Light reception and circadian behavior in 'blind' and 'clock-less' mutants of Neurospora crassa

A period without PER: understanding 24-hour rhythms without classic transcription and translation feedback loops

Since Ronald Konopka and Seymour Benzer's discovery of the gene Period in the 1970s, the circadian rhythm field has diligently investigated regulatory mechanisms and intracellular transcriptional and translation feedback loops involving Period, and these investigations culminated in a 2017 Nobel Prize in Physiology or Medicine for Michael W. Young, Michael Rosbash, and Jeffrey C. Hall. Although research on 24-hour behavior rhythms started with Period, a series of discoveries in the past decade have shown us that post-transcriptional regulation and protein modification, such as phosphorylation and oxidation, are alternatives ways to building a ticking clock.

The Neurospora Circadian System

The eukaryotic filamentous fungus Neurospora crassa has proven to be a durable and dependable model system for the analysis of the cellular and molecular bases of circadian rhythms. Pioneering genetic analyses identified clock genes, and beginning with the cloning of frequency ( frq), work over the past 2 decades has revealed the molecular basis of a core circadian clock feedback loop that has illuminated our understanding of circadian oscillators in microbes, plants, and animals. In this transcription/translation-based feedback loop, a heterodimer of the White Collar-1 (WC-1) and WC-2 proteins acts both as the circadian photoreceptor and, in the dark, as a transcription factor that promotes the expression of the frq gene. FRQ dimerizes and feeds back to block the activity of its activators (making a negative feedback loop), as well as feeding forward to promote the synthesis of its activator, WC-1. Phosphorylation of FRQ by several kinases leads to its ubiquitination and turnover, releasing the WC-1/WC-2 dimer to reactivate frq expression and restart the circadian cycle. Light resetting of the clock can be understood through the rapid light induction of frq expression and temperature resetting through the influence of elevated temperaturesin driving higher levels of FRQ. Several FRQ- and WC-independent, noncircadian FRQ-less oscillators (FLOs) have been described, each of which appears to regulate aspects of Neurospora growth or development. Overall, the FRQ/white collar complex feedback loop appears to coordinate the circadian system through its activity to regulate downstream-target clock-controlled genes, either directly or via regulation of driven FLOs.

Photoperiodism in Neurospora Crassa

Plants and animals use day or night length for seasonal control of reproduction and other biological functions. Overwhelming evidence suggests that this photoperiodic mechanism relies on a functional circadian system. Recent progress has defined how flowering time in plants is regulated by photoperiodic control of output pathways, but the underlying mechanisms of photoperiodism remain to be described. The authors investigate photoperiodism in a genetic model system for circadian rhythms research, Neurospora crassa. They find that both propagation and reproduction respond systematically to photoperiod. Furthermore, a nonreproductive light-regulated function is also enhanced under certain photoperiodic conditions. All of these photoperiodic responses require a functional circadian clock, in that they are absent in a clock mutant. Night break experiments show that measuring night length is one of the mechanisms used for photoperiod assessment. This represents the first formal report of photoperiodism in the fungi.

Analysis of Circadian Rhythms in the Basal Filamentous Ascomycete Pyronema confluens

Many organisms use circadian clocks to adapt to daily changes in the environment. Major insights into the molecular mechanisms of circadian oscillators have been gained through studies of the model organism Neurospora crassa; however, little is known about molecular components of circadian clocks in other fungi. An important part of the N. crassa circadian clock is the frequency (frq) gene, homologs of which can be found in Sordariomycetes, Dothideomycetes, and Leotiomycetes, but not Eurotiomycetes. Recently, we identified a frq homolog in Pyronema confluens, a member of the early-diverging Pezizomycete lineage of filamentous ascomycetes. The P. confluens FRQ shares many conserved domains with the N. crassa FRQ. However, there is no known morphological phenotype showing overt circadian rhythmicity in P. confluens. To investigate whether a molecular clock is present, we analyzed frq transcription in constant darkness, and found circadian oscillation of frq with a peak in the subjective morning. This rhythm was temperature compensated. To identify additional clock-controlled genes, we performed RNA sequencing of two time points (subjective morning and evening). Circadian expression of two morning-specific genes was verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR) over a full time course, whereas expression of two putative morning-specific and five putative evening-specific genes could not be verified as circadian. frq expression was synchronized, but not entrained by light. In summary, we have found evidence for two of the three main properties of circadian rhythms (free-running rhythm, temperature compensation) in P. confluens, suggesting that a circadian clock with rhythmically expressed frq is present in this basal filamentous ascomycete.

