On the role of protein synthesis in the circadian clock of Neurospora crassa

The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species

Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.

To Ub or not to Ub: Regulation of circadian clocks by ubiquitination and deubiquitination

Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to the daily changes of their environment. These clocks generate self-sustained oscillations at the cellular, tissue, and behavioral level. The rhythm-generating mechanism is based on a gene expression network with a delayed negative feedback loop that causes the transcripts to oscillate with a period of approximately 24 hr. This oscillatory nature of the proteins involved in this network necessitates that they are intrinsically unstable, with a short half-life. Hence, post-translational modifications (PTMs) are important to precisely time the presence, absence, and interactions of these proteins at appropriate times of the day. Ubiquitination and deubiquitination are counter-balancing PTMs which play a key role in this regulatory process. In this review, we take a comprehensive look at the roles played by the processes of ubiquitination and deubiquitination in the clock machinery of the most commonly studied eukaryotic models of the circadian clock: plants, fungi, fruit flies, and mammals. We present the effects exerted by ubiquitinating and deubiquitinating enzymes on the stability, but also the activity, localization, and interactions of clock proteins. Overall, these PTMs have key roles in regulating not only the pace of the circadian clocks but also their response to external cues and their control of cellular functions.

A pathway linking translation stress to checkpoint kinase 2 signaling in Neurospora crassa

Checkpoint kinase 2 (CHK-2) is a key component of the DNA damage response (DDR) pathway and its activation mechanism is evolutionarily conserved. We show that PERIOD-4 (PRD-4), the CHK-2 ortholog of Neurospora crassa, is part of an additional signaling pathway that is activated when protein translation is compromised. Translation stress induces phosphorylation of PRD-4 by an upstream kinase distinct from those of the DDR pathway. We present evidence that the activating kinase is mTOR. Translation stress is sensed via a decrease in levels of an unstable inhibitor that antagonizes phosphorylation of PRD-4.

Checkpoint kinase 2 (CHK-2) is a key component of the DNA damage response (DDR). CHK-2 is activated by the PIP3-kinase-like kinases (PI3KKs) ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related protein (ATR), and in metazoan also by DNA-dependent protein kinase catalytic subunit (DNA-PKcs). These DNA damage-dependent activation pathways are conserved and additional activation pathways of CHK-2 are not known. Here we show that PERIOD-4 (PRD-4), the CHK-2 ortholog of Neurospora crassa, is part of a signaling pathway that is activated when protein translation is compromised. Translation stress induces phosphorylation of PRD-4 by a PI3KK distinct from ATM and ATR. Our data indicate that the activating PI3KK is mechanistic target of rapamycin (mTOR). We provide evidence that translation stress is sensed by unbalancing the expression levels of an unstable protein phosphatase that antagonizes phosphorylation of PRD-4 by mTOR complex 1 (TORC1). Hence, Neurospora mTOR and PRD-4 appear to coordinate metabolic state and cell cycle progression.

Principles of the animal molecular clock learned from Neurospora

Study of Neurospora, a model system evolutionarily related to animals and sharing a circadian system having nearly identical regulatory architecture to that of animals, has advanced our understanding of all circadian rhythms. Work on the molecular bases of the Oscillator began in Neurospora before any clock genes were cloned and provided the second example of a clock gene, frq, as well as the first direct experimental proof that the core of the Oscillator was built around a transcriptional translational negative feedback loop (TTFL). Proof that FRQ was a clock component provided the basis for understanding how light resets the clock, and this in turn provided the generally accepted understanding for how light resets all animal and fungal clocks. Experiments probing the mechanism of light resetting led to the first identification of a heterodimeric transcriptional activator as the positive element in a circadian feedback loop, and to the general description of the fungal/animal clock as a single step TTFL. The common means through which DNA damage impacts the Oscillator in fungi and animals was first described in Neurospora. Lastly, the systematic study of Output was pioneered in Neurospora, providing the vocabulary and conceptual framework for understanding how Output works in all cells. This model system has contributed to the current appreciation of the role of Intrinsic Disorder in clock proteins and to the documentation of the essential roles of protein post-translational modification, as distinct from turnover, in building a circadian clock.

Lithium Leads to an Increased FRQ Protein Stability and to a Partial Loss of Temperature Compensation in the Neurospora Circadian Clock

In many organisms, the presence of lithium leads to an increase of the circadian period length. In Neurospora crassa, it was earlier found that lithium results in a decrease of overall growth and increased circadian periods. In this article, the authors show that lithium leads to a reduction of FRQ degradation with elevated FRQ levels and to a partial loss of temperature compensation. At a concentration of 13 mM lithium, FRQ degradation is reduced by about 60% while, surprisingly, the activity of the 20S proteasome remains unaffected. Experiments and model calculations have shown that the stability of FRQ is dependent on its phosphorylation state and that increased FRQ protein stabilities lead to increased circadian periods, consistent with the observed increase of the period when lithium is present. Because in Neurospora the proteasome activity is unaffected by lithium concentrations that lead to significant FRQ stabilization, it appears that lithium acts as an inhibitor of kinases that affect phosphorylation of FRQ and other proteins. A competition between Li+and Mg2+ions for Mg2+-binding sites may be a mechanism to how certain kinases are inhibited by Li+. A possible kinase in this respect is GSK-3, which in other organisms is known to be inhibited by lithium. The partial loss of temperature compensation in the presence of lithium can be understood as an increase in the overall activation energy of FRQ degradation. This increase in activation energy may be related to a reduction in FRQ phosphorylation so that more kinase activity, that is, higher temperature and longer times, is required to achieve the necessary amount of FRQ phosphorylation leading to turnover. Using a modified Goodwin oscillator as a semiquantitative model for the Neurospora clock, the effects of lithium can be described by adding lithium inhibitory terms of FRQ degradation to the model.

