WC-2 mediates WC-1-FRQ interaction within the PAS protein-linked circadian feedback loop of Neurospora

Stoichiometric relationship among clock proteins determines robustness of circadian rhythms

The mammalian circadian oscillator is primarily driven by an essential negative feedback loop comprising a positive component, the CLOCK-BMAL1 complex, and a negative component, the PER-CRY complex. Numerous studies suggest that feedback inhibition of CLOCK-BMAL1 is mediated by time-dependent physical interaction with its direct target gene products PER and CRY, suggesting that the ratio between the negative and positive complexes must be important for the molecular oscillator and rhythm generation. We explored this idea by altering expression of clock components in fibroblasts derived from Per2(Luc) and Per mutant mice, a cell system extensively used to study in vivo clock mechanisms. Our data demonstrate that the stoichiometric relationship between clock components is critical for the robustness of circadian rhythms and provide insights into the mechanistic organization of the negative feedback loop. Our findings may explain why certain mutant mice or cells are arrhythmic, whereas others are rhythmic, and suggest that robustness of circadian rhythms can be increased even in wild-type cells by modulating the stoichiometry.

Regulation of the activity and cellular localization of the circadian clock protein FRQ

Eukaryotic circadian clocks employ autoregulatory negative feedback loops to control daily rhythms. In the filamentous fungus Neurospora, FRQ, FRH, WC-1, and WC-2 are the core components of the circadian negative feedback loop. To close the transcription-based negative feedback loop, the FRQ-FRH complex inhibits the activity of the WC complex in the nucleus by promoting the casein kinases-mediated WC phosphorylation. Despite its essential role in the nucleus, most FRQ is found in the cytoplasm. In this study, we mapped the FRQ regions that are important for its cellular localization. We show that the C-terminal part of FRQ, particularly the FRQ-FRH interaction domain, plays a major role in controlling FRQ localization. Both the mutation of the FRQ-FRH interaction domain and the down-regulation of FRH result in the nuclear enrichment of FRQ, suggesting that FRH regulates FRQ localization via a physical interaction. To study the role of FRQ phosphorylation, we examined the FRQ localization in wild-type as well as an array of FRQ kinase, FRQ phosphatase, and FRQ phosphorylation site mutants. Collectively, our results suggest that FRQ phosphorylation does not play a significant role in regulating its cellular localization. Instead, we find that phosphorylation of FRQ inhibits its transcriptional repressor activity in the circadian negative feedback loop. Such an effect is achieved by inhibiting the ability of FRQ to interact with WCC and casein kinase 1a. Our results indicate that the rhythmic FRQ phosphorylation profile observed is an important part of the negative feedback mechanism that drives robust circadian gene expression.

Genetic and molecular characterization of a blue light photoreceptor MGWC-1 in Magnaporth oryzae

Three key factors involved in successful plant disease development include the presence of a susceptible host, a virulent pathogen, and a disease-conducive environment. Our understanding of how environmental factors influence disease-conducive or disease-suppressive conditions, and how a pathogen advantageously capitalizes on them, is quite limited. Utilizing the model pathosystem Magnaporthe oryzae-Oryza sativa, we found a significant light-dependent disease suppression. Our genetic data suggest that the blue-light receptor MGWC-1 in M. oryzae is involved in light-dependent disease suppression during the dark-phase (disease-conducive light condition) immediately after pathogen-host contact. Sensing "darkness" is accomplished by MGWC-1, a blue-light receptor in M. oryzae. To explore the potential molecular mechanisms of light-dependent disease suppression we performed a genome-wide microarray experiment and identified several groups of gene families that are differentially regulated during the light-to-dark transition. Our genetic and molecular data provide insights into how a fungal pathogen utilizes ambient light signals for successful disease development.

Circadian oscillators in eukaryotes

The biological clock, present in nearly all eukaryotes, has evolved such that organisms can adapt to our planet's rotation in order to anticipate the coming day or night as well as unfavorable seasons. As all modern high-precision chronometers, the biological clock uses oscillation as a timekeeping element. In this review, we describe briefly the discovery, historical development, and general properties of circadian oscillators. The issue of temperature compensation (TC) is discussed, and our present understanding of the underlying genetic and biochemical mechanisms in circadian oscillators are described with special emphasis on Neurospora crassa, mammals, and plants.

Neurospora illuminates fungal photoreception

Light not only is indispensable as an energy source for life on earth but also serves as an essential environmental cue conveying the information of daily and seasonal time to organisms across different kingdoms. Although the molecular mechanisms underlying light responses are actively explored in various light-sensitive organisms, these studies are either hindered by the complexity of the systems or an incomplete familiarity with the light signaling components involved in the scheme. Therefore, study of a simple and well-characterized model system is desirable to expand our knowledge of basic properties underlying the regulation of biological light responses. This review will briefly introduce the basic light sensing machinery in Neurospora crassa, a filamentous fungus, and then focus on the most recent advances in employing Neurospora as a model to study light signaling cascades, photoadaptation, and circadian clock-modulated effects in eukaryotic cells. Also, we will summarize the functions of a number of putative photoreceptors in Neurospora, and discuss the implications of the study of Neurospora to the field of fungal photobiology and some challenges for future studies.

VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase to alter light and clock responses in Neurospora

The photoreceptor and PAS/LOV protein VIVID (VVD) modulates blue-light signaling and influences light and temperature responses of the circadian clock in Neurospora crassa. One of the main actions of VVD on the circadian clock is to influence circadian clock phase by regulating levels of the transcripts encoded by the central clock gene frequency (frq). How this regulation is achieved is unknown. Here we show that VVD interacts with complexes central for circadian clock and blue-light signaling, namely the WHITE-COLLAR complex (WCC) and FREQUENCY-interacting RNA helicase (FRH), a component that complexes with FRQ to mediate negative feedback control in Neurospora. VVD interacts with FRH in the absence of WCC and FRQ but does not seem to control the exosome-mediated negative feedback loop. Instead, VVD acts to modulate the transcriptional activity of the WCC.

Physical interaction between VIVID and white collar complex regulates photoadaptation in Neurospora

Photoadaptation, the ability to attenuate a light response on prolonged light exposure while remaining sensitive to escalating changes in light intensity, is essential for organisms to decipher time information appropriately, yet the underlying molecular mechanisms are poorly understood. In Neurospora crassa, VIVID (VVD), a small LOV domain containing blue-light photoreceptor protein, affects photoadaptation for most if not all light-responsive genes. We report that there is a physical interaction between VVD and the white collar complex (WCC), the primary blue-light photoreceptor and the transcription factor complex that initiates light-regulated transcriptional responses in Neurospora. Using two previously characterized VVD mutants, we show that the level of interaction is correlated with the level of WCC repression in constant light and that even light-insensitive VVD is sufficient partly to regulate photoadaptation in vivo. We provide evidence that a functional GFP-VVD fusion protein accumulates in the nucleus on light induction but that nuclear localization of VVD does not require light. Constitutively expressed VVD alone is sufficient to change the dynamics of photoadaptation. Thus, our results demonstrate a direct molecular connection between two of the most essential light signaling components in Neurospora, VVD and WCC, illuminating a previously uncharacterized process for light-sensitive eukaryotic cells.

A role in the regulation of transcription by light for RCO-1 and RCM-1, the Neurospora homologs of the yeast Tup1-Ssn6 repressor

The activation of gene transcription by light is transient since light-dependent mRNA accumulation ceases after long exposures to light. This phenomenon, photoadaptation, has been observed in plants and fungi, and allows the perception of changes in light intensities. In the fungus Neurosporacrassa photoadaptation involves the transient binding of the photoresponsive White Collar Complex (WCC) to the promoters of light-regulated genes. We show that RCO-1 and RCM-1, the Neurospora homologs of the components of the yeast Tup1-Ssn6 repressor complex, participate in photoadaptation. Mutation in either rco-1 or rcm-1 result in high and sustained accumulation of mRNAs for con-10 and other light-regulated genes after long exposures to light. The mutation of rco-1 increased the sensitivity to light for con-10 activation and delayed synthesis and/or degradation of con-10 and con-6 mRNAs without altering the amount or the light-dependent phosphorylation of the photoreceptor WC-1. RCO-1 and RCM-1 are located in the Neurospora nuclei were they regulate gene transcription. We show that RCO-1 and RCM-1 participate in the light-transduction pathway of Neurospora and has a role in photoadaptation by repressing gene transcription after long exposures to light.

Robustness from flexibility in the fungal circadian clock

Background

Robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. A key challenge is to identify the structures in biological circuits that confer system-level properties such as robustness. Circadian clocks allow organisms to adapt to the predictable changes of the 24-hour day/night cycle by generating endogenous rhythms that can be entrained to the external cycle. In all organisms, the clock circuits typically comprise multiple interlocked feedback loops controlling the rhythmic expression of key genes. Previously, we showed that such architectures increase the flexibility of the clock's rhythmic behaviour. We now test the relationship between flexibility and robustness, using a mathematical model of the circuit controlling conidiation in the fungus Neurospora crassa.

Results

The circuit modelled in this work consists of a central negative feedback loop, in which the frequency (frq) gene inhibits its transcriptional activator white collar-1 (wc-1), interlocked with a positive feedback loop in which FRQ protein upregulates WC-1 production. Importantly, our model reproduces the observed entrainment of this circuit under light/dark cycles with varying photoperiod and cycle duration. Our simulations show that whilst the level of frq mRNA is driven directly by the light input, the falling phase of FRQ protein, a molecular correlate of conidiation, maintains a constant phase that is uncoupled from the times of dawn and dusk. The model predicts the behaviour of mutants that uncouple WC-1 production from FRQ's positive feedback, and shows that the positive loop enhances the buffering of conidiation phase against seasonal photoperiod changes. This property is quantified using Kitano's measure for the overall robustness of a regulated system output. Further analysis demonstrates that this functional robustness is a consequence of the greater evolutionary flexibility conferred on the circuit by the interlocking loop structure.

Conclusions

Our model shows that the behaviour of the fungal clock in light-dark cycles can be accounted for by a transcription-translation feedback model of the central FRQ-WC oscillator. More generally, we provide an example of a biological circuit in which greater flexibility yields improved robustness, while also introducing novel sensitivity analysis techniques applicable to a broader range of cellular oscillators.

Reversible phosphorylation subserves robust circadian rhythms by creating a switch in inactivating the positive element

Reversible phosphorylation of proteins is ubiquitous in circadian systems, but the role it plays in generating rhythmicity is not completely understood. A common mechanism for most circadian rhythms involves a negative feedback loop between the positive and negative elements. Here, we built a minimal model for the Neurospora crassa circadian clock based on the core negative feedback loop and the protein FREQUENCY (FRQ)-dependent phosphorylation of the White Collar Complex (WCC). The model can reproduce basic features of the clock, such as the period length, phase relationship, and entrainment to light/dark cycles. We found that the activity of WCC can be controlled by FRQ in a switchlike manner owing to zero-order ultrasensitivity. WCC is inactivated when FRQ level crosses a threshold from below. As a result, low cooperativity in transcriptional activation is sufficient for circadian rhythms, and the level of active WCC exhibits spiky oscillations. Such oscillations are robust to molecular noise and may subserve controlling circadian output. Therefore, the core negative feedback together with phosphorylation of the positive element can ensure robust circadian rhythms. Our work provides insights into the critical roles of posttranslational modification in circadian clocks.