Using circadian entrainment to find cryptic clocks

Three properties are most often attributed to the circadian clock: a ca. 24-h free-running rhythm, temperature compensation of the circadian rhythm, and its entrainment to zeitgeber cycles. Relatively few experiments, however, are performed under entrainment conditions. Rather, most chronobiology protocols concern constant conditions. We have turned this paradigm around and used entrainment to study the circadian clock in organisms where a free-running rhythm is weak or lacking. We describe two examples therein: Caenorhabditis elegans and Saccharomyces cerevisiae. By probing the system with zeitgeber cycles that have various structures and amplitudes, we can demonstrate the establishment of systematic entrained phase angles in these organisms. We conclude that entrainment can be utilized to discover hitherto unknown circadian clocks and we discuss the implications of using entrainment more broadly, even in model systems that show robust free-running rhythms.

A novel cryptochrome-dependent oscillator in Neurospora crassa

Several lines of evidence suggest that the circadian clock is constructed of multiple molecular feedback oscillators that function to generate robust rhythms in organisms. However, while core oscillator mechanisms driving specific behaviors are well described in several model systems, the nature of other potential circadian oscillators is not understood. Using genetic approaches in the fungus Neurospora crassa, we uncovered an oscillator mechanism that drives rhythmic spore development in the absence of the well-characterized FRQ/WCC oscillator (FWO) and in constant light, conditions under which the FWO is not functional. While this novel oscillator does not require the FWO for activity, it does require the blue-light photoreceptor CRYPTOCHROME (CRY); thus, we call it the CRY-dependent oscillator (CDO). The CDO was uncovered in a strain carrying a mutation in cog-1 (cry-dependent oscillator gate-1), has a period of ∼1 day in constant light, and is temperature-compensated. In addition, cog-1 cells lacking the circadian blue-light photoreceptor WC-1 respond to blue light, suggesting that alternate light inputs function in cog-1 mutant cells. We show that the blue-light photoreceptors VIVID and CRY compensate for each other and for WC-1 in CRY-dependent oscillator light responses, but that WC-1 is necessary for circadian light entrainment.

Interconnections of reactive oxygen species homeostasis and circadian rhythm in Neurospora crassa

SIGNIFICANCE

Both circadian rhythm and the production of reactive oxygen species (ROS) are fundamental features of aerobic eukaryotic cells. The circadian clock enhances the fitness of organisms by enabling them to anticipate cycling changes in the surroundings. ROS generation in the cell is often altered in response to environmental changes, but oscillations in ROS levels may also reflect endogenous metabolic fluctuations governed by the circadian clock. On the other hand, an effective regulation and timing of antioxidant mechanisms may be crucial in the defense of cellular integrity. Thus, an interaction between the circadian timekeeping machinery and ROS homeostasis or signaling in both directions may be of advantage at all phylogenetic levels.

RECENT ADVANCES

The Frequency-White Collar-1 and White Collar-2 oscillator (FWO) of the filamentous fungus Neurospora crassa is well characterized at the molecular level. Several members of the ROS homeostasis were found to be controlled by the circadian clock, and ROS levels display circadian rhythm in Neurospora. On the other hand, multiple data indicate that ROS affect the molecular oscillator.

CRITICAL ISSUES

Increasing evidence suggests the interplay between ROS homeostasis and oscillators that may be partially or fully independent of the FWO. In addition, ROS may be part of a complex cellular network synchronizing non-transcriptional oscillators with timekeeping machineries based on the classical transcription-translation feedback mechanism.

FUTURE DIRECTIONS

Further investigations are needed to clarify how the different layers of the bidirectional interactions between ROS homeostasis and circadian regulation are interconnected.

(Re)inventing the circadian feedback loop

For 20 years, researchers have thought that circadian clocks are defined by feedback loops of transcription and translation. The rediscovery of posttranslational circadian oscillators in diverse organisms forces us to rethink this paradigm. Meanwhile, the original "basic" feedback loops of canonical circadian clocks have swelled to include dozens of additional proteins acting in interlocked loops. We review several self-sustained clock mechanisms and propose that minimum requirements for diurnal timekeeping might be simpler than those of actual free-running circadian oscillators. Thus, complex mechanisms of circadian timekeeping might have evolved from random connections between unrelated feedback loops with independent but limited time-telling capability.