A COMPARISON INVESTIGATION OF THE SIMPLEST MODELS OF CIRCADIAN RHYTHMS

We present three different simplest realistic models of the circadian pacemaker that can be interpreted in molecular terms: Goodwin model, piece-wise Goodwin model and delay model. The main purpose is to investigate how the common parameters in these three model affect the dynamical behavior. In particular, the existence and stability of periodic solutions of three models are studied, and the parameter space where the steady state becomes unstable is given which can be used to compare the effect of parameters on the oscillations of three models. Furthermore, the effects of parameters on the period of periodic solutions and phase response curves are investigated and discussed. Our results confirm that all three models can be used to simulate the realistic circadian rhythms. However, in practice, which model is chosen depends on the real data.

Analysis of posttranslational regulations in the Neurospora circadian clock

Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinases and phosphatases, and the phosphorylation is important for regulating FRQ stability and its function in the circadian negative feedback loop. The degradation of FRQ is mediated by the ubiquitin/proteasome pathway. This article discusses posttranslational regulations of the Neurospora clock and describes the methods used in the studies of FRQ phosphorylation, FRQ kinases and phosphatases, and FRQ degradation.

The effects of temperature change on the circadian clock of Neurospora

The phase resetting of the circadian oscillatory system by pulses of increased temperature (zeitgebers) and the temperature compensation of its period length during longer exposures are major features of the system, but are not well understood in molecular terms. In Neurospora crassa, the effects of pulses of increased temperature on the circadian rhythm of conidiation were determined and possible inputs to the oscillatory system tested, including changes in cyclic 3',5'-adenosine monophosphate (cAMP), inositol 1,4,5-trisphosphate and H+ concentrations, as well as changes of phosphorylation, synthesis and degradation of proteins. Following the kinetics of these parameters during exposure to increased temperature showed transient changes. Experimental manipulation of cAMP, Ca2+ and H+ levels, and of the synthesis and, possibly, degradation of proteins, resulted in phase shifts of the oscillatory system. It is assumed that the temperature signal affects the oscillator(s) by multiple pathways and shifts the whole state of the oscillatory system. Second messenger levels, protein synthesis and protein degradation show adaptation to longer exposures to elevated temperature which may be involved in the temperature compensation of the period length. The temperature compensation is also proposed to involve a shift in the state of all or most oscillator variables.

The genetic basis of the circadian clock: identification of frq and FRQ as clock components in Neurospora

Genetic approaches to the identification of clock components have succeeded in two model systems, Neurospora and Drosophila. In each organism, genes identified through screens for clock-affecting mutations (frq in Neurospora, per in Drosophila) have subsequently been shown to have characteristics of central clock components: (1) mutations in each gene can affect period length and temperature compensation, two canonical characteristics of circadian systems; (2) each gene regulates the timing of its own transcription in a circadian manner; and (3) in the case of frq, constitutively elevated expression will set the phase of the clock on release into normal conditions. Despite clear genetic and molecular similarities, however, the two genes are neither molecular nor temporal homologues. The timing of peak expression is distinct in the two genes, frq expression peaking after dawn and per expression peaking near midnight. Also, although expression of per from a constitutive promoter can rescue rhythmicity in a fly lacking the gene, constitutive expression of frq will not rescue rhythmicity in Neurospora frq-null strains, and in fact causes arrhythmicity when expressed in a wild-type strain. These data suggest that frq is and/or encodes a state variable of the circadian oscillator. Recent molecular genetic analyses of frq have shed light on the origin of temperature compensation and strongly suggest that this property is built into the oscillatory feedback loop rather than appended to it. It seems plausible that clocks are adjusted and reset through adjustments in central clock components such as frq, and, by extension, per.

Circadian clocks: 50 years on

Since the first Cold Spring Harbor meeting on "Biological Clocks" in 1960, the field has progressed from the study of a fascinating but esoteric set of phenomena of interest primarily to a relatively small group of prescient biologists to become recognized as defining a centrally important aspect of biological organization. This change is the consequence of a profound increase in understanding of the mechanisms that generate and control circadian rhythmicity, coupled with the realization that circadian temporal organization is an important component of much of what most organisms do. As such, it impinges on human health, agriculture, and biological conservation, as well as on many more basic aspects of biology at every level. Many of the seminal discoveries of the last 47 years were presented and discussed at this exciting meeting.

