A DOUBLETIME kinase binding domain on the Drosophila PERIOD protein is essential for its hyperphosphorylation, transcriptional repression, and circadian clock function

Natural variation in the Drosophila melanogaster clock gene period modulates splicing of its 3'-terminal intron and mid-day siesta

Drosophila melanogaster exhibits circadian (≅24 hr) regulated morning and evening bouts of activity that are separated by a mid-day siesta. Increases in daily ambient temperature are accompanied by a progressively longer mid-day siesta and delayed evening activity. Presumably, this behavioral plasticity reflects an adaptive response that endows D. melanogaster with the ability to temporally optimize daily activity levels over a wide range of physiologically relevant temperatures. For example, the shift in activity towards the cooler nighttime hours on hot days might minimize the risks associated with exposure to mid-day heat, whereas on cold days activity is favored during the warmer daytime hours. These temperature-induced shifts in the distribution of daily activity are partly based on the thermal sensitive splicing of an intron found in the 3' untranslated region (UTR) of the circadian clock gene termed period (per). As temperature decreases, splicing of this 3'-terminal intron (termed dmpi8) is gradually increased, which is causally linked to a shorter mid-day siesta. Herein we identify several natural polymorphisms in the per 3' UTR from wild-caught populations of flies originating along the east coast of the United States. Two non-intronic closely spaced single nucleotide polymorphisms (SNPs) modulate dmpi8 splicing efficiency, with the least efficiently spliced version associated with a longer mid-day siesta, especially at lower temperatures. Although these SNPs modulate the splicing efficiency of dmpi8 they have little to no effect on its thermal responsiveness, consistent with the notion that the suboptimal 5' and 3' splice sites of the dmpi8 intron are the primary cis-acting elements mediating temperature regulation. Our results demonstrate that natural variations in the per gene can modulate the splicing efficiency of the dmpi8 intron and the daily distribution of activity, providing natural examples for the involvement of dmpi8 splicing in the thermal adaptation of behavioral programs in D. melanogaster.

CULLIN-3 controls TIMELESS oscillations in the Drosophila circadian clock

The ubiquitin ligases CUL-3 and SLMB collaborate to regulate the Drosophila circadian clock by controlling TIMELESS oscillations.

Eukaryotic circadian clocks rely on transcriptional feedback loops. In Drosophila, the PERIOD (PER) and TIMELESS (TIM) proteins accumulate during the night, inhibit the activity of the CLOCK (CLK)/CYCLE (CYC) transcriptional complex, and are degraded in the early morning. The control of PER and TIM oscillations largely depends on post-translational mechanisms. They involve both light-dependent and light-independent pathways that rely on the phosphorylation, ubiquitination, and proteasomal degradation of the clock proteins. SLMB, which is part of a CULLIN-1-based E3 ubiquitin ligase complex, is required for the circadian degradation of phosphorylated PER. We show here that CULLIN-3 (CUL-3) is required for the circadian control of PER and TIM oscillations. Expression of either Cul-3 RNAi or dominant negative forms of CUL-3 in the clock neurons alters locomotor behavior and dampens PER and TIM oscillations in light-dark cycles. In constant conditions, CUL-3 deregulation induces behavioral arrhythmicity and rapidly abolishes TIM cycling, with slower effects on PER. CUL-3 affects TIM accumulation more strongly in the absence of PER and forms protein complexes with hypo-phosphorylated TIM. In contrast, SLMB affects TIM more strongly in the presence of PER and preferentially associates with phosphorylated TIM. CUL-3 and SLMB show additive effects on TIM and PER, suggesting different roles for the two ubiquitination complexes on PER and TIM cycling. This work thus shows that CUL-3 is a new component of the Drosophila clock, which plays an important role in the control of TIM oscillations.

Circadian clocks adjust the physiology and behavior of organisms to the day/night cycle and rely on molecular feedback loops that generate daily oscillations of transcription. In the Drosophila fruit fly, the PERIOD (PER) and TIMELESS (TIM) proteins coordinate the clock–they accumulate during the night, form a complex, and repress their own gene expression in the early morning. The temporal control of this oscillation involves the phosphorylation, ubiquitination, and proteasomal degradation of the PER and TIM proteins. The SUPERNUMERARY LIMBS (SLMB) ubiquitin ligase is known to play a key role in controlling the degradation of phosphorylated PER and TIM. In this study we investigated the role of another ubiquitin ligase, CULLIN-3 (CUL-3). We found that inhibition of CUL-3 activity results in the abolition of rest/activity rhythms in flies and flattens the PER and TIM oscillations. CUL-3 physically interacts and forms a complex with a lowphosphorylated version of TIM in the absence of PER, thereby allowing its accumulation during the night. In contrast, when PER is present SLMB preferentially interacts with phosphorylated TIM, favoring its degradation. The results suggest that CUL-3 and SLMB share the work to control the oscillations of the PER and TIM proteins during the day/night cycle.

Modelling the effect of phosphorylation on the circadian clock of Drosophila

It is by now well known that, at the molecular level, the core of the circadian clock of most living species is a negative feedback loop where some proteins inhibit their own transcription. However, it has recently been shown that post-translational processes, such as phosphorylations, are essential for a correct timing of the clock. Depending on which sites of a circadian protein are phosphorylated, different properties such as degradation, nuclear localization and repressing power can be altered. Furthermore, phosphorylation domains can be related in a positive way, giving rise to consecutive phosphorylations, or in a negative way, hindering phosphorylation at other domains. Here we present a simple mathematical model of a circadian protein having two mutually exclusive domains of phosphorylation. We show that the system has limit cycles that arise from a unique fixed point through a Hopf bifurcation. We find a set of parameters, with realistic values, for which the limit cycle has the same period as the wild type circadian oscillations of the fruit fly. The domains act as a switch, in the sense that alterations in their phosphorylation can alter the period of circadian oscillation in opposite ways, increasing or decreasing the period of the wild type oscillations. In particular, we show that our model is able to reproduce some of the experimental results found for switch-like phosphorylations of the PER protein of the circadian clock of the fly Drosophila melanogaster.