Circadian rhythms in Neurospora crassa: dynamics of the clock component frequency visualized using a fluorescent reporter

The frequency (frq) gene of Neurospora crassa has long been considered essential to the function of this organism's circadian rhythm. Increasingly, deciphering the coupling of core oscillator genes such as frq to the output pathways of the circadian rhythm has become a major focus of circadian research. To address this coupling it is critical to have a reporter of circadian activity that can deliver high resolution spatial and temporal information about the dynamics of core oscillatory proteins such as FRQ. However, due to the difficulty of studying the expression of circadian rhythm genes in aerobic N. crassa cultures, little is known about the dynamics of this gene under physiologically realistic conditions. To address these issues we report a fluorescent fusion to the frq gene using a codon optimized version of the mCherry gene. To trace the expression and accumulation of FRQ-mCherryNC (FRQ-mCh) during the circadian rhythm, growing vegetative hyphae were scanned every hour under confocal microscopy (100x). Fluorescence of FRQ-mCh was detected only at the growing edge of the colony, and located in the cytoplasm and nuclei of vegetative hyphae for a distance of approximately 150-200microm from the apices of leading hyphae. When driven by the frq promoter, apparently there was also a second FRQ entrance into the nucleus during the circadian cycle; however the second entrance had a lower accumulation level than the first entrance. Thus this fluorescent fusion protein has proven useful in tracking the spatial dynamics of the frq protein and has indicated that the dynamics of the FRQ protein's nuclear trafficking may be more complex than previously realized.

FRQ-interacting RNA helicase mediates negative and positive feedback in the Neurospora circadian clock

The Neurospora circadian oscillator comprises FREQUENCY (FRQ) and its transcription activator, the White Collar Complex (WCC). Repression of WCC's transcriptional activity by FRQ via negative feedback is indispensable for clock function. An unbiased genetic screen that targeted mutants with defects in negative feedback regulation yielded a fully viable arrhythmic strain bearing a novel allele of FRQ-interacting RNA helicase (frh), an essential gene that encodes a putative exosome component protein. In the allele, frh(R806H), clock function is completely disturbed, while roles of FRQ-interacting RNA helicase (FRH) essential for viability are left intact. FRH(R806H) still interacts with FRQ, but interaction between the FRQ-FRH(R806H) complex (FFC) and WCC is severely affected. Phosphorylation of WC-1 is reduced in the mutant leading to constantly elevated WCC activity, which breaks the negative feedback loop. WCC levels are considerably reduced in the mutant, especially those of WC-1, consistent both with loss of positive feedback (FRQ-dependent WC-1 stabilization) and with a reduced level of the FRQ-mediated WCC phosphorylation that leads to high WCC activity accompanied by rapid transcription-associated turnover. FRH overexpression promotes WC-1 accumulation, confirming that FRH together with FRQ plays a role in WC-1 stabilization. Identification of a viable allele of frh, displaying virtually complete loss of both negative and positive circadian feedback, positions FRH as a core component of the central oscillator that is permissive for rhythmicity but appears not to modulate periodicity. Moreover, the results suggest that there are clock-specific roles for FRH that are distinct from the predicted essential exosome-associated functions for the protein.

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.

Activity of the circadian transcription factor White Collar Complex is modulated by phosphorylation of SP-motifs

Posttranslational modifications, particularly phosphorylation, regulate activity, stability and localization of proteins in circadian clocks, thereby contributing to a stable oscillation with a period of approximately 24h. The White Collar Complex (WCC) is the central transcription factor of the circadian clock of Neurospora crassa. Its activity is regulated in a circadian manner by rhythmic phosphorylation, mediated by the clock protein Frequency (FRQ). Here we present purification of TAP-tagged WCC and identification of novel phosphorylation sites of WC-1 and WC-2, all of which appear to be proline directed. Exchange of a single WC-2 serine residue (S433) to alanine or aspartate affects WCC-dependent transcription and circadian period, suggesting an important role of WC-2 S433 phosphorylation for WCC activity and circadian timing.

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.

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.

Closing the circadian negative feedback loop: FRQ-dependent clearance of WC-1 from the nucleus

In Neurospora crassa, a transcription factor, WCC, activates the transcription of frq. FRQ forms homodimers as well as complexes with an RNA helicase, FRH, and the WCC, and translocates into the nucleus to inactivate the WCC, closing the time-delayed negative feedback loop. The detailed mechanism for closing this loop, however, remains incompletely understood. In particular within the nucleus, the low amount of FRQ compared with that of WC-1 creates a conundrum: How can the nuclear FRQ inactivate the larger amount of WCC? One possibility is that FRQ might function as a catalytic component in phosphorylation-dependent inhibition. However, in silico experiments reveal that stoichiometric noncatalytic binding and inhibition can generate a robust oscillator, even when nuclear FRQ levels are substantially lower than nuclear WCC, so long as there is FRQ-dependent clearance of WC-1 from the nucleus. Based on this model, we can predict and now demonstrate that WC-1 stability cycles, that WC-1 is stable in the absence of FRQ, and that physical binding between FRQ and WCC is essential for closure of the negative feedback loop. Moreover, and consistent with a noncatalytic clearance-based model for inhibition, appreciable amounts of the nuclear FRQ:WCC complex accumulate at some times of day, comprising as much as 10% of the nuclear WC-1.