Molecular mechanism of suppression of circadian rhythms by a critical stimulus

Circadian singularity behavior (also called suppression of circadian rhythms) is a phenomenon characterized by the abolishment of circadian rhythmicities by a critical stimulus. Here we demonstrate that both temperature step up and light pulse, stimuli that activate the expression of the Neurospora circadian clock gene frequency (frq), can trigger singularity behavior in this organism. The arrhythmicity is transient and is followed by the resumption of rhythm in randomly distributed phases. In addition, we show that induction of FRQ expression alone can trigger singularity behavior, indicating that FRQ is a state variable of the Neurospora circadian oscillator. Furthermore, mutations of frq lead to changes in the amplitude of FRQ oscillation, which determines the sensitivity of the clock to phase-resetting cues. Our results further suggest that the singularity behavior is due to the loss of rhythm in all cells. Together, these data suggest that the singularity behavior is due to a circadian negative feedback loop driven to a steady state after the critical treatment. After the initial arrhythmicity, cell populations are then desynchronized.

How fungi keep time: circadian system in Neurospora and other fungi

The circadian system in Neurospora remains a premier model system for understanding circadian rhythms, and evidence has now begun to accumulate suggesting broad conservation of rhythmicity amongst the filamentous fungi. A well-described transcription-translation-based negative feedback loop involving the FREQUENCY, WHITE COLLAR-1 and WHITE COLLAR-2 proteins is integral to the Neurospora system. Recent advances include descriptions of the surprisingly complex frequency transcription unit, an enhanced appreciation of the roles of kinases and their regulation in the generation of the circadian rhythm and their links to the cell cycle, and strong evidence for an additional WHITE COLLAR-associated feedback loop. Documentation of sequence homologs of integral circadian and photoresponsive proteins amongst the 42 available sequenced fungal genomes suggests unexpected roles for circadian timing among both pathogens and saprophytes.

Analysis of circadian rhythms in Neurospora: overview of assays and genetic and molecular biological manipulation

The eukaryotic filamentous fungus Neurospora crassa is a tractable model system that has provided numerous insights into the molecular basis of circadian rhythms. In the core circadian clock feedback loop, WC-1 and WC-2 interact via PAS domains to heterodimerize, and this complex acts both as the circadian photoreceptor and, in the dark, as a transcription factor that promotes the expression of the frq gene. In the negative step of the loop, dimers of FRQ feed back to block the activity of the WC-1/WC-2 complex (WCC) and, in a positive step, to promote the synthesis of WC-1. Several kinases phosphorylate FRQ, leading to its ubiquitination and turnover, releasing the WC-1/WC-2 dimer to reactivate frq expression and restart the circadian cycle. Light and temperature entrainment of the clock arise from rapid light induction of frq expression and from the effect of elevated temperatures in driving higher levels of FRQ. Noncircadian candidate slave oscillators, termed FRQ-less oscillators (FLOs), have been described, each of which appears to regulate aspects of Neurospora growth or development. Overall, the core FRQ/WCC feedback loop coordinates the circadian system by regulating downstream clock-controlled genes either directly or via regulation of driven FLOs. This article provides a brief synopsis of the system and describes current assays for the Neurospora clock. Methods for genetic and molecular manipulation of the core clock are summarized, and accompanying chapters address more specifically aspects of photobiology and output.

Regulation of the Circadian Oscillator in Xenopus Retinal Photoreceptors by Protein Kinases Sensitive to the Stress-activated Protein Kinase Inhibitor, SB 203580

Circadian rhythms are generated by transcriptional and translational feedback loops. Stress-activated protein kinases (SAPKs) are known to regulate transcription factors in response to a variety of extracellular stimuli. In the present study, we examined whether the SAPKs play a role in the circadian system in cultured Xenopus retinal photoreceptor layers. A 6-h pulse of SB 203580, an inhibitor of SAPKs, reset the circadian rhythm of melatonin in a phase-dependent manner similar to dark pulses. This phase-shifting effect was dose-dependent over the range of 1-100 microm. Treatment with SB 203580 also affected light-induced phase shifts, and light had no effect on the circadian oscillator in the presence of 100 microm SB 203580. In-gel kinase assays showed that SB 203580 selectively inhibited a small group of protein kinases in the photoreceptor cells. These SB 203580-sensitive kinases correspond to two isoforms of phosphorylated p38 MAPK and three isoforms of c-Jun N-terminal kinase (JNK). Further in vitro study demonstrated that SB 203580 also inhibited casein kinase Iepsilon (CKIepsilon), which has been shown to regulate circadian rhythms in several organisms. However, a pharmacological inhibition of CKI reset the circadian oscillator in a phase-dependent manner distinct from that of SB 203580. This argues against a primary role of CKI in the phase-shifting effects of SB 203580. These results suggest that SB 203580 affects the circadian system by inhibiting p38 MAPKs or JNKs and that these protein kinases are candidate cellular signals in the regulation of the circadian oscillator in the Xenopus retinal photoreceptors.

