes must be expressed at the appropriate levels since sustained oscillations only occur in a precise range of parameter values. BioEssays 22:84-93, 2000.

Localization and light-dependent phosphorylation of white collar 1 and 2, the two central components of blue light signaling in Neurospora crassa

In Neurospora crassa only two white collar (wc) mutants, wc-1 and wc-2, have been described that seem to be insensitive to light. The pleiotropic phenotypes of these mutants suggest that they represent two central components of blue light signal transduction. The WC proteins have several characteristics of transcription factors consistent with an involvement in transcriptional control of light-regulated genes. Here, we present a biochemical analysis of WC1 and WC2 polypeptides in N. crassa. Using specific antisera against WC1 and WC2, respectively, the subcellular localization of the WC polypeptides was investigated. The WC1 protein was localized exclusively in the nucleus, whereas WC2 was detected in both the nuclear and cytoplasmic fractions. The nuclear localization of WC1 and WC2 was shown to be independent of light and dimerization between the two proteins. In addition, WC1 and WC2 are phosphorylated in response to light. The phosphorylation of WC1 and WC2 was dependent on functional WC1 and WC2 proteins, respectively, which clearly indicated a correlation between the light-dependent phosphorylation and the function of WC1 and WC2 in blue light signaling. However, the light-specific phosphorylation of the WC proteins revealed different kinetics. The phosphorylation of WC1 was transient whereas the WC2 phosphorylation was shown to be stable under constant light conditions. The analysis of the light-dependent phosphorylation of WC1 and WC2 in wc-2 and wc-1 mutants revealed an epistatic relationship for WC1 and WC2 with WC2 acting downstream of WC1 in the signal transduction pathway of blue light.

GABA synchronizes clock cells within the suprachiasmatic circadian clock

The master clock in the suprachiasmatic nuclei (SCN) is composed of multiple, single-cell circadian clocks. We test the postulate that these individual "clock cells" can be synchronized to each other by the inhibitory transmitter gamma-aminobutyric acid (GABA). For these experiments, we monitored the firing rate rhythm of individual clock cells on fixed multielectrode plates in culture and tested the effects of GABA. The results show that the daily variation in responsiveness of the SCN to phase-shifting agents is manifested at the level of individual neurons. Moreover, GABA, acting through A-type receptors, can both phase shift and synchronize clock cells. We propose that GABA is an important synchronizer of SCN neurons in vivo.

clk-1, mitochondria, and physiological rates

Mutations in the C. elegans maternal-effect gene clk-1 are highly pleiotropic, affecting the duration of diverse developmental and behavioral processes. They result in an average slowing of embryonic and post-embryonic development, adult rhythmic behaviors, reproduction, and aging.(1) CLK-1 is a highly conserved mitochondrial protein,(2,3) but even severe clk-1 mutations affect mitochondrial respiration only slightly.(3) Here, we review the evidence supporting the regulatory role of clk-1 in physiological timing. We also discuss possible models for the action of CLK-1, in particular, one proposing that CLK-1 is involved in the coordination of mitochondrial and nuclear function. BioEssays 22:48-56, 2000.

Theoretical models for circadian rhythms in Neurospora and Drosophila

We examine theoretical models proposed for the molecular mechanism of circadian rhythms in Drosophila. The models are based on the negative feedback exerted by a complex between the PER and TIM proteins on the expression of the per and tim genes. We show that a similar model can account for circadian oscillations in Neurospora, where the protein FRQ negatively regulates the expression of the frq gene. The effect of light on the circadian rhythms is included by considering that it elicits a rise in the rate of TIM degradation in Drosophila, whereas in Neurospora it enhances the rate of frq transcription. The models account for the occurrence of sustained circadian oscillations in continuous darkness in Drosophila and Neurospora. Numerical simulations further indicate that the periodic forcing of circadian oscillations by light-dark cycles can result either in the entrainment to the external periodicity or in aperiodic oscillations (i.e. chaos), depending on the magnitude of the periodic changes in the light-controlled parameter.

