Assay and Characteristics of Circadian Rhythmicity in Liquid Cultures of Neurospora crassa

Suppressing the Neurospora crassa circadian clock while maintaining light responsiveness in continuous stirred tank reactors

Neurospora crassa has been utilized as a model organism for studying biological, regulatory, and circadian rhythms for over 50 years. These circadian cycles are driven at the molecular level by gene transcription events to prepare for environmental changes. N. crassa is typically found on woody biomass and is commonly studied on agar-containing medium which mimics its natural environment. We report a novel method for disrupting circadian gene transcription while maintaining light responsiveness in N. crassa when held in a steady metabolic state using bioreactors. The arrhythmic transcription of core circadian genes and downstream clock-controlled genes was observed in constant darkness (DD) as determined by reverse transcription-quantitative PCR (RT-qPCR). Nearly all core circadian clock genes were up-regulated upon exposure to light during 11hr light/dark cycle experiments under identical conditions. Our results demonstrate that the natural timing of the robust circadian clock in N. crassa can be disrupted in the dark when maintained in a consistent metabolic state. Thus, these data lead to a path for the production of industrial scale enzymes in the model system, N. crassa, by removing the endogenous negative feedback regulation by the circadian oscillator.

Dissecting the mechanisms of the clock in Neurospora

The circadian clock exists to synchronize inner physiology with the external world, allowing life to anticipate and adapt to the continual changes that occur in an organism's environment. The clock architecture is highly conserved, present in almost all major branches of life. Within eukaryotes, the filamentous fungus Neurospora crassa has consistently been used as an excellent model organism to uncover the basic circadian physiology and molecular biology. The Neurospora model has elucidated our fundamental understanding of the clock as nested positive and negative feedback loop, regulated by transcriptional and posttranscriptional processes. This review will examine the basics of circadian rhythms in the model filamentous fungus N. crassa as well as highlight the output of the clock in Neurospora and the reasons that N. crassa has continued to be a strong model for the study of circadian rhythms. It will also synopsize classical and emerging methods in the study of the circadian clock.

Robust entrainment of circadian oscillators requires specific phase response curves

The circadian clocks keeping time in many living organisms rely on self-sustained biochemical oscillations entrained by external cues, such as light, to the 24-h cycle induced by Earth's rotation. However, environmental cues are unreliable due to the variability of habitats, weather conditions, or cue-sensing mechanisms among individuals. A tempting hypothesis is that circadian clocks have evolved so as to be robust to fluctuations in the signal that entrains them. To support this hypothesis, we analyze the synchronization behavior of weakly and periodically forced oscillators in terms of their phase response curve (PRC), which measures phase changes induced by a perturbation applied at different times of the cycle. We establish a general relationship between the robustness of key entrainment properties, such as stability and oscillator phase, on the one hand, and the shape of the PRC as characterized by a specific curvature or the existence of a dead zone, on the other hand. The criteria obtained are applied to computational models of circadian clocks and account for the disparate robustness properties of various forcing schemes. Finally, the analysis of PRCs measured experimentally in several organisms strongly suggests a case of convergent evolution toward an optimal strategy for maintaining a clock that is accurate and robust to environmental fluctuations.

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.

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.

Isolation of total RNA from Neurospora mycelium

In filamentous fungi, including the model organism Neurospora crassa, plentiful biological tissue from which RNA can be extracted may be obtained by allowing fungal spores to germinate and form a mycelium in liquid culture. The mycelium constitutes a mosaic of multinuclear, tubular filaments known as hyphae or mycelia. In general, when exposed to air, fungal hyphae quickly start to develop spores, which are often colorful. However, when submerged in liquid under rapid agitation large amounts of vegetatively growing mycelium can be obtained, which can be easily harvested by means of filtration. To preserve the physiological state of the culture, the mycelium is snap-frozen, and then to free its contents, the mycelium is ground under liquid nitrogen to break all hyphal structures. Here a method to extract high-quality total RNA from Neurospora mycelium using TRIzol reagent is described.