A new mutation affecting FRQ-less rhythms in the circadian system of Neurospora crassa

We are using the fungus Neurospora crassa as a model organism to study the circadian system of eukaryotes. Although the FRQ/WCC feedback loop is said to be central to the circadian system in Neurospora, rhythms can still be seen under many conditions in FRQ-less (frq knockout) strains. To try to identify components of the FRQ-less oscillator (FLO), we carried out a mutagenesis screen in a FRQ-less strain and selected colonies with altered conidiation (spore-formation) rhythms. A mutation we named UV90 affects rhythmicity in both FRQ-less and FRQ-sufficient strains. The UV90 mutation affects FRQ-less rhythms in two conditions: the free-running long-period rhythm in choline-depleted chol-1 strains becomes arrhythmic, and the heat-entrained rhythm in the frq¹⁰ knockout is severely altered. In a FRQ-sufficient background, the UV90 mutation causes damping of the free-running conidiation rhythm, reduction of the amplitude of the FRQ protein rhythm, and increased phase-resetting responses to both light and heat pulses, consistent with a decreased amplitude of the circadian oscillator. The UV90 mutation also has small but significant effects on the period of the conidiation rhythm and on growth rate. The wild-type UV90 gene product appears to be required for a functional FLO and for sustained, high-amplitude rhythms in FRQ-sufficient conditions. The UV90 gene product may therefore be a good candidate for a component of the FRQ-less oscillator. These results support a model of the Neurospora circadian system in which the FRQ/WCC feedback loop mutually interacts with a single FLO in an integrated circadian system.

All eukaryotes (including humans), and some bacteria, have evolved internal biological clocks that control activity and physiology in a daily (circadian) cycle. The molecular oscillators that drive these circadian rhythms are said to depend on rhythmic expression and feedback regulation of a small set of “clock genes.” However, there is increasing evidence that there is more to the story than these well-studied feedback loops. In the fungus Neurospora crassa, rhythms can still be seen in mutants that are missing one of the clock genes, frq. There is currently a controversy as to whether there are many different frq-less oscillators and whether they interact with the frq clock. To identify the molecular mechanism that drives these frq-less rhythms, we started with a frq-less strain and mutagenized it to look for genes that affect the frq-less rhythms. We found a new mutation that not only disrupted two frq-less rhythms but also affected the rhythm when the frq gene is present. Our results suggest there is only one frq-less oscillator, and it interacts with the frq clock. Our new mutation may identify a gene that is critical to both oscillators. We suggest that a similar clock architecture may be common to all organisms.

Effects of prd circadian clock mutations on FRQ-less rhythms in Neurospora

Rhythmic conidiation (spore formation) in Neurospora crassa provides a model system for investigating the molecular mechanisms of circadian rhythmicity. A feedback loop involving the frq, wc-1, and wc-2 gene products (FRQ/ WCC) is an important component of the mechanism; however, rhythmic conidiation can still be observed when these gene products are absent. The nature of the oscillator(s) that drives this FRQ-less rhythmicity (FLO) is an important question in Neurospora circadian biology. We have looked for interactions between FRQ/WCC and FLO by assaying the effects on FRQ-less rhythms of mutations known to affect the period in the presence of FRQ. We assayed 4 prd mutations (prd-1, prd-2, prd-3, and prd-4) under 2 conditions in frq(null) strains: long-period free-running rhythms in chol-1 strains grown without choline, and heat-entrainable rhythms in choline-sufficient conditions. We found effects of all 4 mutations on both types of FRQ-less rhythms. The greatest effects were seen with prd-1 and prd-2, which abolished free-running rhythms in the chol-1; frq(10) backgrounds and significantly affected entrained peak timing under heat-entrainment conditions in frq( 10) backgrounds. The prd-3 and prd-4 mutations had more subtle effects on period and stability of free-running rhythms in the chol-1; frq(10) backgrounds and had little effect on peak timing under heat-entrainment conditions in frq(10) backgrounds. These results, along with previously published evidence for effects of prd mutations on other FRQ-less rhythms, suggest that either there are common components shared between the FRQ/WCC oscillator and several FRQ-less oscillators or that there is a single oscillator driving all conidiation rhythms. We favor a model of the Neurospora circadian system in which a single FRQ-less oscillator drives conidiation and interacts with the FRQ/WCC feedback loop; the output or amplitude of the FRQ-less oscillator can be affected by many gene products and metabolic conditions that reveal FRQ-less rhythmicity. We propose that prd-1 and prd-2 are good candidates for components of the FRQ-less oscillator and that prd-3 and prd-4 act on the system mainly through effects on FRQ/WCC.