Per1 and Per2 gene expression in the rat suprachiasmatic nucleus: circadian profile and the compartment-specific response to light

Expression profiles of rPer1 and rPer2 messenger RNAs, rat homologues of the Drosophila clock gene period, were examined in the rat suprachiasmatic nucleus, a main locus of circadian oscillation, with special reference to the topographical compartmentation of the suprachiasmatic nucleus. Quantitative in situ hybridization of rPer1 and rPer2 messenger RNAs showed a robust circadian rhythm in the suprachiasmatic nucleus, with a characteristic peak/trough profile in each gene: the peak of rPer1 messenger RNA was in the daytime and that of rPer2 messenger RNA was at the transition time of day to night in both light-dark and constant dark conditions. Light exposure at circadian time 16 increased both rPer1 and rPer2 messenger RNAs in the suprachiasmatic nucleus. In a detailed histological analysis, we found that light exposure at circadian time 16 induced the expression of rPer1 and rPer2 genes in neurons limited to the ventrolateral part of the suprachiasmatic nucleus, although the usual circadian rPer1 and rPer2 messenger RNA oscillation in light-dark and constant dark conditions occurred strongly in neurons in the dorsomedial part but weakly in neurons in the ventrolateral part of the suprachiasmatic nucleus. These rPer expression profiles indicate that the two major subpopulations of neurons in the suprachiasmatic nucleus play different roles in the generation of circadian rhythm: a strong autonomous expression ability with no light response in dorsomedial neurons and a strong light responsiveness with a weak autonomous expression in ventrolateral neurons.

Photic induction of mPer1 and mPer2 in cry-deficient mice lacking a biological clock

Mice lacking mCry1 and mCry2 are behaviorally arrhythmic. As shown here, cyclic expression of the clock genes mPer1 and mPer2 (mammalian Period genes 1 and 2) in the suprachiasmatic nucleus and peripheral tissues is abolished and mPer1 and mPer2 mRNA levels are constitutively high. These findings indicate that the biological clock is eliminated in the absence of both mCRY1 and mCRY2 (mammalian cryptochromes 1 and 2) and support the idea that mammalian CRY proteins act in the negative limb of the circadian feedback loop. The mCry double-mutant mice retain the ability to have mPer1 and mPer2 expression induced by a brief light stimulus known to phase-shift the biological clock in wild-type animals. Thus, mCRY1 and mCRY2 are dispensable for light-induced phase shifting of the biological clock.

A pdf neuropeptide gene mutation and ablation of PDF neurons each cause severe abnormalities of behavioral circadian rhythms in Drosophila

The mechanisms by which circadian pacemaker systems transmit timing information to control behavior are largely unknown. Here, we define two critical features of that mechanism in Drosophila. We first describe animals mutant for the pdf neuropeptide gene, which is expressed by most of the candidate pacemakers (LNv neurons). Next, we describe animals in which pdf neurons were selectively ablated. Both sets of animals produced similar behavioral phenotypes. Both sets entrained to light, but both were largely arrhythmic under constant conditions. A minority of each pdf variant exhibited weak to moderate free-running rhythmicity. These results confirm the assignment of LNv neurons as the principal circadian pacemakers controlling daily locomotion in Drosophila. They also implicate PDF as the principal circadian transmitter.

Rapid down-regulation of mammalian period genes during behavioral resetting of the circadian clock