Circadian rhythmicity during prolonged chemostat cultivation of Neurospora crassa

Following exposure to light and attainment of steady-state in the chemostat, Neurospora was grown in constant conditions of darkness at 25 degrees C for 6 days. Biomass samples were taken every 4h for the extraction of RNA and protein, and the state of the circadian clock was assessed by assaying the levels of three rhythmically expressed mRNAs; frequency (frq), antisense frq (qrf) and clock-controlled gene-14 (ccg-14), and by monitoring the clock-controlled rhythm of sporulation. Our results indicate that the Neurospora clock continued to run in the chemostat. This is the longest reported time that Neurospora has been grown in a chemostat in filamentous form and opens up the possibility of studying the response of Neurospora to a range of stimuli in the absence of confounding effects due to; alterations in growth rate, aging, and changing conditions of the growth medium.

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

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

Rhythms of differentiation and diacylglycerol in Neurospora

Although the fungus Neurospora crassa is a relatively simple lower eukaryote, its circadian system may be more complex than previously thought. In this paper we review evidence suggesting that there may be several output pathways coupled in complex ways to a single oscillator, or that there may be more than one oscillator driving independent output pathways. We have described two new rhythms in Neurospora that are not tightly coupled to the rhythm of conidiation bands that is the standard assay for the state of the Neurospora circadian clock. The first is a rhythm in the timing of differentiation, i.e. the production of aerial hyphae and spores. Large regions of the mycelium differentiate synchronously, as if responding to a spatially widespread signal. This rhythm may be distinct from the timer that sets the determination switch controlling the spatial pattern of conidiation bands. The second new rhythm is an oscillation in the levels of the neutral lipid diacylglycerol (DAG). This rhythm is found in all regions of a colony and is not always in phase with the rhythm of conidiation bands. The DAG rhythm shares some characteristics with the differentiation rhythm and has the potential to act as the signal that induces rhythmic differentiation.

Genetic and molecular analysis of circadian rhythms in Neurospora

Over the course of the past 40 years Neurospora has become a well-known and uniquely tractable model system for the analysis of the molecular basis of eukaryotic circadian oscillatory systems. Molecular bases for the period length and sustainability of the rhythm, light, and temperature resetting of the circadian system and for gating of light input and light effects are becoming understood, and Neurospora promises to be a suitable system for examining the role of coupled feedback loops in the clock. Many of these insights have shown or foreshadow direct parallels in mammalian systems, including the mechanism of light entrainment, the involvement of PAS:PAS heterodimers as transcriptional activators in essential clock-associated feedback loops, and dual role of FRQ in the loop as an activator and a repressor; similarities extend to the primary sequence level in at least one case, that of WC-1 and BMAL1. Work on circadian output in Neurospora has identified more than a dozen regulated genes and has been at the forefront of studies aimed at understanding clock control of gene expression.

The Goodwin model: simulating the effect of light pulses on the circadian sporulation rhythm of Neurospora crassa

The Goodwin oscillator is a minimal model that describes the oscillatory negative feedback regulation of a translated protein which inhibits its own transcription. Now, over 30 years later this scheme provides a basic description of the central components in the circadian oscillators of Neurospora, Drosophila, and mammals. We showed previously that Neurospora's resetting behavior by pulses of temperature, cycloheximide or heat shock can be simulated by this model, in which degradation processes play an important role for determining the clock's period and its temperature-compensation. Another important environmental factor for the synchronization is light. In this work, we show that on the basis of a light-induced transcription of the frequency (frq) gene phase response curves of light pulses as well as the influence of the light pulse length on phase shifts can be described by the Goodwin oscillator. A relaxation variant of the model predicts that directly after a light pulse inhibition in frq -transcription occurs, even when the inhibiting factor Z (FRQ) has not reached inhibitory concentrations. This has so far not been experimentally investigated for frq transcription, but it complies with a current model of light-induced transcription of other genes by a phosphorylated white-collar complex. During long light pulses, the relaxational model predicts that the sporulation rhythm is arrested in a steady state of high frq -mRNA levels. However, experimental results indicate the possibility of oscillations around this steady state and more in favor of the results by the original Goodwin model. In order to explain the resetting behavior by two light pulses, a biphasic first-order kinetics recovery period of the blue light receptor or of the light signal transduction pathway has to be assumed.