A role for O-GlcNAcylation in setting circadian clock speed

Post-translational modifications of one or more central "clock" proteins, most notably time-of-day-dependent changes in phosphorylation, are critical for setting the pace of circadian (≅24 h) clocks. In animals, PERIOD (PER) proteins are the key state variable regulating circadian clock speed and undergo daily changes in abundance and cytoplasmic-nuclear distribution that are partly driven by a complex phosphorylation program. Here, we identify O-GlcNAcylation (O-GlcNAc) as a critical post-translational modification in circadian regulation that also contributes to setting clock speed. Knockdown or overexpression of Drosophila O-GlcNAc transferase (ogt) in clock cells either shortens or lengthens circadian behavioral rhythms, respectively. The Drosophila PERIOD protein (dPER) is a direct target of OGT and undergoes daily changes in O-GlcNAcylation, a modification that is mainly observed during the first half of the night, when dPER is predominantly located in the cytoplasm. Intriguingly, the timing of when dPER translocates from the cytoplasm to the nucleus is advanced or delayed in flies, wherein ogt expression is reduced or increased, respectively. Our results suggest that O-GlcNAcylation of dPER contributes to setting the correct pace of the clock by delaying the timing of dPER nuclear entry. In addition, OGT stabilizes dPER, suggesting that O-GlcNAcylation has multiple roles in circadian timing systems.

A master CLOCK hard at work brings rhythm to the transcriptome

In this issue of Genes & Development, Abruzzi et al. (pp. 2374-2386) use chromatin immunoprecipitation (ChIP) tiling array assays (ChIP-chip) to show that physical interactions between circadian (≅24-h) clock machineries and genomes are more widespread than previously thought and provide novel insights into how clocks drive daily rhythms in global gene expression.

A new twist on clock protein phosphorylation: a conformational change leads to protein degradation

Progressive phosphorylation of circadian clock proteins is a hallmark of time-keeping. In this issue of Molecular Cell, Querfurth et al. (2011) demonstrate that phosphorylation of Neurospora FRQ induces a conformational change, which can account for its temporally gated degradation.

The role of natural selection in circadian behaviour: a molecular-genetic approach

Circadian rhythms (~24 h) in biochemistry, physiology and behaviour are found in almost all eukaryotes and some bacteria. The elucidation of the molecular components of the 24 h circadian clock in a number of model organisms in recent years has provided an opportunity to assess the adaptive value of variation in clock genes. Laboratory experiments using artificially generated mutants reveal that the circadian period is adaptive in a 24 h world. Natural genetic variation can also be studied, and there are a number of ways in which the signature of natural selection can be detected. These include the study of geographical patterns of genetic variation, which provide a first indication that selection may be at work, and the use of sophisticated statistical neutrality tests, which examine whether the pattern of variation observed is consistent with a selective rather than a neutral (or drift) scenario. Finally, examining the probable selective agents and their differential effects on the circadian phenotype of the natural variants provides the final compelling evidence for selection. We present some examples of how these types of analyses have not only enlightened the evolutionary study of clocks, but have also contributed to a more pragmatic molecular understanding of the function of clock proteins.

NEMO/NLK phosphorylates PERIOD to initiate a time-delay phosphorylation circuit that sets circadian clock speed

The speed of circadian clocks in animals is tightly linked to complex phosphorylation programs that drive daily cycles in the levels of PERIOD (PER) proteins. Using Drosophila, we identify a time-delay circuit based on hierarchical phosphorylation that controls the daily downswing in PER abundance. Phosphorylation by the NEMO/NLK kinase at the "per-short" domain on PER stimulates phosphorylation by DOUBLETIME (DBT/CK1δ/ɛ) at several nearby sites. This multisite phosphorylation operates in a spatially oriented and graded manner to delay progressive phosphorylation by DBT at other more distal sites on PER, including those required for recognition by the F box protein SLIMB/β-TrCP and proteasomal degradation. Highly phosphorylated PER has a more open structure, suggesting that progressive increases in global phosphorylation contribute to the timing mechanism by slowly increasing PER susceptibility to degradation. Our findings identify NEMO as a clock kinase and demonstrate that long-range interactions between functionally distinct phospho-clusters collaborate to set clock speed.

A key temporal delay in the circadian cycle of Drosophila is mediated by a nuclear localization signal in the timeless protein

Regulated nuclear entry of the Period (PER) and Timeless (TIM) proteins, two components of the Drosophila circadian clock, is essential for the generation and maintenance of circadian behavior. PER and TIM shift from the cytoplasm to the nucleus daily, and the length of time that PER and TIM reside in the cytoplasm is an important determinant of the period length of the circadian rhythm. Here we identify a TIM nuclear localization signal (NLS) that is required for appropriately timed nuclear accumulation of both TIM and PER. Transgenic flies with a mutated TIM NLS produced circadian rhythms with a period of ∼30 hr. In pacemaker cells of the brain, PER and TIM proteins rise to abnormally high levels in the cytoplasm of tim(ΔNLS) mutants, but show substantially reduced nuclear accumulation. In cultured S2 cells, the mutant TIM(ΔNLS) protein significantly delays nuclear accumulation of both TIM and wild-type PER proteins. These studies confirm that TIM is required for the nuclear localization of PER and point to a key role for the TIM NLS in the regulated nuclear accumulation of both proteins.

The novel gene twenty-four defines a critical translational step in the Drosophila clock

Daily oscillations of gene expression underlie circadian behaviours in multicellular organisms1. While attention has been focused on transcriptional and posttranslational mechanisms1–3, other posttranscriptional modes have been less clearly delineated. Here we report mutants of a novel Drosophila gene twenty-four (tyf) that display weak behavioural rhythms. Weak rhythms are accompanied by dramatic reductions in the levels of the clock protein PERIOD (PER) as well as more modest effects on TIMELESS (TIM). Nonetheless, PER induction in pacemaker neurons can rescue tyf mutant rhythms. TYF associates with a 5′-cap binding complex, poly(A)-binding protein (PABP) as well as per and tim transcripts. Furthermore, TYF activates reporter expression when tethered to reporter mRNA even in vitro. Taken together, these data suggest that TYF potently activates PER translation in pacemaker neurons to sustain robust rhythms, revealing a novel and important role for translational control in the Drosophila circadian clock.