The pervasive role of circadian clocks in regulating physiology and behavior is widely recognized. Their adaptive value is their ability to be entrained by environmental cues such that the internal circadian phase is a reliable predictor of solar time. In mammals, both light and nonphotic behavioral cues can entrain the principal oscillator of the hypothalamic suprachiasmatic nuclei (SCN). However, although light can advance or delay the clock during circadian night, behavioral events trigger phase advances during the subjective day, when the clock is insensitive to light. The recent identification of Period (Per) genes in mammals, homologues of dperiod, which encodes a core element of the circadian clockwork in Drosophila, now provides the opportunity to explain circadian timing and entrainment at a molecular level. In mice, expression of mPer1 and mPer2 in the SCN is rhythmic and acutely up-regulated by light. Moreover, the temporal relations between mRNA and protein cycles are consistent with a clock based on a transcriptional/translational feedback loop. Here we describe circadian oscillations of Per1 and Per2 in the SCN of the Syrian hamster, showing that PER1 protein and mRNA cycles again behave in a manner consistent with a negative-feedback oscillator. Furthermore, we demonstrate that nonphotic resetting has the opposite effect to light: acutely down-regulating these genes. Their sensitivity to nonphotic resetting cues supports their proposed role as core elements of the circadian oscillator. Moreover, this study provides an explanation at the molecular level for the contrasting but convergent effects of photic and nonphotic cues on the clock.

Discovery of a putative heme-binding protein family (SOUL/HBP) by two-tissue suppression subtractive hybridization and database searches

In the domestic chicken, Gallus gallus, the retina and pineal gland contain circadian clocks that are directly entrained by environmental light-dark cycles. To identify novel genes that are expressed in the retina and pineal gland, we performed two-tissue suppression subtractive hybridization (SSH). Two-tissue SSH is designed to identify genes expressed in common between two RNA samples while at the same time subtracting out abundant transcripts. Using this method, we identified a novel chicken gene, named ckSoul, that is strongly expressed in the retina and pineal gland. The protein product of ckSoul is similar to a novel heme-binding protein (p22 HBP) and to an uncharacterized mammalian gene in the expressed sequence tag (EST) database. The mouse transcript of this new gene is expressed in the retina and may represent the mammalian ortholog of ckSoul. Molecular analysis of the mammalian and chicken proteins suggests SOUL and HBP are members of a new family of heme-binding proteins.

Cycling vrille expression is required for a functional Drosophila clock

We identified a novel regulatory loop within Drosophila's circadian clock. A screen for clock-controlled genes recovered vrille (vri), a transcription factor essential for embryonic development. vri is expressed in circadian pacemaker cells in larval and adult brains. vri RNA levels oscillate with a circadian rhythm. Cycling is directly regulated by the transcription factors dCLOCK and CYCLE, which are also required for oscillations of period and timeless RNA. Eliminating the normal vri cycle suppresses period and timeless expression and causes long-period behavioral rhythms and arrhythmicity, indicating that cycling vri is required for a functional Drosophila clock. We also show that dCLOCK and VRI independently regulate levels of a neuropeptide, pigment dispersing factor, which appears to regulate overt behavior.

The circadian clock controls the expression pattern of the circadian input photoreceptor, phytochrome B

Developmental and physiological responses are regulated by light throughout the entire life cycle of higher plants. To sense changes in the light environment, plants have developed various photoreceptors, including the red/far-red light-absorbing phytochromes and blue light-absorbing cryptochromes. A wide variety of physiological responses, including most light responses, also are modulated by circadian rhythms that are generated by an endogenous oscillator, the circadian clock. To provide information on local time, circadian clocks are synchronized and entrained by environmental time cues, of which light is among the most important. Light-driven entrainment of the Arabidopsis circadian clock has been shown to be mediated by phytochrome A (phyA), phytochrome B (phyB), and cryptochromes 1 and 2, thus affirming the roles of these photoreceptors as input regulators to the plant circadian clock. Here we show that the expression of PHYB::LUC reporter genes containing the promoter and 5' untranslated region of the tobacco NtPHYB1 or Arabidopsis AtPHYB genes fused to the luciferase (LUC) gene exhibit robust circadian oscillations in transgenic plants. We demonstrate that the abundance of PHYB RNA retains this circadian regulation and use a PHYB::Luc fusion protein to show that the rate of PHYB synthesis is also rhythmic. The abundance of bulk PHYB protein, however, exhibits only weak circadian rhythmicity, if any. These data suggest that photoreceptor gene expression patterns may be significant in the daily regulation of plant physiology and indicate an unexpectedly intimate relationship between the components of the input pathway and the putative circadian clock mechanism in higher plants.