The dst2 gene essential for photomorphogenesis of Coprinopsis cinerea encodes a protein with a putative FAD-binding-4 domain

The fruiting-body primordium of Coprinopsis cinerea exhibits remarkable photomorphogenesis. Under a 12-h light/12-h dark regime, the primordium proceeds to the fruiting-body maturation phase in which the primordium successively undergoes basidiospore formation, stipe elongation and pileus expansion, resulting in the mature fruiting-body. In continuous darkness, however, the primordium never proceeds to the maturation phase: the pileus and stipe tissues at the upper part of the primordium remain rudimentary while the basal part of the primordium elongates, producing the etiolated "dark stipe" phenotype. In our previous studies, blind mutants, which produce dark stipes under light conditions that promote fruiting-body maturation in the wild-type, have been isolated, and two genes, dst1 and dst2, responsible for the mutant phenotype have been identified. In this study we show that the dst2-1 mutant exhibits a blind phenotype during asexual spore production in addition to that in fruiting-body photomorphogenesis. We also reveal that dst2 is predicted to encode a protein with a putative flavin adenine dinucleotide (FAD)-binding-4 domain. The two blind phenotypes, together with the existence of an FAD-binding domain in Dst2, suggest that Dst2 may play a role in perceiving blue light.

Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora

White collar-1 (WC-1) and white collar-2 (WC-2) are essential for light-mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome-wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive. Evidence is shown for photoreception in the absence of the dominant, and here confirmed, white collar complex (WCC) that regulates both types of light responses. VVD primarily modulates late responses, whereas light-responsive submerged protoperithecia-1 (SUB-1), a GATA family transcription factor, is essential for most late light gene expression. After a 15-min light stimulus, the WCC directly binds the sub-1 promoter. Bioinformatics analysis detects many early light response elements (ELREs), as well as identifying a late light response element (LLRE) required for wild-type activity of late light response promoters. The data provide a global picture of transcriptional response to light, as well as illuminating the cis- and trans-acting elements comprising the regulatory signalling cascade that governs the photobiological response.

Rhythmic conidiation in constant light in vivid mutants of Neurospora crassa

In Neurospora crassa, a circadian rhythm of conidiation (asexual spore formation) can be seen on the surface of agar media. This rhythm has a period of 22 hr in constant darkness (D/D). Under constant illumination (L/L), no rhythm is visible and cultures show constant conidiation. However, here we report that strains with a mutation in the vivid (vvd) gene, previously shown to code for the photoreceptor involved in photo-adaptation, exhibit conidiation rhythms in L/L as well as in D/D. The period of the rhythm of vvd strains ranges between 6 and 21 hr in L/L, depending upon the intensity of the light, the carbon source, and the presence of other mutations. Temperature compensation of the period also depends on light intensity. Dark pulses given in L/L shift the phase of the rhythm. Shifts from L/L to D/D show unexpected after effects; i.e., the short period of a vvd strain in L/L gradually lengthens over 2-3 days in D/D. The rhythm in L/L requires the white collar (wc-1) gene, but not the frequency (frq) gene. FRQ protein shows no rhythm in L/L in a vvd strain. The conidiation rhythm in L/L in vvd is therefore driven by a FRQ-less oscillator (FLO).