Understanding circadian rhythmicity in Neurospora crassa: from behavior to genes and back again

Circadian clocks have been described in organisms ranging in complexity from unicells to mammals, in which they function to control daily rhythms in cellular activities and behavior. The significance of a detailed understanding of the clock can be appreciated by its ubiquity and its established involvement in human physiology, including endocrine function, sleep/wake cycles, psychiatric illness, and drug tolerances and effectiveness. Because the clock in all organisms is assembled within the cell and clock mechanisms are evolutionarily conserved, simple eukaryotes provide appropriate experimental systems for dissecting the clock. Significant progress has been made in deciphering the circadian system in Neurospora crassa using both genetic and molecular approaches, and Neurospora has contributed greatly to our understanding of (1) the feedback cycle that comprises a circadian oscillator, (2) the mechanisms by which the clock is kept in synchrony with the environment, and (3) the genes that reside in rhythmic output pathways. Importantly, the lessons learned in Neurospora are relevant to our understanding of clocks in higher eukaryotes.

Evidence against a direct role for inositol phosphate metabolism in the circadian oscillator and the blue-light signal transduction pathway in Neurospora crassa

The inositol-depletion hypothesis proposes that the effects of Li+ on cellular functions are the result of inhibition by Li+ of the inositol monophosphate phosphatase and subsequent depletion of inositol lipids. This mechanism has been proposed to account for the effects of Li+ on the period of the circadian oscillator. Inositol phosphate metabolism has also been proposed as part of the blue-light signal-transduction pathway through which the phase of the circadian oscillator can be reset by light pulses. Four predictions of these two hypotheses have been tested in the fungus Neurospora crassa and all have been found to fail: (1) inositol supplementation does not reverse the effects of Li+ on the period of the circadian rhythm; (2) inositol depletion of an inositol-requiring mutant does not mimic the effects of Li+; (3) depletion of inositol lipids does not inhibit the response to light; and (4) a phase-resetting pulse of light does not increase the levels of inositol phosphates, including Ins(1,4,5)P3.

Neurospora crassa clock-controlled genes are regulated at the level of transcription

Although an extensive number of biological processes are under the daily control of the circadian biological clock, little is known about how the clock maintains its regulatory networks within a cell. An important aspect of this temporal control is the daily control of gene expression. Previously we identified two morning-specific genes that are regulated by the clock through daily control of gene expression (J. Loros, S. Denome, and J.C. Dunlap, Science 243:385-388, 1989). We have now introduced a method for transcriptional analysis in Neurospora crassa and used this nuclear run-on procedure to show that regulation of mRNA abundance for these two morning-specific genes occurs at the level of transcription. This transcriptional regulation by the circadian clock provides a basis for isolating circadian rhythm mutants.

Neurospora crassa clock-controlled genes are regulated at the level of transcription

Although an extensive number of biological processes are under the daily control of the circadian biological clock, little is known about how the clock maintains its regulatory networks within a cell. An important aspect of this temporal control is the daily control of gene expression. Previously we identified two morning-specific genes that are regulated by the clock through daily control of gene expression (J. Loros, S. Denome, and J.C. Dunlap, Science 243:385-388, 1989). We have now introduced a method for transcriptional analysis in Neurospora crassa and used this nuclear run-on procedure to show that regulation of mRNA abundance for these two morning-specific genes occurs at the level of transcription. This transcriptional regulation by the circadian clock provides a basis for isolating circadian rhythm mutants.