Molecular genetic analysis of circadian timekeeping in Drosophila

A genetic screen for mutants that alter circadian rhythms in Drosophila identified the first clock gene-the period (per) gene. The per gene is a central player within a transcriptional feedback loop that represents the core mechanism for keeping circadian time in Drosophila and other animals. The per feedback loop, or core loop, is interlocked with the Clock (Clk) feedback loop, but whether the Clk feedback loop contributes to circadian timekeeping is not known. A series of distinct molecular events are thought to control transcriptional feedback in the core loop. The time it takes to complete these events should take much less than 24h, thus delays must be imposed at different steps within the core loop. As new clock genes are identified, the molecular mechanisms responsible for these delays have been revealed in ever-increasing detail and provide an in-depth accounting of how transcriptional feedback loops keep circadian time. The phase of these feedback loops shifts to maintain synchrony with environmental cycles, the most reliable of which is light. Although a great deal is known about cell-autonomous mechanisms of light-induced phase shifting by CRYPTOCHROME (CRY), much less is known about non-cell autonomous mechanisms. CRY mediates phase shifts through an uncharacterized mechanism in certain brain oscillator neurons and carries out a dual role as a photoreceptor and transcription factor in other tissues. Here, I review how transcriptional feedback loops function to keep time in Drosophila, how they impose delays to maintain a 24-h cycle, and how they maintain synchrony with environmental light:dark cycles. The transcriptional feedback loops that keep time in Drosophila are well conserved in other animals, thus what we learn about these loops in Drosophila should continue to provide insight into the operation of analogous transcriptional feedback loops in other animals.

Two distinct modes of PERIOD recruitment onto dCLOCK reveal a novel role for TIMELESS in circadian transcription

Negative transcriptional feedback loops are a core feature of eukaryotic circadian clocks and are based on rhythmic interactions between clock-specific repressors and transcription factors. In Drosophila, the repression of dCLOCK (dCLK)-CYCLE (CYC) transcriptional activity by dPERIOD (dPER) is critical for driving circadian gene expression. Although growing lines of evidence indicate that circadian repressors such as dPER function, at least partly, as molecular bridges that facilitate timely interactions between other regulatory factors and core clock transcription factors, how dPER interacts with dCLK-CYC to promote repression is not known. Here, we identified a small conserved region on dPER required for binding to dCLK, termed CBD (for dCLK binding domain). In the absence of the CBD, dPER is unable to stably associate with dCLK and inhibit the transcriptional activity of dCLK-CYC in a simplified cell culture system. CBD is situated in close proximity to a region that interacts with other regulatory factors such as the DOUBLETIME kinase, suggesting that complex architectural constraints need to be met to assemble repressor complexes. Surprisingly, when dPER missing the CBD (dPER(ΔCBD)) was evaluated in flies the clock mechanism was operational, albeit with longer periods. Intriguingly, the interaction between dPER(ΔCBD) and dCLK is TIM-dependent and modulated by light, revealing a novel and unanticipated in vivo role for TIM in circadian transcription. Finally, dPER(ΔCBD) does not provoke the daily hyperphosphorylation of dCLK, indicating that direct interactions between dPER and dCLK are necessary for the dCLK phosphorylation program but are not required for other aspects of dCLK regulation.

Of switches and hourglasses: regulation of subcellular traffic in circadian clocks by phosphorylation

Investigation of the phosphorylation of circadian clock proteins has shown that this modification contributes to circadian timing in all model organisms. Phosphorylation alters the stability, transcriptional activity and subcellular localization of clock proteins during the course of a day, such that time-of-day-specific phosphorylation encodes information for measuring time and is crucial for the establishment of an approximately 24-h period. One main feature of molecular timekeeping is the daytime-specific nuclear accumulation of clock proteins, which can be regulated by phosphorylation. Here, we discuss increasing knowledge of how subcellular shuttling is regulated in circadian clocks, on the basis of recent observations in Neurospora crassa showing that clock proteins undergo maturation through sequential phosphorylation. In this model organism, clock proteins are regulated by the phosphorylation-dependent modulation of rapid shuttling cycles that alter their subcellular localization in a time-of-day-specific manner.

A hierarchical phosphorylation cascade that regulates the timing of PERIOD nuclear entry reveals novel roles for proline-directed kinases and GSK-3beta/SGG in circadian clocks

The daily timing of when PERIOD (PER) proteins translocate from the cytoplasm to the nucleus is a critical step in clock mechanisms underpinning circadian rhythms in animals. Numerous lines of evidence indicate that phosphorylation plays a prominent role in regulating various aspects of PER function and metabolism, including changes in its daily stability and subcellular distribution. In this report, we show that phosphorylation of serine 661 (Ser661) by a proline-directed kinase(s) is a key phospho-signal on the Drosophila PER protein (dPER) that regulates the timing of its nuclear accumulation. Mutations that block phosphorylation at Ser661 do not affect dPER stability but delay its nuclear entry in key pacemaker neurons, yielding longer behavioral rhythms. Intriguingly, abolishing phosphorylation at Ser661 also attenuates the extent of dPER hyperphosphorylation in vivo, suggesting the phosphorylated state of Ser661 regulates phosphorylation at other sites on dPER. Indeed, we identify Ser657 as a site that is phosphorylated by the glycogen synthase kinase GSK-3β (SHAGGY; SGG) in a manner dependent on priming at Ser661. Although not as dramatic as mutating Ser661, mutations that abolish phosphorylation at Ser657 also lead to longer behavioral periods, suggesting that a multi-kinase hierarchical phosphorylation module regulates the timing of dPER nuclear entry. Together with evidence in mammalian systems, our findings implicate proline-directed kinases in clock mechanisms and suggest that PER proteins are key downstream targets of lithium therapy, a potent inhibitor of GSK-3β used to treat manic depression, a disorder associated with clock malfunction in humans.

Circadian organization of behavior and physiology in Drosophila

Circadian clocks organize behavior and physiology to adapt to daily environmental cycles. Genetic approaches in the fruit fly, Drosophila melanogaster, have revealed widely conserved molecular gears of these 24-h timers. Yet much less is known about how these cell-autonomous clocks confer temporal information to modulate cellular functions. Here we discuss our current knowledge of circadian clock function in Drosophila, providing an overview of the molecular underpinnings of circadian clocks. We then describe the neural network important for circadian rhythms of locomotor activity, including how these molecular clocks might influence neuronal function. Finally, we address a range of behaviors and physiological systems regulated by circadian clocks, including discussion of specific peripheral oscillators and key molecular effectors where they have been described. These studies reveal a remarkable complexity to circadian pathways in this "simple" model organism.

Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA

Transcriptional feedback loops are central to the generation and maintenance of circadian rhythms. In animal systems as well as Neurospora, transcriptional repression is believed to occur by catalytic post-translational events. We report here in the Drosophila model two different mechanisms by which the circadian repressor PERIOD (PER) inhibits CLOCK/CYCLE (CLK/CYC)-mediated transcription. First, PER is recruited to circadian promoters, which leads to the nighttime decrease of CLK/CYC activity. This decrease is proportional to PER levels on DNA, and PER recruitment probably occurs via CLK. Then CLK is released from DNA and sequestered in a strong, approximately 1:1 PER-CLK off-DNA complex. The data indicate that the PER levels bound to CLK change dynamically and are important for repression, first on-DNA and then off-DNA. They also suggest that these mechanisms occur upstream of post-translational events, and that elements of this two-step mechanism likely apply to mammals.

Mathematical model of the Drosophila circadian clock: loop regulation and transcriptional integration

Eukaryotic circadian clocks include interconnected positive and negative feedback loops. The clock-cycle dimer (CLK-CYC) and its homolog, CLK-BMAL1, are key transcriptional activators of central components of the Drosophila and mammalian circadian networks, respectively. In Drosophila, negative loops include period-timeless and vrille; positive loops include par domain protein 1. Clockwork orange (CWO) is a recently discovered negative transcription factor with unusual effects on period, timeless, vrille, and par domain protein 1. To understand the actions of this protein, we introduced a new system of ordinary differential equations to model regulatory networks. The model is faithful in the sense that it replicates biological observations. CWO loop actions elevate CLK-CYC; the transcription of direct targets responds by integrating opposing signals from CWO and CLK-CYC. Loop regulation and integration of opposite transcriptional signals appear to be central mechanisms as they also explain paradoxical effects of period gain-of-function and null mutations.

Sleep triggered by an immune response in Drosophila is regulated by the circadian clock and requires the NFkappaB Relish

Background

Immune challenge impacts behavior in many species. In mammals, this adaptive behavior is often manifested as an increase in sleep. Sleep has therefore been proposed to benefit the host by enhancing immune function and thereby overcome the challenge. To facilitate genetic studies on the relationship between sleep and immune function, we characterized the effect of the immune response on sleep in Drosophila melanogaster. Behavioral features of sleep as well as the innate immune response signaling pathways are well characterized in flies and are highly conserved in mammals.

Results

An immune response induced by infection with Gram-negative bacteria or by aseptic injury increased sleep in flies. The increase in sleep occurred during the morning hours after treatment and the magnitude of the effect was dependent on the time-of-day of inoculation or injury such that night-time treatment had a stronger effect than that during the daytime. This pattern persisted in constant darkness, indicating a role of the circadian clock. Mutants of the circadian clock gene, period, eliminated the increase in sleep observed in the morning, but instead showed enhanced sleep immediately after injury or infection.

Null mutants of the Nuclear Factor κB (NFκB) Relish, which is central to the innate immune response, do not increase sleep in response to injury or infection at any time of day. Instead, they maintain a normal sleep pattern until they die. Expression of a full-length Relish transgene in the fat bodies of Relish mutants restored the morning increase in sleep during an immune response. Fat bodies are a major site of immune signalling in flies and have a key role in host defense.

Conclusions

These data demonstrate that an immune response increases sleep in flies in a manner that is gated by the circadian clock and that requires the NFκB Relish. These findings support a role of sleep in a recovery process and demonstrate a conserved feature of the Drosophila model of sleep.

Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism

Circadian rhythms in mammals are generated by a transcriptional negative feedback loop that is driven primarily by oscillations of PER and CRY, which inhibit their own transcriptional activators, CLOCK and BMAL1. Current models posit that CRY is the dominant repressor, while PER may play an accessory role. In this study, however, constitutive expression of PER, and not CRY1, severely disrupted the clock in fibroblasts and liver. Furthermore, constitutive expression of PER2 in the brain and SCN of transgenic mice caused a complete loss of behavioral circadian rhythms in a conditional and reversible manner. These results demonstrate that rhythmic levels of PER2, rather than CRY1, are critical for circadian oscillations in cells and in the intact organism. Our biochemical evidence supports an elegant mechanism for the disparity: PER2 directly and rhythmically binds to CLOCK:BMAL1, while CRY only interacts indirectly; PER2 bridges CRY and CLOCK:BMAL1 to drive the circadian negative feedback loop.

Post-translational modifications in circadian rhythms

The pace has quickened in circadian biology research. In particular, an abundance of results focused on post-translational modifications (PTMs) is sharpening our view of circadian molecular clockworks. PTMs affect nearly all aspects of clock biology; in some cases they are essential for clock function and in others, they provide layers of regulatory fine-tuning. Our goal is to review recent advances in clock PTMs, help make sense of emerging themes, and spotlight intriguing (and perhaps controversial) new findings. We focus on PTMs affecting the core functions of eukaryotic clocks, in particular the functionally related oscillators in Neurospora crassa, Drosophila melanogaster, and mammalian cells.

Roles of CLOCK phosphorylation in suppression of E-box-dependent transcription

In mammalian circadian clockwork, the CLOCK-BMAL1 heterodimer activates E-box-dependent transcription, while its activity is suppressed by circadian binding with negative regulators, such as CRYs. Here, we found that the CLOCK protein is kept mostly in the phosphorylated form throughout the day and is partly hyperphosphorylated in the suppression phase of E-box-dependent transcription in the mouse liver and NIH 3T3 cells. Coexpression of CRY2 in NIH 3T3 cells inhibited the phosphorylation of CLOCK, whereas CIPC coexpression markedly stimulated phosphorylation, indicating that CLOCK phosphorylation is regulated by a combination of the negative regulators in the suppression phase. CLOCK-BMAL1 purified from the mouse liver was subjected to tandem mass spectrometry analysis, which identified Ser38, Ser42, and Ser427 as in vivo phosphorylation sites of CLOCK. Ser38Asp and Ser42Asp mutations of CLOCK additively and markedly weakened the transactivation activity of CLOCK-BMAL1, with downregulation of the nuclear amount of CLOCK and the DNA-binding activity. On the other hand, CLOCK Delta 19, lacking the CIPC-binding domain, was far less phosphorylated and much more stabilized than wild-type CLOCK in vivo. Calyculin A treatment of cultured NIH 3T3 cells promoted CLOCK phosphorylation and facilitated its proteasomal degradation. Together, these results show that CLOCK phosphorylation contributes to the suppression of CLOCK-BMAL1-mediated transactivation through dual regulation: inhibition of CLOCK activity and promotion of its degradation.