A putative transcription factor with seven zinc-finger motifs identified in the developing suprachiasmatic nucleus by the differential display PCR method

The suprachiasmatic nucleus (SCN) is a mammalian central circadian pacemaker. This nucleus develops in the last stage of fetal life and matures to make strong synaptic connections within 2 weeks of postnatal life to establish strong oscillation characteristics. To identify factors that initiate the circadian oscillation, we applied a differential display PCR method to developing SCN, and isolated a gene with seven zinc-finger motifs, Lot1, which encodes a gene that appeared at a very high level in the SCN during the early postnatal days. Lot1 mRNA first appeared at postnatal day 1 (P1) at a very high level, and the signal in the SCN continued to be very high until P10 and thereafter rapidly decreased until P20 and was expressed at a very faint level during adulthood. Lot1 mRNA expression was observed only in neurons of the dorsomedial SCN throughout the course of development. During the developmental stage, Lot1 mRNA expression shows a circadian rhythm with a peak in the day time and a trough at night time in both light-dark and constant dark conditions. These observations imply that Lot1 is the first identified putative transcription factor expressed only in the period of active synaptogenesis in the SCN, where Lot1 might play a role in establishing autonomous oscillation.

Sex-linked period genes in the silkmoth, Antheraea pernyi: implications for circadian clock regulation and the evolution of sex chromosomes

Regulation of the period (per) gene is a critical feature of circadian clock function in insects. Here, we show that per is sex-linked in the silkmoth, Antheraea per-nyi. The previously described silkmoth per gene is found on the Z chromosome. Silkmoth per is not dosage compensated at either the RNA or the protein level. Although earlier studies showed the presence of an oscillating endogenous antisense per transcript, we show that this transcript comes from a locus on the female-specific W chromosome. We further demonstrate the presence of a homolog of per on W that encodes a truncated protein. Rhythmicity of male (ZZ) moths demonstrates that neither of the W-linked per-like genes is essential for clock function. The presence of a per allele with duplications on W provides insight into the evolution of the sex chromosomes.

Modeling circadian rhythm generation in the suprachiasmatic nucleus with locally coupled self-sustained oscillators: phase shifts and phase response curves

Circadian rhythm generation in the suprachiasmatic nucleus was modeled by locally coupled self-sustained oscillators. The model is composed of 10,000 oscillators, arranged in a square array. Coupling between oscillators and standard deviation of (randomly determined) intrinsic oscillator periods were varied. A stable overall rhythm emerged. The model behavior was investigated for phase shifts of a 24-h zeitgeber cycle. Prolongation of either the dark or the light phase resulted in a lengthening of the period, whereas shortening of the dark or the light phase shortened the period. The model's response to shifts in the light-dark cycle was dependent only on the extent of the shift and was insensitive to changes in parameters. Phase response curves (PRC) and amplitude response curves were determined for single and triple 5-h light pulses (1000 lux). Single pulses lead to type 1 PRCs with larger phase shifts for weak coupling. Triple pulses generally evoked type 1 PRCs with the exception of weak coupling, where a type 0 PRC was observed.

Circadian systems and metabolism

Circadian systems direct many metabolic parameters and, at the same time, they appear to be exquisitely shielded from metabolic variations. Although the recent decade of circadian research has brought insights into how circadian periodicity may be generated at the molecular level, little is known about the relationship between this molecular feedback loop and metabolism both at the cellular and at the organismic level. In this theoretical paper, we conjecture about the interdependence between circadian rhythmicity and metabolism. A mathematical model based on the chemical reactions of photosynthesis demonstrates that metabolism as such may generate rhythmicity in the circadian range. Two additional models look at the possible function of feedback loops outside of the circadian oscillator. These feedback loops contribute to the robustness and sustainability of circadian oscillations and to compensation for long- and short-term metabolic variations. The specific circadian property of temperature compensation is put into the context of metabolism. As such, it represents a general compensatory mechanism that shields the clock from metabolic variations.