A circadian clock in Neurospora: how genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a day

Neurospora has proven to be a tractable model system for understanding the molecular bases of circadian rhythms in eukaryotes. At the core of the circadian oscillatory system is a negative feedback loop in which two transcription factors, WC-1 and WC-2, act together to drive expression of the frq gene. WC-2 enters the promoter region of frq coincident with increases in frq expression and then exits when the cycle of transcription is over, whereas WC-1 can always be found there. FRQ promotes the phosphorylation of the WCs, thereby decreasing their activity, and phosphorylation of FRQ then leads to its turnover, allowing the cycle to reinitiate. By understanding the action of light and temperature on frq and FRQ expression, the molecular basis of circadian entrainment to environmental light and temperature cues can be understood, and recently a specific role for casein kinase 2 has been found in the mechanism underlying circadian temperature-compensation. These data promise molecular explanations for all of the canonical circadian properties of this model system, providing biochemical answers and regulatory logic that may be extended to more complex eukaryotes including humans.

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.

Interlocked feedback loops of the circadian clock of Neurospora crassa

Circadian clocks drive daily rhythms in physiology and behaviour, and thus allow organisms to better adapt to rhythmic changes in the environment. Circadian oscillators are cell-autonomous systems, which generate via transcriptional, post-transcriptional, translational and post-translational control mechanisms a daily activity-rhythm of a circadian transcription factor complex. According to recent models, this complex of transcription factors controls directly or indirectly expression of a large number of genes, and thus generates the potential to modulate physiological processes in a rhythmic fashion. The basic principles of the generation of circadian oscillation are similar in all eukaryotic systems. The circadian clock of the filamentous fungus Neurospora crassa is well characterized at the molecular level. Focusing on the molecular properties, interactions and post-translational modifications of the core Neurospora clock proteins WHITE COLLAR-1, WHITE COLLAR-2, FREQUENCY and VIVID, this review summarizes our knowledge of the molecular basis of circadian time keeping in Neurospora. Moreover, we discuss the mechanisms by which environmental cues like light and temperature entrain and reset this circadian system.

Isoform switching facilitates period control in the Neurospora crassa circadian clock

A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neurospora crassa circadian network incorporating experimental work showing that temperature alters the balance of translation between a short and long form of the FREQUENCY (FRQ) protein. This is used to discuss period control and functionality for the Neurospora system. The model reproduces a broad range of key experimental data on temperature dependence and rhythmicity, both in wild-type and mutant strains. We present a simple mechanism utilising the presence of the FRQ isoforms (isoform switching) by which period control could have evolved, and argue that this regulatory structure may also increase the temperature range where the clock is robustly rhythmic.

Simulating dark expressions and interactions of frq and wc-1 in the Neurospora circadian clock

Circadian rhythms are considered to play an essential part in the adaptation of organisms to their environments. The occurrence of circadian oscillations appears to be based on the presence of transcriptional-translational negative feedback loops. In Neurospora crassa, the protein FREQUENCY (FRQ) is part of such a negative feedback loop apparently by a direct interaction with its transcription factor WHITE COLLAR-1 (WC-1). Based on the observation that nuclear FRQ levels are significantly lower than nuclear WC-1 levels, it was suggested that FRQ would act more like a catalyst in inhibiting WC-1 rather than binding to WC-1 and making an inactive FRQ:WC-1 complex. Intrigued by this hypothesis, we constructed a model for the Neurospora circadian clock, which includes expression of the frq and the wc-1 genes and their possible interactions. The model suggests that even small amounts of nuclear FRQ-protein are capable of inhibiting frq transcription in a rhythmic manner by binding to WC-1 and promoting its degradation. Our model predicts the importance of a FRQ dependent degradation of WC-1 in closing the negative feedback loop. The model shows good agreement with experimental levels in nuclear and cytosolic FRQ and WC-1, their phase relationships, and several clock mutant phenotypes.

The Neurospora crassa circadian clock

The filamentous fungus Neurospora crassa is one of a handful of model organisms that has proven tractable for dissecting the molecular basis of a eukaryotic circadian clock. Work on Neurospora and other eukaryotic and prokaryotic organisms has revealed that a limited set of clock genes and clock proteins are required for generating robust circadian rhythmicity. This molecular clockwork is tuned to the daily rhythms in the environment via light- and temperature-sensitive pathways that adjust its periodicity and phase. The circadian clockwork in turn transduces temporal information to a large number of clock-controlled genes that ultimately control circadian rhythms in physiology and behavior. In summarizing our current understanding of the molecular basis of the Neurospora circadian system, this chapter aims to elucidate the basic building blocks of model eukaryotic clocks as we understand them today.

Execution of the circadian negative feedback loop in Neurospora requires the ATP-dependent chromatin-remodeling enzyme CLOCKSWITCH

In the Neurospora circadian system, the transcription factors White Collar-1 (WC-1) and White Collar-2 (WC-2) activate expression of frq, whose gene product inhibits its own expression. The WC proteins are thought to form an obligate complex; however, chromatin immunoprecipitation (ChIP) indicates that WC-2 binds to the frq promoter in a rhythmic fashion, whereas WC-1 is bound continuously. Small oscillations in histone acetylation are detected over the circadian cycle with a marked reduction upon light-induced activation. Nuclease accessibility experiments indicate chromatin rearrangement at the frq promoter; therefore, 19 genes with homology to ATP-dependent chromatin-remodeling enzymes were deleted and the strains examined for clock phenotypes. One gene, designated clockswitch (csw-1), is required for clock function; its product localizes to the frq promoter, is required for proper frq expression, and has an impact on chromatin structure. The data suggest that CSW-1 regulates accessibility of promoter DNA, thus generating the sharp transition from the transcriptionally active to the repressed state.