A role for the PERIOD:PERIOD homodimer in the Drosophila circadian clock

Circadian clocks in eukaryotes rely on transcriptional feedback loops, in which clock genes repress their own transcription resulting in molecular oscillations with a period of ∼24 h. In Drosophila, the clock proteins Period (PER) and Timeless (TIM) operate in such a feedback loop, whereby they first accumulate in the cytoplasm of clock cells as a heterodimer. Nuclear translocation of the complex or the individual PER and TIM proteins is followed by repression of per and tim transcription, whereby PER seems to act as the prime repressor. We found that in addition to PER:TIM complexes, functional PER:PER homodimers exist in flies. Specific disruption of PER homodimers results in drastically impaired behavioral and molecular rhythmicity, pointing the biological importance of this clock protein complex. Analysis of PER subcellular distribution and repressor competence in the PER dimer mutant revealed defects in PER nuclear translocation and a disruption of rhythmic period transcription. The striking similarity of these phenotypes with that of reduced CKII activity suggests that the formation or function of the PER dimer is closely linked to this kinase. Our results confirm a previous structural model for PER and provide strong evidence that PER homodimers are important for circadian clock function.

The current models of circadian clocks in flies and mammals involve the formation of complexes between clock proteins in the cytoplasm. These complexes are usually heterodimers (that is, made up of two different clock proteins) and appear to enter the nucleus at certain times of the circadian day in order to shut down their own gene expression by deactivating specific transcription factors. After progressive phosphorylation the repressor proteins eventually are degraded so that a new cycle of transcription can begin. Here we present evidence that in addition to heterodimeric complexes, the clock protein PERIOD (PER) also forms homodimers (pairs of identical proteins). Based on a structural model a PER mutant was designed, which is not able to form homodimers but can still bind to its partner TIMELESS (TIM). Flies expressing this mutant PER protein show abnormal clock function in regard to PER nuclear translocation, repressor activity, and behavioral rhythms. The circadian clock model in flies therefore needs to be extended by adding the PER:PER homodimer as a functional unit. Recent structural studies with mammalian PER proteins suggest that homodimers between clock proteins are an important general feature of eukaryotic clocks.

The circadian molecular clock model needs to be extended by adding the PERIOD:PERIOD homodimer as a functional unit in rhythm generation in Drosophila. Blocking this dimerization leads to faulty nuclear localization, reduced repressor activity, and impaired behavioral rhythms.

Modeling the Drosophila melanogaster circadian oscillator via phase optimization

The circadian clock, which coordinates daily physiological behaviors of most organisms, maintains endogenous (approximately 24 h) cycles and simultaneously synchronizes to the 24-h environment due to its inherent robustness to environmental perturbations coupled with a sensitivity to specific environmental stimuli. In this study, the authors develop a detailed mathematical model that characterizes the Drosophila melanogaster circadian network. This model incorporates the transcriptional regulation of period, timeless, vrille , PAR-domain protein 1, and clock gene and protein counterparts. The interlocked positive and negative feedback loops that arise from these clock components are described primarily through mass-action kinetics (with the exception of regulated gene expression) and without the use of explicit time delays. System parameters are estimated via a genetic algorithm-based optimization of a cost function that relies specifically on circadian phase behavior since amplitude measurements are often noisy and do not account for the unique entrainment features that define circadian oscillations. Resulting simulations of this 29-state ordinary differential equation model comply with fitted wild-type experimental data, demonstrating accurate free-running (23.24-h periodic) and entrained (24-h periodic) circadian dynamics. This model also predicts unfitted mutant phenotype behavior by illustrating short and long periodicity, robust oscillations, and arrhythmicity. This mechanistic model also predicts light-induced circadian phase resetting (as described by the phase-response curve) that are in line with experimental observations.

DOUBLETIME plays a noncatalytic role to mediate CLOCK phosphorylation and repress CLOCK-dependent transcription within the Drosophila circadian clock

Circadian clocks keep time via gene expression feedback loops that are controlled by time-of-day-specific changes in the synthesis, activity, and degradation of transcription factors. Within the Drosophila melanogaster circadian clock, DOUBLETIME (DBT) kinase is necessary for the phosphorylation of PERIOD (PER), a transcriptional repressor, and CLOCK (CLK), a transcriptional activator, as CLK-dependent transcription is being repressed. PER- and DBT-containing protein complexes feed back to repress CLK-dependent transcription, but how DBT promotes PER and CLK phosphorylation and how PER and CLK phosphorylation contributes to transcriptional repression have not been defined. Here, we show that DBT catalytic activity is not required for CLK phosphorylation or transcriptional repression and that PER phosphorylation is dispensable for repressing CLK-dependent transcription. These results support a model in which DBT plays a novel noncatalytic role in recruiting additional kinases that phosphorylate CLK, thereby repressing transcription. A similar mechanism likely operates in mammals, given the conserved activities of PER, DBT, and CLK orthologs.

Activating PER repressor through a DBT-directed phosphorylation switch

Protein phosphorylation plays an essential role in the generation of circadian rhythms, regulating the stability, activity, and subcellular localization of certain proteins that constitute the biological clock. This study examines the role of the protein kinase Doubletime (DBT), a Drosophila ortholog of human casein kinase I (CKI)ɛ/δ. An enzymatically active DBT protein is shown to directly phosphorylate the Drosophila clock protein Period (PER). DBT-dependent phosphorylation sites are identified within PER, and their functional significance is assessed in a cultured cell system and in vivo. The per^S mutation, which is associated with short-period (19-h) circadian rhythms, alters a key phosphorylation target within PER. Inspection of this and neighboring sequence variants indicates that several DBT-directed phosphorylations regulate PER activity in an integrated fashion: Alternative phosphorylations of two adjoining sequence motifs appear to be associated with switch-like changes in PER stability and repressor function.