Translational and transcriptional inhibitors block serotonergic phase advances of the suprachiasmatic nucleus circadian pacemaker in vitro

The mammalian circadian pacemaker is located in the suprachiasmatic nucleus (SCN). Various inputs modulate pacemaker phase, including the serotonergic (5HTergic) input from the midbrain raphe. 5HT phase-advances the SCN pacemaker when applied during mid subjective day. In vitro studies indicate that 5HT advances the mammalian circadian pacemaker through a process that includes stimulating 5HT7 receptors, activating protein kinase A, and opening K+ channels. How these cytoplasmic and membrane events translate into a shift in the molecular core of the circadian oscillator is not known. To further understand this process, the authors investigated whether 5HTergic phase advances require transcription or translation. Using two reversible translational inhibitors, anisomycin and cycloheximide, the authors show that inhibiting protein synthesis blocks 5HTergic phase shifts. The authors further show that the transcriptional inhibitor 5,6-dichloro-1-beta-ribobenzimidazole also blocks 5HTergic phase shifts. These results are similar to those found previously with respect to 5HTergic modulation of the Aplysia ocular circadian clock, and suggest that 5HT may phase-shift the SCN pacemaker through increasing transcription and translation of specific proteins.

Epistatic and synergistic interactions between circadian clock mutations in Neurospora crassa

We identified a series of epistatic and synergistic interactions among the circadian clock mutations of Neurospora crassa that indicate possible physical interactions among the various clock components encoded by these genes. The period-6 (prd-6) mutation, a short-period temperature-sensitive clock mutation, is epistatic to both the prd-2 and prd-3 mutations. The prd-2 and prd-3 long-period mutations show a synergistic interaction in that the period length of the double mutant strain is considerably longer than predicted. In addition, the prd-2 prd-3 double mutant strain also exhibits overcompensation to changes in ambient temperature, suggesting a role in the temperature compensation machinery of the clock. The prd-2, prd-3, and prd-6 mutations also show significant interactions with the frq(7) long-period mutation. These results suggest that the gene products of prd-2, prd-3, and prd-6 play an important role in both the timing and temperature compensation mechanisms of the circadian clock and may interact with the FRQ protein.

Circadian rhythms in Neurospora: a new measurement, the reset zone

The authors define a new feature of a circadian rhythm, the reset zone, and point out its usefulness for predictions concerning oscillator behavior. The reset zone measures the responses of a circadian system to resetting pulses. It can be easily determined from a phase transition curve (PTC), which is simply a phase response curve (PRC) replotted as new phase versus old phase (Winfree's format). The reset zone is the range of new phases seen in such a plot and has two potentially useful characteristics: its size and its midpoint. A series of experiments with Neurospora involving temperature pulses indicated that the size of the reset zone changed in a nonlinear way in response to both the duration of 40 degrees C pulses and to the magnitude of temperature change for 3-h pulses. Other existing data are replotted to show how the reset zone size varies with growth temperature and with the period of different clock mutants. Employing exclusively reset zone data within the framework of a limit cycle displacement model, an equation is formulated that predicts the relative changes in the values of state variables of the oscillator for changes in any given environmental condition, such as temperature. Examples are also drawn from other organisms, such as hamsters, Gonyalaux, Kalanchoe, and Drosophila, illustrating the usefulness of the reset zone measurement. It can be used as a numerical scale for assessing the strength of a pulse, for comparing the relative effects of a given pulse applied to different organisms or mutants, for determining the directionality of the changes in state variables produced by various types of pulses, and possibly for measuring clock amplitude.

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.

The Goodwin oscillator: on the importance of degradation reactions in the circadian clock

This article focuses on the Goodwin oscillator and related minimal models, which describe negative feedback schemes that are of relevance for the circadian rhythms in Neurospora, Drosophila, and probably also in mammals. The temperature behavior of clock mutants in Neurospora crassa and Drosophila melanogaster are well described by the Goodwin model, at least on a semi-quantitative level. A similar semi-quantitative description has been found for Neurospora crassa phase response curves with respect to moderate temperature pulses, heat shock pulses, and pulses of cycloheximide. A characteristic feature in the Goodwin and related models is that degradation of clock-mRNA and clock protein species plays an important role in the control of the oscillator's period. As predicted by this feature, recent experimental results from Neurospora crassa indicate that the clock (FRQ) protein of the long period mutant frq7 is degraded approximately twice as slow as the corresponding wild-type protein. Quantitative RT-PCR indicates that experimental frq7-mRNA concentrations are significantly higher than wild-type levels. The latter findings cannot be modeled by the Goodwin oscillator. Therefore, a threshold inhibition mechanism of transcription is proposed.