A genetic network for the clock of Neurospora crassa

A diverse array of organisms from bacteria to humans may have evolved the ability to tell time in the presence or absence of external environmental cues. In the lowly bread mould, Neurospora crassa, biomolecular reactions involving the white-collar-1 (wc-1), white-collar-2 (wc-2), and frequency (frq) genes and their products constitute building blocks of a biological clock. Here we use genetic network models to explain quantitatively, from a systems perspective, how these building blocks interact, and how a complex trait like clock oscillation emerges from these interactions. We use a recently developed method of genetic network identification to find an ensemble of oscillating network models quantitatively consistent with available RNA and protein profiling data on the N. crassa clock. Predicted key features of the N. crassa clock system are a dynamically frustrated closed feedback loop, cooperativity in frq gene activation, and/or WC-1/WC-2 protein complex deactivation and substantial posttranscriptional enhancement of wc-1 RNA lifetime. Measuring the wc-1 mRNA lifetime provides a critical test of the genetic networks.

Circadian output, input, and intracellular oscillators: insights into the circadian systems of single cells

Circadian output comprises the business end of circadian systems in terms of adaptive significance. Work on Neurospora pioneered the molecular analysis of circadian output mechanisms, and insights from this model system continue to illuminate the pathways through which clocks control metabolism and overt rhythms. In Neurospora, virtually every strain examined in the context of rhythms bears the band allele that helps to clarify the overt rhythm in asexual development. Recent cloning of band showed it to be an allele of ras-1 and to affect a wide variety of signaling pathways yielding enhanced light responses and asexual development. These can be largely phenocopied by treatments that increase levels of intracellular reactive oxygen species. Although output is often unidirectional, analysis of the prd-4 gene provided an alternative paradigm in which output feeds back to affect input. prd-4 is an allele of checkpoint kinase-2 that bypasses the requirement for DNA damage to activate this kinase; FRQ is normally a substrate of activated Chk2, so in Chk2(PRD-4), FRQ is precociously phosphorylated and the clock cycles more quickly. Finally, recent adaptation of luciferase to fully function in Neurospora now allows the core FRQ/WCC feedback loop to be followed in real time under conditions where it no longer controls the overt rhythm in development. This ability can be used to describe the hierarchical relationships among FRQ-Less Oscillators (FLOs) and to see which are connected to the circadian system. The nitrate reductase oscillator appears to be connected, but the oscillator controlling the long-period rhythm elicited upon choline starvation appears completely disconnected from the circadian system; it can be seen to run with a very long noncompensated 60-120-hour period length under conditions where the circadian FRQ/WCC oscillator continues to cycle with a fully compensated circadian 22-hour period.

Fungal photoreceptors: sensory molecules for fungal development and behaviour

Light regulates fungal development and behaviour and activates metabolic pathways. In addition, light is one of the many signals that fungi use to perceive and interact with the environment. In the ascomycete Neurospora crassa blue light is perceived by the white collar (WC) complex, a protein complex formed by WC-1 and WC-2. WC-1 is a protein with a flavin-binding domain and a zinc-finger domain, and interacts with WC-2, another zinc-finger domain protein. The WC complex operates as a photoreceptor and a transcription factor for blue-light responses in Neurospora. Proteins similar to WC-1 and WC-2 have been described in other fungi, suggesting a general role for the WC complex as a fungal receptor for blue light. The ascomycete Aspergillus nidulans uses red light perceived by a fungal phytochrome as a signal to regulate sexual and asexual development. In addition, other photoreceptors, rhodopsins and cryptochromes, have been identified in fungi, but their functional relevance has not been elucidated. The investigation of fungal light responses provides an opportunity to understand how fungi perceive the environment and to identify the mechanisms involved in the regulation by light of cellular development and metabolism.

Western blotting

Western blotting is one of the most commonly used biochemical techniques to detect a specific protein from a mixture of proteins such as tissue extracts. Antibodies to the specific antigen are used to detect the protein. The mixture of proteins is resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to a membrane. A specific antigen immobilized on the membrane is detected and visualized by a primary antibody, a secondary antibody-peroxidase conjugate, and a chemiluminescent reagent.

Complexity of the Neurospora crassa circadian clock system: multiple loops and oscillators

Organisms from bacteria to humans use a circadian clock to control daily biochemical, physiological, and behavioral rhythms. We review evidence from Neurospora crassa that suggests that the circadian clock is organized as a network of genes and proteins that form coupled evening- and morning-specific oscillatory loops that can function autonomously, respond differently to environmental inputs, and regulate phase-specific outputs. There is also evidence for coupled morning and evening oscillator loops in plants, insects, and mammals, suggesting conservation of clock organization. From a systems perspective, fungi provide a powerful model organism for investigating oscillator complexity, communication between oscillators, and addressing reasons why the system has evolved to be so complex.

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.

CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop

The eukaryotic circadian oscillators consist of circadian negative feedback loops. In Neurospora, it was proposed that the FREQUENCY (FRQ) protein promotes the phosphorylation of the WHITE COLLAR (WC) complex, thus inhibiting its activity. The kinase(s) involved in this process is not known. In this study, we show that the disruption of the interaction between FRQ and CK-1a (a casein kinase I homolog) results in the hypophosphorylation of FRQ, WC-1, and WC-2. In the ck-1a(L) strain, a knock-in mutant that carries a mutation equivalent to that of the Drosophila dbt(L) mutation, FRQ, WC-1, and WC-2 are hypophosphorylated. The mutant also exhibits ~32 h circadian rhythms due to the increase of FRQ stability and the significant delay of FRQ progressive phosphorylation. In addition, the levels of WC-1 and WC-2 are low in the ck-1a(L) strain, indicating that CK-1a is also important for the circadian positive feedback loops. In spite of its low accumulation in the ck-1a(L) strain, the hypophosphorylated WCC efficiently binds to the C-box within the frq promoter, presumably because it cannot be inactivated through FRQ-mediated phosphorylation. Furthermore, WC-1 and WC-2 are also hypophosphorylated in the cka(RIP) strain, which carries the disruption of the catalytic subunit of casein kinase II. In the cka(RIP) strain, WCC binding to the C-box is constantly high and cannot be inhibited by FRQ despite high FRQ levels, resulting in high levels of frq RNA. Together, these results suggest that CKI and CKII, in addition to being the FRQ kinases, mediate the FRQ-dependent phosphorylation of WCs, which inhibit their activity and close the circadian negative feedback loop.

Transcriptional and post-transcriptional regulation of the circadian clock of cyanobacteria and Neurospora

Circadian clocks are self-sustained oscillators modulating rhythmic transcription of large numbers of genes. Clock-controlled gene expression manifests in circadian rhythmicity of many physiological and behavioral functions. In eukaryotes, expression of core clock components is organized in a network of interconnected positive and negative feedback loops. This network is thought to constitute the pacemaker that generates circadian rhythmicity. The network of interconnected loops is embedded in a supra-net via a large number of interacting factors that affect expression and function of core clock components on transcriptional and post-transcriptional levels. In particular, phosphorylation and dephosphorylation of clock components are critical processes ensuring robust self-sustained circadian rhythmicity and entrainment of clocks to external cues. In cyanobacteria, three clock proteins have the capacity to generate a self-sustained circadian rhythm of autophosphorylation and dephosphorylation independent of transcription and translation. This phosphorylation rhythm regulates the function of these clock components, which then facilitate rhythmic gene transcription, including negative feedback on their own genes. In this article, we briefly present the mechanism of clock function in cyanobacteria. We then discuss in detail the contribution of transcriptional feedback and protein phosphorylation to various functional aspects of the circadian clock of Neurospora crassa.

Molecular mechanism of light responses in Neurospora: from light-induced transcription to photoadaptation

Blue light regulates many molecular and physiological activities in a large number of organisms. In Neurospora crassa, a eukaryotic model system for studying blue-light responses, the transcription factor and blue-light photoreceptor WHITE COLLAR-1 (WC-1) and its partner WC-2 are central to blue-light sensing. Neurospora's light responses are transient, that is, following an initial acute phase of induction, light-regulated processes are down-regulated under continuous illumination, a phenomenon called photoadaptation. The molecular mechanism(s) of photoadaptation are not well understood. Here we show that a common mechanism controls the light-induced transcription of immediate early genes (such as frq, al-3, and vvd) in Neurospora, in which light induces the binding of identical large WC-1/WC-2 complexes (L-WCC) to the light response elements (LREs) in their promoters. Using recombinant proteins, we show that the WC complexes are functional without the requirement of additional factors. In vivo, WCC has a long period photocycle, indicating that it cannot be efficiently used for repeated light activation. Contrary to previous expectations, we demonstrate that the light-induced hyperphosphorylation of WC proteins inhibits bindings of the L-WCC to the LREs. We show that, in vivo, due to its rapid hyperphosphorylation, L-WCC can only bind transiently to LREs, indicating that WCC hyperphosphorylation is a critical process for photoadaptation. Finally, phosphorylation was also shown to inhibit the LRE-binding activity of D-WCC (dark WC complex), suggesting that it plays an important role in the circadian negative feedback loop.

Degradation of the Neurospora circadian clock protein FREQUENCY through the ubiquitin–proteasome pathway

Phosphorylation of the Neurospora circadian clock protein FREQUENCY (FRQ) promotes its degradation through the ubiquitin–proteasome pathway. Ubiquitination of FRQ requires FWD-1 (F-box/WD-40 repeat-containing protein-1), which is the substrate-recruiting subunit of an SCF (SKP/Cullin/F-box)-type ubiquitin ligase. In the fwd-1 mutant strains, FRQ degradation is defective, resulting in the accumulation of hyperphosphorylated FRQ and the loss of the circadian rhythmicities. The CSN (COP9 signalosome) promotes the function of SCF complexes in vivo. But in vitro, deneddylation of cullins by CSN inhibits SCF activity. In Neurospora, the disruption of the csn-2 subunit impairs FRQ degradation and compromises the normal circadian functions. These defects are due to the dramatically reduced levels of FWD-1 in the csn-2 mutant, a result of its rapid degradation. Other components of the SCFFWD−1 complex, SKP-1 and CUL-1 are also unstable in the mutant. These results establish important roles for SCFFWD−1 and CSN in the circadian clock of Neurospora and suggest that they are conserved components of the eukaryotic circadian clocks. In addition, these findings resolve the CSN paradox and suggest that the major function of CSN is to maintain the stability of SCF ubiquitin ligases in vivo.