Most proteins involved in circadian transcriptional feedback loops undergo reversible chemical modifications (called phosphorylation) that regulate their activity in a time-of-day–dependent manner. Doubletime (DBT), a Drosophila kinase, phosphorylates the circadian transcriptional repressor PERIOD (PER). Mutations of dbt shorten or lengthen the period of circadian behavioral rhythms, or abolish the rhythms altogether in flies. A mutation of the human ortholog of dbt, casein kinase I (CKI)δ, has been associated with certain forms of a heritable sleep disorder. The disorder may reflect altered activity of a human PER protein, as the syndrome can also be caused by mutation of a CKIɛ/δ phosphorylation site within PER2. In this study, we locate DBT-directed phosphorylation sites in the Drosophila PER protein, including a DBT target region of PER that was previously shown to regulate DBT activity. Two PER domains within this region appear to serve as alternative targets for DBT. Phosphorylation of the upstream domain seems to suppress phosphorylation elsewhere in the region, producing a stable PER protein with little activity as a transcriptional repressor. However, when phosphorylation of the upstream domain is blocked, downstream DBT targets appear to be phosphorylated, producing a highly active, but short-lived repressor. Our results suggest that ordered patterns of DBT-directed phosphorylation contribute to the timing of PER's function and disappearance, and thus influence the pace of the circadian clock.

Two phosphorylation domains inDrosophila PERIOD protein interact in a switch-like fashion with each other and the kinase DOUBLETIME to regulate PER's stability and activity as a transcriptional repressor in the circadian transcriptional feedback loop.

Control of WHITE COLLAR localization by phosphorylation is a critical step in the circadian negative feedback process

Reversible protein phosphorylation has critical functions in the eukaryotic circadian negative feedback loops. In Neurospora, the FREQUENCY protein closes the circadian negative feedback loop by promoting the phosphorylation of its transcription activator, the WHITE COLLAR complex (WCC) and consequently inhibiting WCC activity. Here we show that protein phosphatase 4 is a novel component of the Neurospora clock by regulating both processes of the circadian negative feedback loop. The disruption of pp4 results in short period rhythms with low amplitude. In addition to its role in regulating FRQ phosphorylation and stability, PP4 also dephosphorylates and activates WCC. In contrast to PP2A, another phosphatase that activates WCC, PP4 has a major function in promoting nuclear entry of WCC. PKA, a WC kinase, inhibits WC nuclear localization. Furthermore, the FRQ-dependent WC phosphorylation promotes WCC cytosolic localization. Together, these results revealed WCC nucleocytoplasmic shuttling as an important step in the circadian negative feedback process and delineated the FRQ-dependent WCC inhibition as a two-step process: the inhibition of WCC DNA-binding activity followed by sequestration of WCC into the cytoplasm.

TIMELESS is an important mediator of CK2 effects on circadian clock function in vivo

Circadian oscillations in clock components are central to generation of self-sustained 24-h periodicity. In the Drosophila molecular clock, accumulation, phosphorylation, and degradation of PERIOD (PER) and TIMELESS (TIM) proteins govern period length. Yet little is known about the kinases that phosphorylate TIM in vivo. It has been shown previously that the protein kinase CK2 phosphorylates TIM in vitro. Here, we identify a role for CK2 in TIM regulation in vivo. Induction of a dominant-negative CK2alpha, CK2alpha(Tik) (Tik), increases TIM protein and tim transcript levels, reduces oscillation amplitude, and results in persistent cytoplasmic TIM localization. Exposure to light and subsequent TIM degradation results in an increase in the fraction of the transcriptional repressor PER that is nuclear and suppression of per and tim RNA levels. TIM protein, but not tim transcript, levels are elevated in Tik mutants in a per(01) background. In contrast, Tik effects on PER are undetectable in a tim(01) background, suggesting that TIM is required for CK2 effects on PER. To identify potential CK2 target sites, we assayed TIM phosphorylation rhythms in a deletion mutant that removes a conserved serine-rich domain and found that TIM protein does not show robust rhythmic changes in mobility by Western blotting, a hallmark of rhythmic phosphorylation. The period lengthening effects in Tik heterozygotes are reduced in a tim(UL) mutant that disrupts a putative CK2 phosphorylation site. Together, these data indicate that TIM is an important mediator of CK2 effects on circadian rhythms.

Drosophila and vertebrate casein kinase Idelta exhibits evolutionary conservation of circadian function

Mutations lowering the kinase activity of Drosophila Doubletime (DBT) and vertebrate casein kinase Iepsilon/delta (CKIepsilon/delta) produce long-period, short-period, and arrhythmic circadian rhythms. Since most ckI short-period mutants have been isolated in mammals, while the long-period mutants have been found mostly in Drosophila, lowered kinase activity may have opposite consequences in flies and vertebrates, because of differences between the kinases or their circadian mechanisms. However, the results of this article establish that the Drosophila dbt mutations have similar effects on period (PER) protein phosphorylation by the fly and vertebrate enzymes in vitro and that Drosophila DBT has an inhibitory C-terminal domain and exhibits autophosphorylation, as does vertebrate CKIepsilon/delta. Moreover, expression of either Drosophila DBT or the vertebrate CKIdelta kinase carrying the Drosophila dbt(S) or vertebrate tau mutations in all circadian cells leads to short-period circadian rhythms. By contrast, vertebrate CKIdelta carrying the dbt(L) mutation does not lengthen circadian rhythms, while Drosophila DBT(L) does. Different effects of the dbt(S) and tau mutations on the oscillations of PER phosphorylation suggest that the mutations shorten the circadian period differently. The results demonstrate a high degree of evolutionary conservation of fly and vertebrate CKIdelta and of the functions affected by their period-shortening mutations.

The phospho-occupancy of an atypical SLIMB-binding site on PERIOD that is phosphorylated by DOUBLETIME controls the pace of the clock

A common feature of animal circadian clocks is the progressive phosphorylation of PERIOD (PER) proteins, which is highly dependent on casein kinase Idelta/epsilon (CKIdelta/epsilon; termed DOUBLETIME [DBT] in Drosophila) and ultimately leads to the rapid degradation of hyperphosphorylated isoforms via a mechanism involving the F-box protein, beta-TrCP (SLIMB in Drosophila). Here we use the Drosophila melanogaster model system, and show that a key step in controlling the speed of the clock is phosphorylation of an N-terminal Ser (S47) by DBT, which collaborates with other nearby phosphorylated residues to generate a high-affinity atypical SLIMB-binding site on PER. DBT-dependent increases in the phospho-occupancy of S47 are temporally gated, dependent on the centrally located DBT docking site on PER and partially counterbalanced by protein phosphatase activity. We propose that the gradual DBT-mediated phosphorylation of a nonconsensus SLIMB-binding site establishes a temporal threshold for when in a daily cycle the majority of PER proteins are tagged for rapid degradation. Surprisingly, most of the hyperphosphorylation is unrelated to direct effects on PER stability. We also use mass spectrometry to map phosphorylation sites on PER, leading to the identification of a number of "phospho-clusters" that explain several of the classic per mutants.