Molecular and behavioral analysis of four period mutants in Drosophila melanogaster encompassing extreme short, novel long, and unorthodox arrhythmic types

Of the mutationally defined rhythm genes in Drosophila melanogaster, period (per) has been studied the most. We have molecularly characterized three older per mutants-perT, perClk, and per04-along with a novel long-period one (perSLIH). Each mutant is the result of a single nucleotide change. perT, perClk, and perSLIH are accounted for by amino acid substitutions; per04 is altered at a splice site acceptor and causes aberrant splicing. perSLIH exhibits a long period of 27 hr in constant darkness and entrains to light/dark (L/D) cycles with a later-than-normal evening peak of locomotion. perSLIH males are more rhythmic than females. perSLIH's clock runs faster at higher temperatures and slower at lower ones, exhibiting a temperature-compensation defect opposite to that of perLong. The per-encoded protein (PER) in the perT mutant cycles in L/D with an earlier-than-normal peak; this peak in perSLIH is later than normal, and there was a slight difference in the PER timecourse of males vs. females. PER in per04 was undetectable. Two of these mutations, perSLIH and perClk, lie within regions of PER that have not been studied previously and may define important functional domains of this clock protein.

Modeling temperature compensation in chemical and biological oscillators

All physicochemical and biological oscillators maintain a balance between destabilizing reactions (as, for example, intrinsic autocatalytic or amplifying reactions) and stabilizing processes. These two groups of processes tend to influence the period in opposite directions and may lead to temperature compensation whenever their overall influence balances. This principle of "antagonistic balance" has been tested for several chemical and biological oscillators. The Goodwin negative feedback oscillator appears of particular interest for modeling the circadian clocks in Neurospora and Drosophila and their temperature compensation. Remarkably, the Goodwin oscillator not only gives qualitative, correct phase response curves for temperature steps and temperature pulses, but also simulates the temperature behavior of Neurospora frq and Drosophila per mutants almost quantitatively. The Goodwin oscillator predicts that circadian periods are strongly dependent on the turnover of the clock mRNA or clock protein. A more rapid turnover of clock mRNA or clock protein results, in short, a slower turnover in longer period lengths.

Temperature compensation and membrane composition in Neurospora crassa

The link between temperature compensation of the circadian rhythm and temperature-induced adjustment of membrane composition in Neurospora crassa is briefly reviewed. In common with most organisms, Neurospora responds to changes in growth temperature by adjusting its lipid composition, primarily by increasing the degree of unsaturation of its fatty acids at low temperature. This may result in maintenance of either membrane fluidity or phase transition behavior over a range of temperatures. In Neurospora, there are three mutations (frq, cel, and chol-1) that affect temperature compensation of the circadian rhythm; cel and chol-1 are defective in lipid synthesis, and frq interacts with the other two in double-mutant strains. This suggests that lipid metabolism may play a role in temperature compensation of the rhythm, and that the FRQ gene product may also be involved in membrane function, either in regulating lipid composition or as a sensor responding to changes in lipid composition.

Genetics and molecular analysis of circadian rhythms

The first part of this review summarizes the two best understood aspects of the two best understood circadian systems, the feedback oscillators of Neurospora and Drosophila, concentrating on what we know about the frequency (frq), period (per) and timeless (tim) genes. In the second part, the general circadian genetic and molecular literature is surveyed, with an eye to describing what is known from a variety of systems about input to the oscillator (entrainment), and how the oscillator might work and be temperature compensated, in emerging systems including Synechococcus, Gonyaulax, Arabidopsis, hamsters, and mice. Finally, the conversation of the molecular components of clocks is analyzed: both frq and per are widely conserved in their respective phylogenetic classes. Pharmacological data suggests that most other organisms use a day-phased oscillator of the type seen in Neurospora rather than a night-phased oscillator such as in Drosophila.

Quantitative two-dimensional gel electrophoretic analysis of clock-controlled proteins in cultured chick pineal cells: circadian regulation of tryptophan hydroxylase

The progression of the circadian oscillator through its cycle and the circadian rhythm of melatonin production in dissociated chick pineal cultures both require daily de novo protein synthesis during defined circadian phases. To identify specific proteins involved in these two processes, we have performed a quantitative two-dimensional polyacrylamide gel electrophoretic screen of proteins that are synthesized at different times of the day in chick pineal cell cultures. Out of approximately 700 proteins analyzed, we have identified several proteins whose levels of 35S incorporation oscillate in a light/dark cycle. One protein of 56 kDa, pI 6 (p56) undergoes a diurnal oscillation that parallels the melatonin rhythm, reaching a peak early in the night and falling to minimal levels during the day. A second protein of 22 kDa, pI 4.5 (p22) also expresses a diurnal rhythm in 35S incorporation; however, it peaks at the end of the night. The oscillations of both proteins persist, with a reduced amplitude, in constant darkness. Furthermore, the phases of the p56 and p22 rhythms are regulated by the light/dark cycle. Both p56 and p22 appear to be under direct control of the chick pineal circadian oscillator, and therefore can be described as "clock-controlled proteins." We have identified p56 as tryptophan hydroxylase by microsequencing and western blotting. Chick pineal tryptophan hydroxylase also expresses a 24-h oscillation in abundance both in vitro and in vivo. The rhythm in tryptophan hydroxylase expression represents a newly discovered level of regulation of the melatonin synthesis pathway by the circadian clock in chick pineal cells.