Different period gene repeats take 'turns' at fine-tuning the circadian clock

The repetitive region of the circadian clock gene period in Drosophila pseudoobscura consists predominantly of a pentapeptide sequence whose consensus is NSGAD. In D. melanogaster, this region is replaced by a dipeptide Thr-Gly repeat, which plays a role in the thermal stability of the circadian phenotype. The Thr-Gly repeat has been shown to form a type II or III beta-turn, whose conformational monomer is (Thr-Gly)3. Here we report, using conformational analyses, that both an NSGAD pentapeptide, and a polymer of the same sequence, form type II beta-turns. Thus two peptide sequences, whose amino-acid composition is very different, nevertheless form the same secondary structure. The implications of these structures for clock function are discussed.

Pituitary adenylyl cyclase-activating peptide: a pivotal modulator of glutamatergic regulation of the suprachiasmatic circadian clock

The circadian clock in the suprachiasmatic nucleus (SCN) of the hypothalamus organizes behavioral rhythms, such as the sleep-wake cycle, on a near 24-h time base and synchronizes them to environmental day and night. Light information is transmitted to the SCN by direct retinal projections via the retinohypothalamic tract (RHT). Both glutamate (Glu) and pituitary adenylyl cyclase-activating peptide (PACAP) are localized within the RHT. Whereas Glu is an established mediator of light entrainment, the role of PACAP is unknown. To understand the functional significance of this colocalization, we assessed the effects of nocturnal Glu and PACAP on phasing of the circadian rhythm of neuronal firing in slices of rat SCN. When coadministered, PACAP blocked the phase advance normally induced by Glu during late night. Surprisingly, blocking PACAP neurotransmission, with either PACAP6-38, a specific PACAP receptor antagonist, or anti-PACAP antibodies, augmented the Glu-induced phase advance. Blocking PACAP in vivo also potentiated the light-induced phase advance of the rhythm of hamster wheel-running activity. Conversely, PACAP enhanced the Glu-induced delay in the early night, whereas PACAP6-38 inhibited it. These results reveal that PACAP is a significant component of the Glu-mediated light-entrainment pathway. When Glu activates the system, PACAP receptor-mediated processes can provide gain control that generates graded phase shifts. The relative strengths of the Glu and PACAP signals together may encode the amplitude of adaptive circadian behavioral responses to the natural range of intensities of nocturnal light.

Similarity of the C. elegans developmental timing protein LIN-42 to circadian rhythm proteins

The Caenorhabditis elegans heterochronic genes control the relative timing and sequence of many events during postembryonic development, including the terminal differentiation of the lateral hypodermis, which occurs during the final (fourth) molt. Inactivation of the heterochronic gene lin-42 causes hypodermal terminal differentiation to occur precociously, during the third molt. LIN-42 most closely resembles the Period family of proteins from Drosophila and other organisms, proteins that function in another type of biological timing mechanism: the timing of circadian rhythms. Per mRNA levels oscillate with an approximately 24-hour periodicity. lin-42 mRNA levels also oscillate, but with a faster rhythm; the oscillation occurs relative to the approximately 6-hour molting cycles of postembryonic development.

Circadian clocks: A cry in the dark?

Cryptochrome proteins are key components of the circadian systems of both Drosophila and mammals. In Drosophila, they appear to be responsible for the entrainment of the circadian clock by the light-dark cycle, while in mammals they perform an important role in rhythm generation itself.