Thermosensitive splicing of a clock gene and seasonal adaptation

Similar to many diurnal animals, the daily distribution of activity in Drosophila exhibits a bimodal pattern with clock-controlled morning and evening peaks separated by a midday "siesta." In prior work, we showed that the thermosensitive splicing of a 3'-terminal intron in the RNA product from the Drosophila period (per) gene (dper) is critical for temperature-induced adjustments in the timing of evening activity. Cold temperatures enhance the splicing efficiency of this intron (termed dmpi8, Drosophila melanogaster per intron 8), an event that stimulates the daily accumulation of dper RNA and protein, leading to earlier evening activity. Conversely, warm temperatures attenuate dmpi8 splicing efficiency contributing to delayed evening activity, likely ensuring that flies avoid activity during the hot midday sun when they are at increased risk of desiccation. Here, we discuss the underlying molecular mechanisms governing the thermosensitive splicing of dmpi8 and how it contributes to seasonal changes in the daily activity patterns of Drosophila. On a broader perspective, RNA-RNA interactions likely have fundamental roles in the thermal adaptation of life forms to the daily and seasonal changes in temperature.

A PER/TIM/DBT interval timer for Drosophila's circadian clock

Circadian rhythms in Drosophila are supported by a negative feedback loop, in which PERIOD (PER) and Timeless (TIM) shut down their own transcription as they translocate once a day from the cytoplasm of clock-containing cells to the nucleus. Period length is partially determined by an interval of cytoplasmic retention of the TIM and PER proteins. To study this process, we examined PER/TIM/Doubletime (DBT) physical interactions and nuclear translocation by imaging individual cultured Drosophila cells. Using live cell video microscopy and green fluorescent protein (GFP) tags, we observed dynamic patterns of stability and localization for DBT, PER, and TIM that resembled those previously found in vivo. These studies suggest that a cytoplasmic interval timer regulates nuclear translocation of these proteins. The cultured cell assay provides a potent system to study interactions among new and known genes involved in the generation of circadian behavior.

Circadian transcription contributes to core period determination in Drosophila

The Clock–Cycle (CLK–CYC) heterodimer constitutes a key circadian transcription complex in Drosophila. CYC has a DNA-binding domain but lacks an activation domain. Previous experiments also indicate that most of the transcriptional activity of CLK–CYC derives from the glutamine-rich region of its partner CLK. To address the role of transcription in core circadian timekeeping, we have analyzed the effects of a CYC–viral protein 16 (VP16) fusion protein in the Drosophila system. The addition of this potent and well-studied viral transcriptional activator (VP16) to CYC imparts to the CLK–CYC-VP16 complex strongly enhanced transcriptional activity relative to that of CLK–CYC. This increase is manifested in flies expressing CYC-VP16 as well as in S2 cells. These flies also have increased levels of CLK–CYC direct target gene mRNAs as well as a short period, implicating circadian transcription in period determination. A more detailed examination of reporter gene expression in CYC-VP16–expressing flies suggests that the short period is due at least in part to a more rapid transcriptional phase. Importantly, the behavioral effects require a period (per) promoter and are therefore unlikely to be merely a consequence of generally higher PER levels. This indicates that the CLK–CYC-VP16 behavioral effects are a consequence of increased per transcription. All of this also suggests that the timing of transcriptional activation and not the activation itself is the key event responsible for the behavioral effects observed in CYC-VP16-expressing flies. The results taken together indicate that circadian transcription contributes to core circadian function in Drosophila.

The existence of circadian clocks, which allow organisms to predict daily changes in their environments, have been recognized for centuries, yet only recently has the molecular machinery responsible for their generation been uncovered. The current model in animals posits that interlocked feedback loops of transcription-translation produce these 24-hour rhythms. In fruit flies, the transcription loop contains a key activator complex, composed of the transcription factors Clock and Cycle. This CLK-CYC complex stimulates the synthesis of repressor proteins like Period and Timeless, which repress the activator complex. The synthesis–repression cycle takes precisely 24 hours under environmental conditions that influence the circadian period. An almost identical process relies on the ortholog proteins CLK-BMAL in mammals. Recent findings have challenged the transcription-translation feedback model and suggest that circadian transcription is an output process and that the post-translational modification of clock proteins is the real central pacemaker mechanism. In the present study, we have manipulated the levels and strength of the CLK-CYC complex. The results demonstrate that its activity is vital for proper period determination and thus indicate that the transcriptional feedback loop is part of the core circadian mechanism.

Organisms keep circadian rhythms and use interlocked transcriptional-translational feedback loops as part of the mechanism. This study highlights the importance of transcription for timekeeping.

G protein-coupled receptor kinase 2 is required for rhythmic olfactory responses in Drosophila

BACKGROUND

The Drosophila circadian clock controls rhythms in the amplitude of odor-induced electrophysiological responses that peak during the middle of night. These rhythms are dependent on clocks in olfactory sensory neurons (OSNs), suggesting that odorant receptors (ORs) or OR-dependent processes are under clock control. Because responses to odors are initiated by heteromeric OR complexes that form odor-gated and cyclic-nucleotide-activated cation channels, we tested whether regulators of ORs were under circadian-clock control.

RESULTS

The levels of G protein-coupled receptor kinase 2 (Gprk2) messenger RNA and protein cycle in a circadian-clock-dependent manner with a peak around the middle of the night in antennae. Gprk2 overexpression in OSNs from wild-type or cyc(01) flies elicits constant high-amplitude electroantennogram (EAG) responses to ethyl acetate, whereas Gprk2 mutants produce constant low-amplitude EAG responses. ORs accumulate to high levels in the dendrites of OSNs around the middle of the night, and this dendritic localization of ORs is enhanced by GPRK2 overexpression at times when ORs are primarily localized in the cell body.