Resetting the Drosophila clock by photic regulation of PER and a PER-TIM complex

Circadian clocks can be reset by light stimulation. To investigate the mechanism of this phase shifting, the effects of light pulses on the protein and messenger RNA products of the Drosophila clock gene period (per) were measured. Photic stimuli perturbed the timing of the PER protein and messenger RNA cycles in a manner consistent with the direction and magnitude of the phase shift. In addition, the recently identified clock protein TIM (for timeless) interacted with PER in vivo, and this association was rapidly decreased by light. This disruption of the PER-TIM complex in the cytoplasm was accompanied by a delay in PER phosphorylation and nuclear entry and disruption in the nucleus by an advance in PER phosphorylation and disappearance. These results suggest a mechanism for how a unidirectional environmental signal elicits a bidirectional clock response.

The genetic and molecular dissection of a prototypic circadian system

A great deal is known about this archetypal circadian system, and it is likely that Neurospora will represent the first circadian system in which it will be possible to provide a complete description of the flow of information from the photoreceptor, through the components of oscillator, out to a terminal aspect of regulation. In Neurospora the strongest case has been made for there being a state variable of clock identified (Hall, 1995), it has now been shown that light resetting of the clock is mediated by the rapid light induction of the gene encoding this state variable, and a number of defined clock-regulated output genes have been identified, in two of which the clock-specific parts of the promoters have been localized. In addition to the importance of these factoids themselves, our efforts towards understanding of this system has allowed the development of tools and paradigms (e.g. Loros et al., 1989; Loros and Dunlap, 1991; Aronson et al., 1994a) that will help to pave the way for proving the identity of clock components in more complex systems, for understanding how clocks are regulated by entraining factors, and for showing how time information eventually is used to regulate the behaviors of clock cells, and of whole organisms.

The circadian clock: from molecules to behaviour

Circadian rhythms are a cardinal feature of living organisms. The stereotypical organization of homeostatic, endocrine and behavioural variables around the 24-hour cycle constitutes one of the most conserved attributes among species. It is now well established that circadian rhythmicity is not a learned behaviour, but is genetically transmitted and therefore subject to genetic manipulations. Recent advances in the circadian field have demonstrated that circadian oscillations are cell autonomous, that the circadian mechanism operates through a negative feedback loop and that a growing number of genes is under circadian control. Furthermore, single-gene mutations have been isolated in mammals that have profound effects on circadian behaviour. The production and mapping of one of these mutations in the mouse, an organism about which there exists a wealth of genetic information, should accelerate the elucidation of the molecular events involved in the generation of circadian rhythms in mammals.

An ultrashort clock mutation at the period locus of Drosophila melanogaster that reveals some new features of the fly's circadian system

A rhythm mutant of Drosophila melanogaster was induced by chemical mutagenesis and isolated by testing for locomotor activity rhythms, which in the new variant had periods of approximately 16 hr. The sex-linked mutation responsible for this ultrashort period causes 20-hr rhythms when heterozygous with a normal X. This semidominance notwithstanding, the new mutation was revealed to be an allele of the period (per) gene by noncomplementation with per-null variants, in the sense that females heterozygous for perT (as the ultrafast-clock allele is called) and per- exhibited periods that were much shorter than in the case of perT/+. These tests also revealed in a clearer manner than in previous cases that two "doses" of a fast-clock per mutation lead to appreciably shorter periods than those exhibited by one-dose females whose other per allele is a loss-of-function variant. In light-dark cycles (LD 12:12), flies carrying perT in a genotypic condition leading to free-running periods that are 8 hr faster than normal nevertheless entrained, by phase-shifting that large number of hours each day; the evening peak of locomotor activity was, however, many hours earlier than normal. The use of a newly developed device for monitoring Drosophila eclosion automatically showed that perT exhibits a very marginal emergence rhythm at 25 degrees C, but periodicity of ca. 17-18 hr at 19 degrees. Staining of the per-encoded protein (PER) in sections of perT versus normal pharate adults revealed for the first time that the immunohistochemically detected signal cycles in its intensity in wild-type, in a manner that is similar to the PER rhythm previously demonstrated in adults. The staining cycle in pharate adults expressing perT differed from that of wild-type. Temperature compensation of the adult activity rhythm of perT was found to be faulty, in that periods became appreciably shorter as the flies were heated. However, the mutant exhibited a normal degree of period lengthening when its locomotor activity was monitored in the presence of heavy water. The perT mutation interacted with the long-period Andante allele of the dusky locus in a manner that was anomalous (in comparison to dyAnd interactions with per+ or another short-period per mutation). This and other unique features of perT are discussed from the standpoint of the new mutation's heuristic value, including that which may stimulate a deeper understanding of the period gene's action at the molecular level.

Negative feedback defining a circadian clock: autoregulation of the clock gene frequency

The frequency (frq) locus of Neurospora crassa was originally identified in searches for loci encoding components of the circadian clock. The frq gene is now shown to encode a central component in a molecular feedback loop in which the product of frq negatively regulated its own transcript, which resulted in a daily oscillation in the amount of frq transcript. Rhythmic messenger RNA expression was essential for overt rhythmicity in the organism and no amount of constitutive expression rescued normal rhythmicity in frq loss-of-function mutants. Step reductions in the amount of FRQ-encoding transcript set the clock to a specific and predicted phase. These results establish frq as encoding a central component in a circadian oscillator.