Characterization of npas3, a novel basic helix-loop-helix PAS gene expressed in the developing mouse nervous system

Here we describe the cloning and expression pattern of a new bHLH-PAS domain gene, Npas3. Npas3 shares 50.2% amino acid sequence identity with Npas1 and a lesser similarity with other members of the bHLH-PAS domain family of transcription factors. Northern blot analysis detected Npas3 mRNA between 11.5 and 17.5 d.p.c. in embryonic development and exclusively in the adult brain. Whole-mount and section in situ hybridization assays revealed expression of Npas3 between 9.5 and 11.5 d.p.c. in the developing neural tube. In addition, Npas3 mRNA was expressed throughout the neuroepithelium of the developing central nervous system between 10. 5 and 12.5 d.p.c. Interestingly, at 14.5 d.p.c., the expression of Npas3 mRNA became restricted to the neopallial layer of the cortex. At 12.5 d.p.c., Npas3 mRNA was evident in nonneural tissues such as the developing dermis and mesenchyme surrounding the otic and nasal placodes. Expression was also detected in the developing cardiac valves, limb and developing kidney.

The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis

A wide range of processes in plants, including expression of certain genes, is regulated by endogenous circadian rhythms. The circadian clock-associated 1 (CCA1) and the late elongated hypocotyl (LHY) proteins have been shown to be closely associated with clock function in Arabidopsis thaliana. The protein kinase CK2 can interact with and phosphorylate CCA1, but its role in the regulation of the circadian clock remains unknown. Here we show that plants overexpressing CKB3, a regulatory subunit of CK2, display increased CK2 activity and shorter periods of rhythmic expression of CCA1 and LHY. CK2 is also able to interact with and phosphorylate LHY in vitro. Additionally, overexpression of CKB3 shortened the periods of four known circadian clock-controlled genes with different phase angles, demonstrating that many clock outputs are affected. This overexpression also reduced phytochrome induction of an Lhcb gene. Finally, we found that the photoperiodic flowering response, which is influenced by circadian rhythms, was diminished in the transgenic lines, and that the plants flowered earlier on both long-day and short-day photoperiods. These data demonstrate that CK2 is involved in regulation of the circadian clock in Arabidopsis.

Interlocked feedback loops within the Drosophila circadian oscillator

Drosophila Clock (dClk) is rhythmically expressed, with peaks in mRNA and protein (dCLK) abundance early in the morning. dClk mRNA cycling is shown here to be regulated by PERIOD-TIMELESS (PER-TIM)-mediated release of dCLK- and CYCLE (CYC)-dependent repression. Lack of both PER-TIM derepression and dCLK-CYC repression results in high levels of dClk mRNA, which implies that a separate dClk activator is present. These results demonstrate that the Drosophila circadian feedback loop is composed of two interlocked negative feedback loops: a per-tim loop, which is activated by dCLK-CYC and repressed by PER-TIM, and a dClk loop, which is repressed by dCLK-CYC and derepressed by PER-TIM.

Light-independent role of CRY1 and CRY2 in the mammalian circadian clock

Cryptochrome (CRY), a photoreceptor for the circadian clock in Drosophila, binds to the clock component TIM in a light-dependent fashion and blocks its function. In mammals, genetic evidence suggests a role for CRYs within the clock, distinct from hypothetical photoreceptor functions. Mammalian CRY1 and CRY2 are here shown to act as light-independent inhibitors of CLOCK-BMAL1, the activator driving Per1 transcription. CRY1 or CRY2 (or both) showed light-independent interactions with CLOCK and BMAL1, as well as with PER1, PER2, and TIM. Thus, mammalian CRYs act as light-independent components of the circadian clock and probably regulate Per1 transcriptional cycling by contacting both the activator and its feedback inhibitors.

Calbindin expression in the hamster SCN is influenced by circadian genotype and by photic conditions

Circadian rhythmicity in mammals, is controlled by the suprachiasmatic nuclei (SCN) of the hypothalamus. We previously described a discrete subnucleus in the core of the hamster SCN containing calbindin-D28k-positive cells which are fos-positive in response to a light pulse. Ablation of this subnucleus results in loss of circadian locomotor rhythmicity even when other parts of the SCN are spared. Here we show that Tau mutant hamsters have significantly more calbindin-D28k in the SCN than do wild type hamsters, and that SCN calbindin-immunoreactivity in the SCN increases in the dark. This is correlated with changes in magnitude of light mediated phase shifts in locomotion. The data are consistent with a role for calbindin cells in light mediated entrainment and phase shifting.