Delay-induced stochastic oscillations in gene regulation

The small number of reactant molecules involved in gene regulation can lead to significant fluctuations in intracellular mRNA and protein concentrations, and there have been numerous recent studies devoted to the consequences of such noise at the regulatory level. Theoretical and computational work on stochastic gene expression has tended to focus on instantaneous transcriptional and translational events, whereas the role of realistic delay times in these stochastic processes has received little attention. Here, we explore the combined effects of time delay and intrinsic noise on gene regulation. Beginning with a set of biochemical reactions, some of which are delayed, we deduce a truncated master equation for the reactive system and derive an analytical expression for the correlation function and power spectrum. We develop a generalized Gillespie algorithm that accounts for the non-Markovian properties of random biochemical events with delay and compare our analytical findings with simulations. We show how time delay in gene expression can cause a system to be oscillatory even when its deterministic counterpart exhibits no oscillations. We demonstrate how such delay-induced instabilities can compromise the ability of a negative feedback loop to reduce the deleterious effects of noise. Given the prevalence of negative feedback in gene regulation, our findings may lead to new insights related to expression variability at the whole-genome scale.

Circuit topology and the evolution of robustness in two-gene circadian oscillators

Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules, with similar results. This suggests that the same principles govern the evolution of robustness on different levels of biological organization. The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness.

Protein kinase C modulates light responses in Neurospora by regulating the blue light photoreceptor WC-1

The Neurospora protein kinase C (NPKC) is a regulator of light responsive genes. We have studied the function of NPKC in light response by investigating its biochemical and functional interaction with the blue light photoreceptor white-collar 1 (WC-1), showing that activation of NPKC leads to a significant decrease in WC-1 protein levels. Furthermore, we show that WC-1 and NPKC interact in a light-regulated manner in vivo, and that protein kinase C (PKC) phosphorylates WC-1 in vitro. We designed dominant negative and constitutively active forms of PKC which are able to induce either a large increase of WC-1 protein level or a strong reduction respectively. Moreover, these changes in PKC activity result in an altered light response. As WC-1 is a key component of Neurospora circadian clock and regulates the clock oscillator component FRQ we investigated the effect of NPKC-mutated forms on FRQ levels. We show that changes in PKC activity affect FRQ levels and the robustness of the circadian clock. Together these data identify NPKC as a novel component of the Neurospora light signal transduction pathway that modulates the circadian clock.

Transcriptional Feedback of Neurospora Circadian Clock Gene by Phosphorylation-Dependent Inactivation of Its Transcription Factor

The circadian clock protein Frequency (FRQ) feedback-regulates its own expression by inhibiting its transcriptional activator, White Collar Complex (WCC). We present evidence that FRQ regulates the bulk of WCC through modulation of its phosphorylation status rather than via direct complex formation. In the absence of FRQ, WCC is hypophosphorylated and transcriptionally active, while WCC is hyperphosphorylated and transcriptionally inactive when FRQ is expressed. The phosphorylation status of WCC changes rhythmically over a circadian cycle. Dephosphorylation and activation of WCC depend on protein phosphatase 2A (PP2A), and WCC is a substrate of PP2A in vitro. Hypophosphorylated WCC binds to the clock box of the frq promoter even in the presence of FRQ, while binding of hyperphosphorylated WCC is compromised even when FRQ is depleted. We propose that negative feedback in the circadian clock of Neurospora is mediated by FRQ, which rhythmically promotes phosphorylation of WCC, functionally equivalent to a cyclin recruiting cyclin-dependent kinase to its targets.

The COP9 signalosome regulates the Neurospora circadian clock by controlling the stability of the SCFFWD-1 complex

The COP9 signalosome (CSN) promotes the function of SCF-type cullin-based ubiquitin ligase complexes in vivo. Paradoxically, removal of the Nedd8 modification of cullins by CSN inhibits the ubiquitin ligase activity of SCF complexes in vitro. Ubiquitination-mediated degradation of the Neurospora circadian clock protein FREQUENCY (FRQ) is critical for clock function. Ubiquitination of FRQ requires FWD-1, the substrate-recruiting subunit of an SCF complex. Here we show that disruption of a subunit of CSN (csn-2) impairs the degradation of FRQ and compromises its normal circadian expression. A FRQ-independent oscillator drives conidiation in the csn-2 mutant, resulting in a 2-d conidiation rhythm that persists in constant darkness (DD), constant light (LL), light-to-dark (LD) transitions, and temperature cycles. Strikingly, the levels of FWD-1 are drastically reduced in csn-2 mutant, explaining the impaired degradation of FRQ. Reduction of FWD-1 levels in the mutant requires its F-box, suggesting that its degradation is due to autoubiquitination. In addition, SKP-1 and CUL-1 of the SCF(FWD-1) complex are also unstable in the mutant. Therefore, our results establish an important role of CSN in the circadian clock of Neurospora. Our findings also reconcile the CSN paradox and suggest that a major function of CSN is to maintain the stability of SCF ubiquitin ligases in vivo.