PAS is a dimerization domain common to Drosophila period and several transcription factors

Mutations in the period gene product (PER) can shorten or lengthen the circadian rhythms of Drosophila melanogaster, but its biochemical activity has not been established. PER contains a motif of approximately 270 amino acids whose function is unknown (termed PAS) and which is also present in three transcription factors of the basic-helix-loop-helix (bHLH) type, in the D. melanogaster single-minded gene product (SIM), and in both subunits of the mammalian dioxin receptor complex. We show here that the PER PAS functions in vitro as a novel protein dimerization motif and that it can mediate associations between different members of the PAS protein family. The dimerization efficiency is decreased by several missense mutations in the PAS domain, including the original perL mutation, which lengthens circadian periods from 24 h to 29 h (ref. 1). The results indicate that the PAS domain may function as a dimerization domain in both SIM and the dioxin receptor complex, and that PER may regulate circadian gene transcription partly by interacting with the PAS domain of bHLH--PAS-containing transcription factors.

Stopping the circadian pacemaker with inhibitors of protein synthesis

The requirement for protein synthesis in the mechanism of a circadian pacemaker was investigated by using inhibitors of protein synthesis. Continuous treatment of the ocular circadian pacemaker of the mollusc Bulla gouldiana with anisomycin or cycloheximide substantially lengthened (up to 39 and 52 hr, respectively) the free-running period of the rhythm. To determine whether high concentrations of inhibitor could stop the pacemaker, long pulse treatments of various durations (up to 44 hr) were applied and the subsequent phase of the rhythm was assayed. The observed phases of the rhythm after the treatments were a function of the time of the end of the treatment pulse, but only for treatments which spanned subjective dawn. The results provide evidence that protein synthesis is required in a phase-dependent manner for motion of the circadian pacemaker to continue.

Molecular analysis of the Neurospora clock: cloning and characterization of the frequency and period-4 genes

Genetic analysis of Neurospora crassa has identified many mutants that affect the biological clock. In this article we review the cloning of two of these genes, frq and prd-4. Both genes were isolated using a chromosome walk technique. Subcloning experiments and subsequent Northern analysis of frq implicate the importance of two transcripts that emanate from this locus. In preliminary data, no protein-coding region is evident in the smaller transcript; the larger transcript contains a 962-amino acid open reading frame. The open reading frame shows limited homology to per, a clock gene identified in Drosophila. Sequence analysis of all existing frq alleles suggests that the defect in each case lies within the open reading frame. Successful cloning of the prd-4 gene required walking a distance of greater than 40 kb. A physical map of this region has been constructed using restriction analysis. The dominance-recessive relationship of prd-4 and prd-4+ was established by examining the period lengths of strains harboring a wide range of prd-4/prd-4+ nuclear ratios.

Amplitude model for the effects of mutations and temperature on period and phase resetting of the Neurospora circadian oscillator

This paper analyzes published and unpublished data on phase resetting of the circadian oscillator in the fungus Neurospora crassa and demonstrates a correlation between period and resetting behavior in several mutants with altered periods: As the period increases, the apparent sensitivity to resetting by light and by cycloheximide decreases. Sensitivity to resetting by temperature pulses may also decrease. We suggest that these mutations affect the amplitude of the oscillator and that a change in amplitude is responsible for the observed changes in both period and resetting by several stimuli. As a secondary hypothesis, we propose that temperature compensation of period in Neurospora can be explained by changes in amplitude: As temperature increases, the compensation mechanism may increase the amplitude of the oscillator to maintain a constant period. A number of testable predictions arising from these two hypotheses are discussed. To demonstrate these hypotheses, a mathematical model of a time-delay oscillator is presented in which both period and amplitude can be increased by a change in a single parameter. The model exhibits the predicted resetting behavior: With a standard perturbation, a smaller amplitude produces type 0 resetting and a larger amplitude produces type 1 resetting. Correlations between period, amplitude, and resetting can also be demonstrated in other types of oscillators. Examples of correlated changes in period and resetting behavior in Drosophila and hamsters raise the possibility that amplitude changes are a general phenomenon in circadian oscillators.

Closely watched clocks: molecular analysis of circadian rhythms in Neurospora and Drosophila

Circadian rhythms represent a type of cellular regulation common to most eukaryotes. Analysis of the genetic basis of this phenomenon is beginning to provide information about how clocks function at the molecular level. Surprisingly, the first two cloned 'clock genes', one from a fruit fly and one from a fungus, share some common characteristics both genetically and in the nature of the proteins they encode. In related work, the recent identification and molecular analysis of clock-controlled genes is revealing how biological clocks control gene expression, and may pave the way for the isolation of novel 'clock genes' in the future.