Circadian entrainment of Neurospora crassa

The circadian clock evolved under entraining conditions, yet most circadian experiments and much circadian theory are built around free-running rhythms. The interpretation of entrainment experiments is certainly more complex than that of free-running rhythms due to the relationship between exogenous and endogenous cycles. Here, we systematically describe entrainment in the simplest of the traditional eukaryotic model systems in circadian research, Neurospora crassa. This fungus forms a mass of spores (bands of conidia) each day. Over a wide range of photoperiods, these bands begin to appear at midnight, suggesting integration of neither dawn nor dusk signals alone. However, when symmetrical light/dark cycles (T cycles, each with 50% light) are applied, dusk determines the time of conidiation with a uniform, period-dependent delay in phase. This "forced" synchronization appears to be specific for the zeitgeber light because similar experiments, but using temperature, result in systematic entrainment, with bands appearing relatively later in shorter cycles and earlier in longer cycles. We find that the molecular mechanism of entrainment primarily concerns posttranscriptional regulation. Finally, we have used Neurospora to investigate acute effects of zeitgeber stimuli known as "masking."

Circadian clock: time for a phase shift of ideas?

A recent study shows that cycling of cryptochrome proteins is dispensable for circadian clock function in mammalian cells. Is it time for a paradigm shift in how we think about the circadian clock mechanism?

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.

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.

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.

Transcriptional feedback oscillators: maybe, maybe not

The molecular mechanism of circadian rhythmicity is usually modeled by a transcription/translation feedback oscillator in which clock proteins negatively feed back on their own transcription to produce rhythmic levels of clock protein mRNAs, which in turn cause the production of rhythmic levels of clock proteins. This mechanism has been applied to all model organisms for which molecular data are available. This review summarizes the increasing number of anomalous observations that do not fit the standard molecular mechanism for the model organisms Acetabularia, Synechococcus, Drosophila, Neurospora, and mouse. The anomalies fall into 2 classes: observations of rhythmicity in the organism when transcription of clock genes is held constant, and rhythmicity in the organism when clock gene function is missing in knockout mutants. It is concluded that the weight of anomalies is now so large that the standard transcription/translation mechanism is no longer an adequate model for circadian oscillators. Rhythmic transcription may have other functions in the circadian system, such as participating in input and output pathways and providing robustness to the oscillations. It may be most useful to think in terms of a circadian system that uses a noncircadian oscillator consisting of metabolic feedback loops, which acquires its circadian properties from additional regulatory molecules such as the products of canonical clock genes.

Circadian clock genes frequency and white collar-1 are not essential for entrainment to temperature cycles in Neurospora crassa

The fungus Neurospora crassa is a model system for investigating the mechanism of circadian rhythmicity, and the core of its circadian oscillator is thought to be a transcription/translation feedback loop involving the products of the frq (frequency), wc-1 (white-collar-1) and wc-2 (white-collar-2) genes. Several reports of rhythmicity in frq and wc null mutants have raised questions about how central the FRQ/WC loop is to the circadian system of Neurospora. Several research groups have attempted to answer this question by looking for entrainment of the conidiation banding rhythm in frq null mutants. Because the frq mutants are blind to light and cannot be entrained to light/dark cycles, these groups have used symmetric temperature cycles of equal-duration cool and warm phases to entrain the rhythm. Under these conditions, the direct effects of temperature on conidiation (masking effects) can compromise observations of the endogenous rhythm. I have reexamined this question by using short heat pulses to clearly separate masking from endogenous rhythms, and I have assayed entrainment in both frq and wc-1 null mutants. I found similar patterns of entrainment in the wild type and both mutant strains. Strong masking effects were found in the frq mutant but not in the wc-1 mutant. I conclude that a rapidly damping temperature-entrainable oscillator is present in the null mutants. A single temperature-entrainable oscillator may drive the conidiation rhythm in all strains, and additional properties such as light sensitivity and temperature compensation may be conferred by the intact FRQ/WC loop in the WT strain.

Phosphorylation-dependent maturation of Neurospora circadian clock protein from a nuclear repressor toward a cytoplasmic activator

Frequency (FRQ) is a central component of interconnected negative and positive limbs of feedback loops of the circadian clock of Neurospora. In the negative limb, FRQ inhibits its transcriptional activator White Collar Complex (WCC) and in the positive limb, FRQ supports accumulation of WCC. We show that these conflicting functions are confined to distinct subcellular compartments and coordinated in temporal fashion. Inactivation of the transcriptional activator WCC requires nuclear FRQ and occurs early after the onset of FRQ expression. Support of WCC accumulation requires cytosolic FRQ and occurs on a post-translational level, when high amounts of FRQ have accumulated. The transcriptional function of FRQ in the negative loop and its post-translational function in the positive loop are independent and associated with distinct regions of FRQ. Phosphorylation of FRQ at the PEST-2 region triggers its maturation from a nuclear repressor toward a cytoplasmic activator.