Differential regulation of mammalian period genes and circadian rhythmicity by cryptochromes 1 and 2

Cryptochromes regulate the circadian clock in animals and plants. Humans and mice have two cryptochrome (Cry) genes. A previous study showed that mice lacking the Cry2 gene had reduced sensitivity to acute light induction of the circadian gene mPer1 in the suprachiasmatic nucleus (SCN) and had an intrinsic period 1 hr longer than normal. In this study, Cry1(-/-) and Cry1(-/-)Cry2(-/-) mice were generated and their circadian clocks were analyzed at behavioral and molecular levels. Behaviorally, the Cry1(-/-) mice had a circadian period 1 hr shorter than wild type and the Cry1(-/-)Cry2(-/-) mice were arrhythmic in constant darkness (DD). Biochemically, acute light induction of mPer1 mRNA in the SCN was blunted in Cry1(-/-) and abolished in Cry1(-/-)Cry2(-/-) mice. In contrast, the acute light induction of mPer2 in the SCN was intact in Cry1(-/-) and Cry1(-/-)Cry2(-/-) animals. Importantly, in double mutants, mPer1 expression was constitutively elevated and no rhythmicity was detected in either 12-hr light/12-hr dark or DD, whereas mPer2 expression appeared rhythmic in 12-hr light/12-hr dark, but nonrhythmic in DD with intermediate levels. These results demonstrate that Cry1 and Cry2 are required for the normal expression of circadian behavioral rhythms, as well as circadian rhythms of mPer1 and mPer2 in the SCN. The differential regulation of mPer1 and mPer2 by light in Cry double mutants reveals a surprising complexity in the role of cryptochromes in mammals.

Remembrance of things PAS: regulation of development by bHLH-PAS proteins

Strange fits of passion I have knownellipsis (W Wordsworth, 'Strange fits of passion'.) bHLH-PAS proteins are regulators of developmental and physiological events that are well conserved between vertebrates and invertebrates. Recent studies using mouse knockouts of bHLH-PAS genes have provided novel insight into the roles of hypoxia inducible factors in controlling oxygen-regulated development and homeostasis, and the role of Single-minded-1 in regulating development and transcription in the hypothalamus. The Drosophila spineless and vertebrate Aryl hydrocarbon receptor bHLH-PAS orthologs both function in chemosensory processes, but in fundamentally different ways. Spineless controls antennal, limb, and sensory cell development, whereas the Aryl hydrocarbon receptor regulates the response to toxin metabolism. Structural analyses of the PAS domain provide insight into how this interaction domain can act as ligand-binding environmental sensor and signal transducer.

Natural allelic variation identifies new genes in the Arabidopsis circadian system

We have analysed the circadian rhythm of Arabidopsis thaliana leaf movements in the accession Cvi from the Cape Verde Islands, and in the commonly used laboratory strains Columbia (Col) and Landsberg (erecta) (Ler), which originated in Northern Europe. The parental lines have similar rhythmic periods, but the progeny of crosses among them reveal extensive variation for this trait. An analysis of 48 Ler/Cvi recombinant inbred lines (RILs) and a further 30 Ler/Col RILs allowed us to locate four putative quantitative trait loci (QTLs) that control the period of the circadian clock. Near-isogenic lines (NILs) that contain a QTL in a small, defined chromo- somal region allowed us to confirm the phenotypic effect and to map the positions of three period QTLs, designated ESPRESSO, NON TROPPO and RALENTANDO. Quantitative trait loci at the locations of RALENTANDO and of a fourth QTL, ANDANTE, were identified in both Ler/Cvi and Ler/Col RIL populations. Some QTLs for circadian period are closely linked to loci that control flowering time, including FLC. We show that flc mutations shorten the circadian period such that the known allelic variation in the MADS-box gene FLC can account for the ANDANTE QTL. The QTLs ESPRESSO and RALENTANDO identify new genes that regulate the Arabidopsis circadian system in nature, one of which may be the flowering-time gene GIGANTEA.