The cellular mechanism of circadian rhythms--a view on evidence, hypotheses and problems

A stable period length is a characteristic property of circadian oscillations. The question about whether higher frequency oscillators (0.5-8 hr) contribute to or establish the stable circadian periodicity cannot be answered at present. A sequential coupling of quantal subcycles appears possible on the basis of known "ultradian" oscillations. There is, however, no supporting evidence for such a concept. Phase response curves of the circadian clock derived from various perturbing pulses allow qualitative conclusions concerning the perturbed clock process. Deductions from computer simulations also allow conclusions about the phase of this oscillatory process. The distinction between processes (a) essential to the clock mechanism, (b) maintaining and controlling the clock (inputs) and (c) depending on the clock (outputs) on the basis of "oscillatory" and "change of psi or tau after perturbation" seems to be useful but not stringent. Protein synthesis may be an essential or input process. Oscillatory changes of this process may be due to periodic translational control or RNA-supply. Circadian changes in protein concentration and/or activity may depend on periodic synthesis, proteolysis, covalent modifications or aggregations. Specific essential proteins have not been identified conclusively. The large overlap between the group of agents and treatments that phase shift the clock and the group that induces stress proteins suggest that the latter may play a role in the controlling (input) or essential domain. The role of membranes in the clock mechanism is not clear: concepts assuming an essential function are based on circumstantial evidence. The membrane potential as well as Ca2+ may be involved in either input or essential function. Ca(2+)-calmodulin may also be important as concluded from inhibitor experiments. It is tempting to assume that a calmodulin-dependent kinase is part of a periodic protein phosphorylation process, yet it is not clear whether the periodic protein phosphorylation that has been observed is essential or is just another output process.

Temperature dependence of phase response curves for drug-induced phase shifts

The effectiveness of drugs active in phase-shifting the circadian rhythm of bioluminescent glow in the unicellular dinoflagellate Gonyaulax polyedra differs, depending upon the time of drug exposure (as pulses). For two drugs tested--cycloheximide and anisomycin, both inhibitors of cytosolic protein synthesis--this function, referred to as the drug phase response curve (dPRC), differs, depending upon the ambient temperature. Since dPRCs may differ at different drug concentrations, the effects observed may be attributable to differences in the effectiveness of or recovery from the drugs at different temperatures.

Comparison of Phase Shifts of the Circadian Rhythm of K Uptake in Lemna gibba G3 by Various Amino Acid Analogs

Phase shifts of the circadian rhythm of K(+) uptake by Lemna gibba G3, caused by pulse administration of various amino acids analogs, were examined and compared. The various phase shifts were not due to any disturbance in the biosynthesis of amino acids, since the effective time of day and direction of the phase shift caused by analogs were not correlated with the standard amino acid which was modified. Effective analogs could be classified into three groups. The first group was effective during the middle subjective day and caused both advances and delays in phase. The second group was effective early in the subjective night, causing large delays and small phase advance. Analogs in the third group shifted the phase as did cycloheximide and were effective at the subjective dawn. Since the analogs of the third group were known to inhibit protein synthesis, it is likely that they shift the phase by lowering the level of some protein(s) important for the clock. By contrast, since the analogs in groups 1 and 2 are known to generate abnormal proteins, the different phase-shifting patterns caused by analogs in groups 1 and 2 suggest that at least two other proteins are important for the circadian timing loop. The amino acid analogs shift the phase as a result of their incorporation into these proteins instead of the standard amino acid. This probably alters the structure and/or activities of these proteins.

The Neurospora clock gene frequency shares a sequence element with the Drosophila clock gene period

The isolation and characterization of single gene mutations affecting the circadian biological clocks of several organisms has left little doubt that circadian rhythms can be subjected to classical genetical analysis. Many of these mutations occur at the same few genetic loci (frequency (frq) in the fungus Neurospora, and period (per) in fruit fly Drosophila); these loci represent the best studied clock-affecting genes known. Mutant strains are usually affected in more than one basic clock property, suggesting an inter-relatedness at the molecular level among these basic properties that would not have been predicted a priori. The extensive background information available concerning the frq locus provides a basis for the molecular dissection of the Neurospora circadian clock--the most minimal circadian system thus far described. We report here the cloning and analysis of the frq locus and show it to be larger and more complex than would have been predicted from the available genetic data. Complete rescue of all of the pleiotropic mutant phenotypes of the recessive frq allele requires transformation with a 7.7-kilobase (kb) region of DNA encoding at least two transcripts. Sequence analysis of this region has allowed the identification of a common element between frq and per which, given the background similarities in their classical genetic characteristics, suggests the possibility of a common element in the clock mechanisms of these two organisms.

Molecular cloning of genes under control of the circadian clock in Neurospora

To investigate the regulation of messenger RNA abundance by circadian clocks, genomic and complementary DNA libraries were screened with complementary DNA probes enriched, by means of sequential rounds of subtractive hybridization, for sequences complementary to transcripts specific to either early morning or early evening cultures of Neurospora. Only two morning-specific genes were identified through this protocol. RNA blot analysis verified that the abundance of the transcripts arising from these genes oscillates with a period of 21.5 hours in a clock wild-type strain and 29 hours in the long-period clock mutant strain frq7. Genetic mapping through the use of restriction fragment length polymorphisms shows the two genes, ccg-1 and ccg-2, to be unlinked. These data provide a view of the extent of clock control of gene expression.