Demasking biological oscillators: properties and principles of entrainment exemplified by the Neurospora circadian clock

Oscillations are found throughout the physical and biological worlds. Their interactions can result in a systematic process of synchronization called entrainment, which is distinct from a simple stimulus-response pattern. Oscillators respond to stimuli at some times in their cycle and may not respond at others. Oscillators can also be driven if the stimulus is strong (or if the oscillator is weak); i.e., they restart their cycle every time they receive a stimulus. Stimuli can also directly affect rhythms without entraining the underlying oscillator (masking): Drivenness and masking are often difficult to distinguish. Here we use the circadian biological clock to explore properties of entrainment. We confirm previous results showing that the residual circadian system in Neurospora can be entrained in a mutant of the clock gene frequency (frq(9), a strain deficient in producing a functional FRQ protein). This finding has implications for understanding the evolution of circadian programs. By comparing data sets from independent studies, we develop a template for analyzing, modeling, and dissecting the interactions of entrained and masked components. These insights can be applied to oscillators of all periodicities.

Circadian rhythms in microorganisms: new complexities

Recent advances in understanding circadian (daily) rhythms in the genera Neurospora, Gonyaulax, and Synechococcus are reviewed and new complexities in their circadian systems are described. The previous model, consisting of a unidirectional flow of information from input to oscillator to output, has now expanded to include multiple input pathways, multiple oscillators, multiple outputs; and feedback from oscillator to input and output to oscillator. New posttranscriptional features of the frq/white-collar oscillator (FWC) of Neurospora are described, including protein phosphorylation and degradation, dimerization, and complex formation. Experimental evidence is presented for frq-less oscillator(s) (FLO) downstream of the FWC. Mathematical models of the Neurospora system are also discussed.

Entrainment dissociates transcription and translation of a circadian clock gene in neurospora

Circadian systems coordinate the daily sequence of events in cells, tissues, and organisms. In constant conditions, the biological clock oscillates with its endogenous period, whereas it is synchronized to the 24 hr light:dark cycle in nature. Here, we investigate light entrainment of Neurospora crassa to photoperiods that mimic seasonal changes. Clock gene (frequency, or frq) RNA levels directly reflect the light environment in all photoperiods, whereas the FRQ protein follows neither RNA levels nor light transitions. Induction of frq RNA and protein can be dissociated by as much as 6 hr, depending on photoperiod. The phase of entrainment at the physiological level (e.g., asexual spore development) correlates with FRQ protein. Thus, a dissociation of transcription, translation, and protein stability is fundamental to circadian entrainment of Neurospora. Our findings suggest that simple feedback models are insufficient to explain the molecular circadian mechanisms under entrained conditions and that clock control of light input pathways involves posttranscriptional regulation. The regulators mediating the dissociation between RNA and protein levels are still unknown and will be the key to understanding both circadian timing at the molecular level and how the clock exerts control over many cellular processes.

Reactive oxygen species affect photomorphogenesis in Neurospora crassa

In Neurospora crassa, several biological phenomena such as the synthesis of carotenoids in the mycelia and polarity of perithecia are regulated by light. We found that a sod-1 mutant, with a defective Cu,Zn-type superoxide dismutase (SOD), showed accelerated light-dependent induction of carotenoid accumulation in the mycelia compared with the wild type. The initial rate of light-induced carotenoid accumulation in the sod-1 mutant was faster than that in the vvd mutant known to accumulate high concentrations. This acceleration was suppressed by treatment with antioxidant reagents. Light-induced transcription of genes involved in carotenoid synthesis, al-1, -2, and -3, was sustained in the sod-1 mutant, whereas it was transient in the wild type. Moreover sod-1 was defective in terms of light-induced polarity of perithecia. By genetic analysis, the enhancement in light-inducible carotenoid synthesis in sod-1 was dependent on the wild type alleles of wc-1 and wc-2. However, the sod-1;vvd double mutant showed additive effects on the carotenoid accumulation in the mycelia. These results suggested that intracellular reactive oxygen species regulated by SOD-1 could affect the light-signal transduction pathway via WC proteins.

VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation

Blue light regulates many physiological and developmental processes in fungi. Most of the blue light responses in the ascomycete Neurospora crassa are dependent on the two blue light regulatory proteins White Collar (WC)-1 and -2. WC-1 has recently been shown to be the first fungal blue light photoreceptor. In the present study, we characterize the Neurospora protein VIVID. VIVID shows a partial sequence similarity with plant blue light photoreceptors. In addition, we found that VIVID non-covalently binds a flavin chromophore. Upon illumination with blue light, VIVID undergoes a photocycle indicative of the formation of a flavin-cysteinyl adduct. VVD is localized in the cytoplasm and is only present after light induction. A loss-of-function vvd mutant was insensitive to increases in light intensities. Furthermore, mutational analysis of the photoactive cysteine indicated that the formation of a flavin-cysteinyl adduct is essential for VIVID functions in vivo. Our results show that VIVID is a second fungal blue light photoreceptor which enables Neurospora to perceive and respond to daily changes in light intensity.

Combining theoretical and experimental approaches to understand the circadian clock

This review is intended as a summary of our work carried out as part of the German Research Association (DFG) Center Program on Circadian Rhythms. Over the last six years, our approach to understanding circadian systems combined theoretical and experimental tools, and Gonyaulax and Neurospora have proven ideal for these efforts. Both of these model organisms demonstrate that even simple circadian systems can have multiple light input pathways and more than one rhythm generator. They have both been used to elaborate basic circadian features in conjunction with formal models. The models introduce the "zeitnehmer," i.e., a clock-regulated input pathway, to the conceptual framework of circadian systems, and proposes networks of individual feedbacks as the basis for circadian rhythmicity.

The frequency gene is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa

The circadian clock of Neurospora broadly regulates gene expression and is synchronized with the environment through molecular responses to changes in ambient light and temperature. It is generally understood that light entrainment of the clock depends on a functional circadian oscillator comprising the products of the wc-1 and wc-2 genes as well as those of the frq gene (the FRQ/WCC oscillator). However, various models have been advanced to explain temperature regulation. In nature, light and temperature cues reinforce one another such that transitions from dark to light and/or cold to warm set the clock to subjective morning. In some models, the FRQ/WCC circadian oscillator is seen as essential for temperature-entrained clock-controlled output; alternatively, this oscillator is seen exclusively as part of the light pathway mediating entrainment of a cryptic "driving oscillator" that mediates all temperature-entrained rhythmicity, in addition to providing the impetus for circadian oscillations in general. To identify novel clock-controlled genes and to examine these models, we have analyzed gene expression on a broad scale using cDNA microarrays. Between 2.7 and 5.9% of genes were rhythmically expressed with peak expression in the subjective morning. A total of 1.4-1.8% of genes responded consistently to temperature entrainment; all are clock controlled and all required the frq gene for this clock-regulated expression even under temperature-entrainment conditions. These data are consistent with a role for frq in the control of temperature-regulated gene expression in N. crassa and suggest that the circadian feedback loop may also serve as a sensor for small changes in ambient temperature.

Molecular mechanisms of entrainment in the Neurospora circadian clock

Light and temperature are 2 of the most important environmental influences on all circadian clocks, and Neurospora provides an excellent system for understanding their effects. Progress made in the past decade has led to a basic molecular understanding of how the Neurospora clock works and how environmental factors influence it. The purpose of this review is to summarize what we currently know about the molecular mechanism of light and temperature entrainment in Neurospora.

The art of entrainment

The circadian system actively synchronizes the temporal sequence of biological functions with the environment. The oscillatory behavior of the system ensures that entrainment is not passive or driven and therefore allows for great plasticity and adaptive potential. With the tools at hand, we now can concentrate on the most important circadian question: How is the complex task of entrainment achieved by anatomical, cellular, and molecular components? Understanding entrainment is equal to understanding the circadian system. The results of this basic research will help us to understand temporal ecology and will allow us to improve conditions for humans in industrialized societies.