On the role of Ca2(+)-calmodulin-dependent and cAMP-dependent protein phosphorylation in the circadian rhythm of Neurospora crassa

Pulses of some Ca2+ channel blockers (dantrolene, Co2+, nifedipine) and calmodulin inhibitors (chlorpromazine) lead to medium (maximally 5-9 h) phase shifts of the circadian conidiation rhythm of Neurospora crassa. Pulses of high Ca2+, or of low Ca2+, a Ca2+ ionophore (A23187) together with Ca2+, and other Ca2+ channel blockers (La3+, diltiazem), however, caused only minor phase shifts. The effect of these substances (A 23187) and of different temperatures on the Ca2+ release from isolated vacuoles was analyzed by using the fluorescent dye Fura-2. A 23187 and higher temperatures increased the release drastically, whereas dantrolene decreased the permeation of Ca2+ (Cornelius et al., 1989). Pulses of 8-PCTP-cAMP, IBMX and of the cAMP antagonist RP-cAMPS, also caused medium (maximally 6-9 h) phase shifts of the conidiation rhythm. The phase response curve of the agonist was almost 180 degrees out of phase with the antagonist PRC. In spite of some variability in the PRCs of these series of experiments all showed maximal shifts during ct 0-12. The variability of the response may be due to circadian changes in the activity of phosphodiesterases: After adding cAMP to mycelial extracts HPLC analysis of cAMP metabolites showed significant differences during a circadian period with a maximum at ct 0. Protein phosphorylation was tested mainly in an in vitro phosphorylation system (with 35S-thio gamma-ATP). The results showed circadian rhythmic changes predominantly in proteins of 47/48 kDa. Substances and treatments causing phase-shifts of the conidiation rhythm also caused changes in the phosphorylation of these proteins: an increase was observed when Ca2+ or cAMP were added, whereas a decrease occurred upon addition of a calmodulin inhibitor (TFP) or pretreatment of the mycelia with higher (42 degrees C) temperatures. Altogether, the results indicate that Ca2(+)-calmodulin-dependent and cAMP-dependent processes play an important, but perhaps not essential, role in the clock mechanism of Neurospora. Ca2+ calmodulin and the phosphorylation state of the 47/48-kDa proteins may have controlling or essential functions for this mechanism.

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

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

Possible link between circadian rhythm and heat shock response in Neurospora crassa

3-h pulses of elevated temperatures (30 degrees C, 35 degrees C, 40 degrees C) phase shift the circadian conidiation rhythm of Neurospora crassa. The phase and amplitude of the phase response curves (PRC) were measured in wild type (frq+) and frequency mutants (frq 1, frq 7). The dose dependence of the phase shifts was compared to the dose dependence of total protein synthesis inhibition and heat shock protein induction in the three strains. All processes showed an almost linear dependence on temperature. These experiments and other available data suggest that a temperature increase may act on the circadian rhythm by a process belonging to the heat shock response.

Phase shifting of the circadian conidiation rhythm in Neurospora crassa by calmodulin antagonists

The effects of chemicals capable of antagonizing the functions of calmodulin, such as trifluoperazine, chlorpromazine, imipramine, alprenolol, W7, and W13, on the circadian conidiation rhythm of Neurospora crassa were examined. Trifluoperazine, at a 30-microM concentration, was most effective in shifting the phase of the conidiation rhythm and caused a maximum phase delay at circadian time (CT) 6 and maximum phase advance at CT 9. Chlorpromazine was less effective than trifluoperazine, and a 300-microM concentration of chlorpromazine was required for a similar phase shift. Imipramine, at a 1-mM concentration, caused only a small phase shift, while alprenolol had little effect on biological clock function. W7 and W13 caused phase delays longer than 10 hr at CT 6 and caused a phase advance of about 5 hr at CT 10 when present at a 200-microM concentration. However, W5 and W12, the dechlorinated homologues of W7 and W13, had no effects on clock function at the same concentration. Calmodulin was assayed by measurements of stimulation of cyclic nucleotide diphosphodiesterase activity. Calmodulin content remained constant in trifluoperazine-sensitive and trifluoperazine-insensitive phases for two cycles following the light-dark transition.