CONCLUSIONS

These results support a model in which circadian-clock-dependent rhythms in GPRK2 abundance control the rhythmic accumulation of ORs in OSN dendrites, which in turn control rhythms in olfactory responses. The enhancement of OR function by GPRK2 contrasts with the traditional role of GPRKs in desensitizing activated receptors and suggests that GPRK2 functions through a fundamentally different mechanism to modulate OR activity.

Ac-ing the clock

Circadian clock proteins are modified in many different ways. The best-studied posttranslational modification is phosphorylation, with well-known kinases and phosphatases regulating the function and stability of clock proteins. Degradation of these proteins usually involves ubiquitylation or sumoylation, and some of the relevant E3 ligases are known. In addition, Hirayama et al. recently identified acetylation as a clock regulatory mechanism.

Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop

Regulation of circadian clock components by phosphorylation plays essential roles in clock functions and is conserved from fungi to mammals. In the Neurospora circadian negative feedback loop, FREQUENCY (FRQ) protein inhibits WHITE COLLAR (WC) complex activity by recruiting the casein kinases CKI and CKII to phosphorylate the WC proteins, resulting in the repression of frq transcription. On the other hand, CKI and CKII progressively phosphorylate FRQ to promote FRQ degradation, a process that is a major determinant of circadian period length. Here, by using whole-cell isotope labeling and quantitative mass spectrometry methods, we show that the WC-1 phosphorylation events critical for the negative feedback process occur sequentially-first by a priming kinase, then by the FRQ-recruited casein kinases. We further show that the cyclic AMP-dependent protein kinase A (PKA) is essential for clock function and inhibits WC activity by serving as a priming kinase for the casein kinases. In addition, PKA also regulates FRQ phosphorylation, but unlike CKI and CKII, PKA stabilizes FRQ, similar to the stabilization of human PERIOD2 (hPER2) due to the phosphorylation at the familial advanced sleep phase syndrome (FASPS) site. Thus, PKA is a key clock component that regulates several critical processes in the circadian negative feedback loop.

Dominant-negative CK2alpha induces potent effects on circadian rhythmicity

Circadian clocks organize the precise timing of cellular and behavioral events. In Drosophila, circadian clocks consist of negative feedback loops in which the clock component PERIOD (PER) represses its own transcription. PER phosphorylation is a critical step in timing the onset and termination of this feedback. The protein kinase CK2 has been linked to circadian timing, but the importance of this contribution is unclear; it is not certain where and when CK2 acts to regulate circadian rhythms. To determine its temporal and spatial functions, a dominant negative mutant of the catalytic alpha subunit, CK2α^Tik, was targeted to circadian neurons. Behaviorally, CK2α^Tik induces severe period lengthening (∼33 h), greater than nearly all known circadian mutant alleles, and abolishes detectable free-running behavioral rhythmicity at high levels of expression. CK2α^Tik, when targeted to a subset of pacemaker neurons, generates period splitting, resulting in flies exhibiting both long and near 24-h periods. These behavioral effects are evident even when CK2α^Tik expression is induced only during adulthood, implicating an acute role for CK2α function in circadian rhythms. CK2α^Tik expression results in reduced PER phosphorylation, delayed nuclear entry, and dampened cycling with elevated trough levels of PER. Heightened trough levels of per transcript accompany increased protein levels, suggesting that CK2α^Tik disturbs negative feedback of PER on its own transcription. Taken together, these in vivo data implicate a central role of CK2α function in timing PER negative feedback in adult circadian neurons.

The molecular mechanism that governs organization of physiology and behavior into 24-h rhythms is a conserved transcriptional feedback process that is strikingly similar across distinct phyla. Notably, cyclic phosphorylation of negative feedback regulators is critical to time molecular rhythms. Indeed, mutation of a putative phosphoacceptor site in the human PERIOD2 gene, a key negative regulator, is associated with Advanced Sleep Phase Syndrome. This study reveals a critical role for the protein kinase CK2 for setting the period of behavioral and molecular oscillations in Drosophila. Circadian phenotypes due to CK2 disruption are due to a direct requirement in adult circadian pacemakers. These findings further demonstrate that CK2 modification of the negative feedback regulator PERIOD alters its cyclical phosphorylation, protein abundance, nuclear translocation, and transcriptional repression activity. These studies place CK2 as a central kinase in circadian timing.

A small conserved domain of Drosophila PERIOD is important for circadian phosphorylation, nuclear localization, and transcriptional repressor activity

We identify in this study a 27-amino-acid motif which is conserved between the Drosophila melanogaster period protein (PER) and the three mammalian PERs. Characterization of PER lacking this motif (PER Delta) shows that it is important for phosphorylation of Drosophila PER by casein kinase I epsilon (CKI epsilon; doubletime protein or DBT) and CKII. S2 cell assays indicate that the domain also contributes significantly to PER nuclear localization as well as to PER transcriptional repressor activity. These two phenomena appear linked, since PER Delta transcriptional repressor activity in S2 cells was restored when nuclear localization was facilitated. Two less direct assays of PER Delta activity in flies can be interpreted similarly. The separate assay of nuclear import and export suggests that the domain functions in part to facilitate PER phosphorylation within the cytoplasm, which in turn promotes nuclear entry. As there is evidence that the kinases also function within the nucleus to promote transcriptional repression, we suggest that there is a subsequent collaboration between phosphorylated PER and the kinases to repress CLK-CYC activity, probably through the phosphorylation of CLK. This is then followed by additional PER phosphorylation, which occurs within the nucleus and leads to PER degradation.

Posttranslational control of the Neurospora circadian clock

The eukaryotic circadian clocks are composed of autoregulatory circadian negative feedback loops that include both positive and negative elements. Investigations of the Neurospora circadian clock system have elucidated many of the basic mechanisms that underlie circadian rhythms, including negative feedback and light and temperature entrainment common to all eukaryotic clocks. The conservation of the posttranslational regulators in divergent circadian systems suggests that the processes mediating the modification and degradation of clock proteins may be the common foundation that allows the evolution of circadian clocks in eukaryotic systems. In this chapter, we summarize recent studies of the Neurospora circadian clock with emphasis on posttranslational regulation in the circadian negative feedback loop.