Functional conservation of light, oxygen, or voltage domains in light sensing

In Neurospora, the flavin adenine dinucleotide-containing protein WHITE COLLAR-1 is the blue-light photoreceptor for the circadian clock and other light responses. The putative chromophore-binding domain of WC-1, its light, oxygen, or voltage (LOV) domain, is similar to the LOV domains found in the plant phototropins, the Neurospora VIVID (VVD) protein, and the Arabidopsis FKF1 and its related proteins. Studies of the plant phototropins have identified 11 flavin-contacting residues that are also conserved in the LOV domains of WC-1, VVD, and FKF1. In this study, by mutating the putative WC-1 flavin-binding sites, we show that these sites are important for the light function of the protein, suggesting that the WC-1 LOV domain adapts a structure similar to that of the phototropin LOV domains. By creating a Neurospora strain in which the LOV domain of WC-1 is swapped with that of VVD, we show that the LOV domain of VVD partially replaces the function of the WC-1 LOV domain, suggesting that VVD is a wc-dependent photoreceptor in Neurospora. Furthermore, we show that the Neurosporastrains containing a chimeric WC-1 protein with the LOV domain from FKF1 or phot1 can also sense light, suggesting that FKF1 and its related proteins are light sensors in Arabidopsis. Taken together, our data suggest that these LOV domains are structurally similar protein modules involved in blue-light sensing.

The network of time: understanding the molecular circadian system

The circadian clock provides a temporal structure that modulates biological functions from the level of gene expression to performance and behaviour. Pioneering work on the fruitfly Drosophila has provided a basis for understanding how the temporal sequence of daily events is controlled in mammals. New insights have come from work on mammals, specifically from studying the daily activity profiles of clock mutant mice; from more detailed recordings of clock gene expression under different experimental conditions and in different tissues; and from the discovery and analysis of a growing number of additional clock genes. These new results are moving the model paradigm away from a simple negative feedback loop to a molecular network. Understanding the coupling and interactions of this network will help us to understand the evolution of the circadian system, advance medical diagnosis and treatment, improve the health of shift workers and frequent travellers, and will generally enable the treatment of clock-related pathologies.

WHITE COLLAR-1, a multifunctional neurospora protein involved in the circadian feedback loops, light sensing, and transcription repression of wc-2

WHITE COLLAR-1 (WC-1) and WC-2, the two PAS domain-containing transcription factors, are the positive elements of the circadian feedback loops in Neurospora. In addition, both proteins are essential components for the light input of various blue light responses, including the light entrainment of the circadian clock. Recently, we identified WC-1 as the blue light photoreceptor responsible for these light responses. In this study, we show that the formation of the FRQ-WC complex in vivo, a step critical in closing the circadian negative feedback loop, requires WC-1. In addition, we show that WC-1 negatively regulates the expression of wc-2 at the level of the transcription, forming another interacting loop. In a wc-1 mutant, we demonstrate that there is alternative protein initiation of WC-1, and the requirements of WC-1 for the light induction of frq and other genes differ significantly, suggesting the existence of different WC complexes in the cell. Consistent with this interpretation, our results show that there are at least two different types of WC-1/WC-2 complexes in vivo, and that the larger WC-1/WC-2 complex contains more than one WC-1 molecule. Using a series of wc-1 mutants, we show that the WC-1 PASC domain and its C-terminal region are essential for the formation of the WC-1/WC-2 complex. Functional analyses reveal that the DNA-binding domain of WC-1 is required only for the activation of frq in the dark and not for the light function of the protein, confirming that WC-1 is a multifunctional protein with separable protein domains.

Roles for WHITE COLLAR-1 in circadian and general photoperception in Neurospora crassa

The transcription factors WHITE COLLAR-1 (WC-1) and WHITE COLLAR-2 (WC-2) interact to form a heterodimeric complex (WCC) that is essential for most of the light-mediated processes in Neurospora crassa. WCC also plays a distinct non-light-related role as the transcriptional activator in the FREQUENCY (FRQ)/WCC feedback loop that is central to the N. crassa circadian system. Although an activator role was expected for WC-1, unanticipated phenotypes resulting from some wc-1 alleles prompted a closer examination of an allelic series for WC-1 that has uncovered roles for this central regulator in constant darkness and in response to light. We analyzed the phenotypes of five different wc-1 mutants for expression of FRQ and WC-1 in constant darkness and following light induction. While confirming the absolute requirement of WC-1 for light responses, the data suggest multiple levels of control for light-regulated genes.