On the role of energy metabolism in Neurospora circadian clock function

Neurospora crassa (bdA) mycelia were kept in liquid culture. Without rhythmic conidiation the levels of adenine nucleotides undergo circadian changes in constant darkness. Maxima occur 12-17 hr and 33-35 hr after initiation of the rhythm, i.e., at CT 0-6 hr. Pulses of metabolic inhibitors such as vanadate (Na3Vo4), molybdate (Na2MoO4 : 2 H2O), N-ethylmaleimide (NEM), azide (NaN3), cyanide (NaCN) and oligomycin phase shift the circadian conidiation rhythm of Neurospora crassa. Maximal advance phase shifts are observed at about CT 6 with all inhibitors. Pulses of N,N'dicyclohexylcarbodiimide (DCCD) and light phase shift the conidiation rhythm following a phase response curve different from those of the other agents (maximal advance at about CT 18-24). The phase shifts with DCCD and light are significantly larger in the wild type compared to the mitochrondrial mutant poky. Such differences are not found in PRCs of the protein synthesis inhibitor cycloheximide. [31P] NMR spectra of wild type Neurospora crassa and the clock mutants frq 1 and frq 7 which differ in their circadian period lengths did not reveal differences in the concentrations of adenine nucleotides, pyridine nucleotides or sugar phosphates. Starvation causes drastic changes of the levels of adenine nucleotides, phosphate and mobile polyphosphate without effecting phase or period length of the circadian rhythm.

Effects of Respiratory Inhibitors on Respiration, ATP Contents, and the Circadian Conidiation Rhythm of Neurospora crassa

Effects of respiratory inhibitors on the circadian clock, respiratory activity, and ATP content were examined in Neurospora crassa. All inhibitors, potassium cyanide, sodium azide, antimycin A, and carbonyl cyanide m-chlorophenyl hydrazone (CCCP), shifted the phase of the conidiation rhythm. All the phase response curves were similar and resembled that for cycloheximide, but were different from the phase response curve for light. Phase shifting by azide and CCCP was proportional to the lowering of respiratory activity and ATP content, but such a correlation was not observed for cyanide and antimycin A. In particular, cyanide at a concentration of 0.5 millimolar completely depleted ATP of the cultures but did not significantly shift their phase. Their results suggest that large shifts caused by these inhibitors are not due to a decrease in energy from respiratory activity.

Calcium Inhibits Phase Shifting of the Circadian Conidiation Rhythm of Neurospora crassa by the Calcium Ionophore A23187

Effects of the calcium ionophore, A23187, and antimycin A on the circadian conidiation rhythm of Neurospora crassa were examined. A23187 at a concentration of 1 mum in medium not containing divalent cations delayed the phase by 10 hours at CT 10 and advanced it by 5 hours at CT 14 (CT 12 corresponds to the time that discs are transferred from light to dark). This phase shifting was completely inhibited by addition of 0.1 millimolar CaCl(2) but not by MgCl(2) at any concentrations examined.Antimycin A inhibited respiration by 90% at a concentration of 0.2 micrograms per milliliter and lowered the ATP content by 85%. Antimycin A alone caused small phase advances but in combination with A23187 resulted in a large phase delay at CT 10. This phase shifting was not reversed by addition of CaCl(2) lower than 10 millimolar.

Chronobiology at the cellular and molecular levels: models and mechanisms for circadian timekeeping