The dst1 gene involved in mushroom photomorphogenesis of Coprinus cinereus encodes a putative photoreceptor for blue light

The homobasidiomycete Coprinus cinereus exhibits remarkable photomorphogenesis during fruiting-body development. Under proper light conditions, fruiting-body primordia proceed to the maturation phase in which basidia in the pileus undergo meiosis, producing sexual spores, followed by stipe elongation and pileus expansion for efficient dispersal of the spores. In the continuous darkness, however, the primordia do not proceed to the maturation phase but are etiolated: the pileus and stipe tissues at the upper part of the primordium remain rudimentary and the basal part of the primordium elongates, producing "dark stipe." In this study we genetically analyzed five strains that produce dark stipes even if light conditions promoting the maturation are given and then characterized one of them, Uar801 (dst1-1). The dst1 gene was cloned as a DNA fragment that rescues the dst1-1 mutation. Dst1 is predicted to be a protein of 1175 amino acids that contains two PAS domains, a coiled-coil structure, and a putative, glutamine-rich, transcriptional activation domain (AD). One of the PAS domains exhibits significant similarity to the LOV domains of known blue-light receptors, suggesting that Dst1 is a blue-light receptor of C. cinereus. The dst1-1 mutation is predicted to truncate the putative AD in the C-terminal region.

Functional consequences of a CKIdelta mutation causing familial advanced sleep phase syndrome

Familial advanced sleep phase syndrome (FASPS) is a human behavioural phenotype characterized by early sleep times and early-morning awakening. It was the first human, mendelian circadian rhythm variant to be well-characterized, and was shown to result from a mutation in a phosphorylation site within the casein kinase I (CKI)-binding domain of the human PER2 gene. To gain a deeper understanding of the mechanisms of circadian rhythm regulation in humans, we set out to identify mutations in human subjects leading to FASPS. We report here the identification of a missense mutation (T44A) in the human CKIdelta gene, which results in FASPS. This mutant kinase has decreased enzymatic activity in vitro. Transgenic Drosophila carrying the human CKIdelta-T44A gene showed a phenotype with lengthened circadian period. In contrast, transgenic mice carrying the same mutation have a shorter circadian period, a phenotype mimicking human FASPS. These results show that CKIdelta is a central component in the mammalian clock, and suggest that mammalian and fly clocks might have different regulatory mechanisms despite the highly conserved nature of their individual components.

Light-independent Phosphorylation of WHITE COLLAR-1 Regulates Its Function in the Neurospora Circadian Negative Feedback Loop

Phosphorylation is a major regulatory mechanism controlling circadian clocks. In the Neurospora circadian clock, the PER-ARNT-SIM (PAS) domain-containing transcription factor, WHITE COLLAR (WC)-1, acts both as the blue light photoreceptor of the clock and as a positive element in the circadian negative feedback loop in constant darkness, by activating the transcription of the frequency (frq) gene. To understand the role of WC-1 phosphorylation, five in vivo WC-1 phosphorylation sites, located immediately downstream of the WC-1 zinc finger DNA binding domain, were identified by tandem mass spectrometry using biochemically purified endogenous WC-1 protein. Mutations of these phosphorylation sites suggest that they are major WC-1 phosphorylation sites under constant conditions but are not responsible for the light-induced hyperphosphorylation of WC-1. Although phosphorylation of these sites does not affect the light function of WC-1, strains carrying mutations of these sites show short period, low amplitude, or arrhythmic conidiation rhythms in constant darkness. Furthermore, normal or slightly higher levels of frq mRNA and FRQ proteins were observed in a mutant strain containing mutations of all five sites despite its low WC-1 levels. Together, these data suggest that phosphorylation of these sites negatively regulates the function of WC-1 in the circadian negative feedback loop and is important for the function of the Neurospora circadian clock.

A nitrate-induced frq-less oscillator in Neurospora crassa

When nitrate is the only nitrogen source, Neurospora crassa's nitrate reductase (NR) shows endogenous oscillations in its nitrate reductase activity (NRA) on a circadian time scale. These NRA oscillations can be observed in darkness or continuous light conditions and also in a frq(9) mutant in which no functional FRQ protein is formed. Even in a white-collar-1 knockout mutant, NRA oscillations have been observed, although with a highly reduced amplitude. This indicates that the NRA oscillations are not a simple output rhythm of the white-collar-driven frq oscillator but may be generated by another oscillator that contains the nit-3 autoregulatory negative feedback loop as a part. In this negative feedback loop, a product in the reaction chain catalyzed by nitrate reductase, probably glutamine, induces repression of the nitrate reductase gene and thus downregulates its own production. This is the first example of an endogenous, nutritionally induced daily rhythm with known molecular components that is observed in the absence of an intact FRQ protein.

A genetic selection for circadian output pathway mutations in Neurospora crassa

In most organisms, circadian oscillators regulate the daily rhythmic expression of clock-controlled genes (ccgs). However, little is known about the pathways between the circadian oscillator(s) and the ccgs. In Neurospora crassa, the frq, wc-1, and wc-2 genes encode components of the frq-oscillator. A functional frq-oscillator is required for rhythmic expression of the morning-specific ccg-1 and ccg-2 genes. In frq-null or wc-1 mutant strains, ccg-1 mRNA levels fluctuate near peak levels over the course of the day, whereas ccg-2 mRNA remains at trough levels. The simplest model that fits the above observations is that the frq-oscillator regulates a repressor of ccg-1 and an activator of ccg-2. We utilized a genetic selection for mutations that affect the regulation of ccg-1 and ccg-2 by the frq-oscillator. We find that there is at least one mutant strain, COP1-1 (circadian output pathway derived from ccg-1), that has altered expression of ccg-1 mRNA, but normal ccg-2 expression levels. However, the clock does not appear to simply regulate a repressor of ccg-1 and an activator of ccg-2 in two independent pathways, since in our selection we identified three mutant strains, COP1-2, COP1-3, and COP1-4, in which a single mutation in each strain affects the expression levels and rhythmicity of both ccg-1 and ccg-2.