This review considers cellular chronobiology and examines, at least in a superficial way, several classes of models and mechanisms that have been proposed for circadian rhythmicity and some of the experimental approaches that have appeared to be most productive. After a brief discussion of temporal organization and the metabolic, epigenetic, and circadian time domains, the general properties of circadian rhythms are enumerated. A survey of independent oscillations in isolated organs, tissues, and cells is followed by a review of selected circadian rhythms in eukaryotic microorganisms, with particular emphasis placed on the rhythm of cell division in the algal flagellate Euglena as a model system illustrating temporal differentiation. In the ensuing section, experimental approaches to circadian clock mechanisms are considered. The dissection of the clock by the use of chemical inhibitors is illustrated for the rhythm of bioluminescence in the marine dinoflagellate Gonyaulax and for the rhythm of photosynthetic capacity in the unicellular green alga Acetabularia. Alternatively, genetic analysis of circadian oscillators is considered in the green alga Chlamydomonas and in the bread mold Neurospora, both of which have yielded clock mutants and mutants having biochemical lesions that exhibit altered clock properties. On the basis of the evidence generated by these experimental approaches, several classes of biochemical and molecular models for circadian clocks have been proposed. These include strictly molecular models, feedback loop (network) models, transcriptional (tape-reading) models, and membrane models; some of their key elements and predictions are discussed. Finally, a number of general unsolved problems at the cellular level are briefly mentioned: cell cycle interfaces, the evolution of circadian rhythmicity, the possibility of multiple cellular oscillators, chronopharmacology and chronotherapy, and cell-cycle clocks in development and aging.

Changes in Intracellular pH Are Not Correlated with the Circadian Rhythm of Neurospora

Intracellular pH (pH(i)) was measured during the circadian cycle of Neurospora. Internal pH of Neurospora cultures in liquid medium was assayed by the 5,5-dimethyl-2,4-oxazolidinedione method and gave values for pH(i) which were similar to those previously obtained by other workers using pH-microelectrodes with agar-grown cultures. Cytoplasmic pH changed in liquid medium cultures, but these changes were not related to the circadian clock. Furthermore, treatments which raise or lower pH(i) do not phase-shift the circadian rhythm. These results indicate that pH(i) plays no specific role in regulating the circadian clock of Neurospora.

Cycloheximide and heat shock induce new polypeptide synthesis in Neurospora crassa

Treatment of Neurospora crassa with 0.1 microgram of cycloheximide per ml, a concentration which inhibited protein synthesis by about 70%, resulted in the greatly enhanced synthesis of at least three polypeptide bands with estimated molecular weights of 88,000, 30,000, and 28,000. A temperature shift from 25 to 37 degrees C resulted in the appearance of a single new polypeptide band of 70,000 daltons, the same size as the major heat shock-induced proteins observed in species of Drosophila and Dictyostelium. Synthesis of the cycloheximide-stimulated polypeptide bands was on cytoplasmic ribosomes rather than on mitochondrial ribosomes, as incorporation of isotope into the polypeptide bands was inhibited by 1.0 microgram of cycloheximide per ml but not by 1 mg of chloramphenicol per ml. In a mutant with cycloheximide-resistant ribosomes, 0.1 microgram of cycloheximide per ml failed to alter the pattern of protein synthesis from that of the controls. It is suggested that the new synthesis of the polypeptide bands reflects specific mechanisms of adaptation to different kinds of environmental stress, including inhibition of protein synthesis and temperature increases.

Cycloheximide and heat shock induce new polypeptide synthesis in Neurospora crassa

Treatment of Neurospora crassa with 0.1 microgram of cycloheximide per ml, a concentration which inhibited protein synthesis by about 70%, resulted in the greatly enhanced synthesis of at least three polypeptide bands with estimated molecular weights of 88,000, 30,000, and 28,000. A temperature shift from 25 to 37 degrees C resulted in the appearance of a single new polypeptide band of 70,000 daltons, the same size as the major heat shock-induced proteins observed in species of Drosophila and Dictyostelium. Synthesis of the cycloheximide-stimulated polypeptide bands was on cytoplasmic ribosomes rather than on mitochondrial ribosomes, as incorporation of isotope into the polypeptide bands was inhibited by 1.0 microgram of cycloheximide per ml but not by 1 mg of chloramphenicol per ml. In a mutant with cycloheximide-resistant ribosomes, 0.1 microgram of cycloheximide per ml failed to alter the pattern of protein synthesis from that of the controls. It is suggested that the new synthesis of the polypeptide bands reflects specific mechanisms of adaptation to different kinds of environmental stress, including inhibition of protein synthesis and temperature increases.

Phase Shifting of the Circadian Clock by Diethylstilbestrol and Related Compounds in Neurospora crassa

Phase shifts of the circadian conidiation rhythm in Neurospora crassa were induced by 3-hour treatments of mycelia in liquid medium with diethylstilbestrol (DES), dienestrol (DIE), hexestrol (HEX), diethylstilbestroldipropionate (DESP), and dienestroldiacetate (DIEA). Over a 24-hour period beginning 24 hours after the transition from light to constant dark, maximum phase shifts occurred about 36 hours. DES was the most effective of the drugs tested, giving 10-hour phase advances at 20 micromolar. DIE and HEX caused similar phase shifts as DES at 40 micromolar. The two derivatives of the last, DESP and DIEA, were much less effective in shifting phase; only a few hours of phase advance result from treatments at 80 micromolar concentrations.The activity of isolated plasma membrane ATPase was inhibited by DES and partially by HEX, but not by DIE, DESP, or DIEA. O(2) consumption of the mycelia was inhibited equally by DES, DIE, and HEX, while DIEA and DESP had little effect. Phase-shifts by DES cannot be interpreted as evidence that plasma membrane ATPase is a component of the circadian clock.

Light-induced phase shifting of the circadian clock in Neurospora crassa requires ammonium salts at high pH

Effects of external ionic conditions on light induced phase shifting of the circadian rhythm of conidiation in Neurospora crassa were examined in simple buffer solutions for discerning effects of individual ions. Mycelia were cultured to liquid media of different pHs and then transferted to 10 mM piperazine-N,N'-bis(2-ethanesulmonic acid) (Pipes) buffer of various pHs and irradiated with while light. The phase of the rhythm of dark controls was not changed by transfer from medium to buffer. When mycelia were cultured in media of pH above 6.7, light did not advance the phase of the clock in Pipes buffer alone. However, light-induced phase advance was restored when an ammonium salt was added to buffer of pH higher than 7.6. An amination-defective mutant, bd am, showed the same response to ammonium nitrate as the wild-type strain, bd. Ammonium must be present before light irradiation for restoration of phase shifting. Free-amino-acid pools in the cells were changed by treatment with Pipes buffer: aspartle acid, glutamic acid, ammonia, glutamine and ornithine levels decreased, while lysine and histidine increased. Addition of ammonium nitrate to Pipes buffer resulted in further changes in amino-acid pools; lysine, histidine, arginine, alanine and ornithine decreased, and glutamine levels increased. Irradiation did not result in significant changes in amino acid pools.

Effects of Membrane ATPase Inhibitors on Light-Induced Phase Shifting of the Circadian Clock in Neurospora crassa

Effects of several membrane ATPase inhibitors on light-induced phase shifting of the circadian conidiation rhythm in Neurospora crassa were examined using mycelial discs in liquid culture. Suppression of phase shifting by the inhibitors was strongly dependent on the pH of the liquid medium in which the discs were cultured during the time from light-dark transition (beginning of free-run) to light irradiation. When discs were cultured in pH 6.7 medium, azide, the inhibitors of plasma membrane ATPase (diethylstilbestrol and N, N'-dicyclohexylcarbodiimide), and ethanol completely suppressed the effect of light on the clock. In contrast, mycelial discs cultured in pH 5.7 medium were fully phase-shifted by light in the presence of the same and even higher concentrations of the chemicals. However, sensitivity to light of the discs cultured in relatively acidic medium was eight times higher than that of the discs cultured at neutral pH. Oligomycin and venturicidin, inhibitors of mitochondrial ATPase, did not suppress phase shifting by light at either pH.

Genetic Evidence That Protein Synthesis Is Required for the Circadia Clock of Neurospora

Small doses of cycloheximide given at intervals (pulses) cause phase shifts of the circadian clock of Neurospora. The effects of this drug on the clock are mediated through its inhibition of protein synthesis, since two cycloheximide-resistant mutants whose 80S ribosomes are resistant to cycloheximide showed no phase shift after exposure to the durg.