Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora

Phenotypic analyses of ΔwcoA and ΔwcoB mutants in Fusarium fujikuroi reveal dark and light-dependent functions as a white-collar complex

The Fusarium fujikuroi fungus, known as a biotechnological source of gibberellins, has a complex secondary metabolism that responds to various environmental signals, including the availability of light and nitrogen. White collar complex proteins, consisting of the flavoprotein WC1 and its partner WC2, are widespread in fungi where they play a central role in the regulation of numerous genes in response to light. Fusarium fungi possess one copy of each WC gene, named wcoA and wcoB in F. fujikuroi. Function of WcoA was previously investigated for the phenotypic effects of its mutation and the consequences on the transcriptome. In this work we have obtained deletion mutants of the wcoA and wcoB genes in IMI58289 genetic background and the expression of some light-regulated genes related to photobiology, development, and stress, as well as genes for key enzymes of secondary metabolism have been analyzed. The results show that several investigated genes require both WcoA and WcoB to be induced by light, and in some cases, also to be correctly expressed in darkness. The regulatory alterations observed in the wcoA or wcoB mutants are mostly coincidental, indicating the functioning of the encoded proteins as a complex. On the other hand, the diversity of effects on different genes of secondary metabolism, as well as the differences of these effects with those previously observed in another wild-type strain, indicate a high functional versatility of the predicted white-collar complex in the genus Fusarium.

Circadian clock is critical for fungal pathogenesis by regulating zinc starvation response and secondary metabolism

Circadian clocks are known to modulate host immune responses to pathogen infections, yet their role in influencing pathogen pathogenesis remains unclear. Here, we investigated the role of circadian clocks in regulating the pathogenesis of the fungal pathogen Fusarium oxysporum, which has multiple genes homologous to the Neurospora crassa frq due to gene duplication events, with Fofrq1 being the primary circadian clock gene. The pathogenesis of F. oxysporum in plants is controlled by its circadian clock, with infections causing severe disease symptoms at dawn. Notably, disruption of clock genes dramatically reduces fungal pathogenicity. Circadian clocks regulate the rhythmic expression of several transcription factors, including FoZafA, which enables the pathogen to adapt to zinc starvation within the plant, and FoCzf1, which governs the production of the toxin fusaric acid. Together, our findings highlight the critical roles of circadian clocks in F. oxysporum pathogenicity by regulating zinc starvation response and secondary metabolite production.

Circadian clock control of interactions between eIF2α kinase CPC-3 and GCN1 with ribosomes regulates rhythmic translation initiation

Misregulation of the activity of GCN2, the kinase that phosphorylates and inactivates translation initiation factor eIF2α, has been implicated in several health disorders, underscoring the need to determine the mechanisms controlling GCN2 activation. During nutrient starvation, increased uncharged tRNA levels trigger GCN1 and GCN20 proteins to mediate the binding of uncharged tRNA to GCN2 to activate the kinase to phosphorylate eIF2α. Under constant conditions, activation of the Neurospora crassa homolog of GCN2, CPC-3, is controlled by the circadian clock. However, how the circadian clock controls the rhythmic activity of CPC-3 was not known. We found that the clock regulates CPC-3 and GCN1 interaction with ribosomes and show that these interactions are necessary for clock regulation of CPC-3 activity. CPC-3 activity rhythms, and the rhythmic interaction of CPC-3 and GCN1 with ribosomes, are abolished in a temperature-sensitive valyl-tRNA synthetase mutant (un-3ts) that has high levels of uncharged tRNAVal at all times of the day. Disrupting the interaction between GCN1 and uncharged tRNA in the absence of GCN20 altered rhythmic CPC-3 activity, indicating that the clock controls the interaction between uncharged tRNA and GCN1. Together, these data support that circadian rhythms in mRNA translation through CPC-3 activity require rhythms in uncharged tRNA levels that drive the rhythmic interaction between CPC-3 and GCN1 with ribosomes. This regulation uncovers a fundamental mechanism to ensure temporal coordination between peak cellular energy levels and the energetically demanding process of mRNA translation.

Circadian rhythms: pervasive, and often times evasive

Most circadian texts begin by stating that clocks are pervasive throughout the tree of life. Indeed, clock mechanisms have been described from cyanobacteria to humans, representing a notable example of convergent evolution: yet, there are several phyla in animals, protists or within fungi and bacteria, in which homologs of some-or all-known clock components seem to be absent, posing inevitable questions about the evolution of circadian systems. Moreover, as we move away from model organisms, there are several taxa in which core clock elements can be identified at the genomic levels. However, the functional description of those putative clocks has been hard to achieve, as rhythmicity is not observed unless defined abiotic or nutritional cues are provided. The mechanisms 'conditioning' the functionality of clocks remain uncertain, emphasizing the need to delve further into non-model circadian systems. As the absence of evidence is not evidence of absence, the lack of known core-clock homologs or of observable rhythms in a given organism, cannot be an a priori criterion to discard the presence of a functional clock, as rhythmicity may be limited to yet untested experimental conditions or phenotypes. This article seeks to reflect on these topics, highlighting some of the pressing questions awaiting to be addressed.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Uncovering the circadian transcriptome of Nasonia vitripennis: insights into a non-canonical insect model

The study of the circadian clock has greatly benefited from using Drosophila as a model system. Yet accumulating evidence suggests that the fly might not be the canonical insect model. Here, I have analysed the circadian transcriptome of the jewel wasp Nasonia vitripennis by using RNA-seq in both constant darkness and constant light (in contrast to flies, the wasps are rhythmic under continuous light). I identify approximately 6% of the transcriptome as cycling under constant conditions, revealing a bimodal distribution of phases and low cycling amplitude. I examine the biological processes under circadian control in Nasonia, identifying clock control of functions such as metabolism, light response and a variety of neural processes, drawing comparisons between Nasonia and Drosophila. Although there was little similarity between cycling genes in Drosophila and Nasonia, the functions fulfilled by cycling transcripts were similar in both species. Interestingly, of the known Drosophila core clock genes, only Pdp1e, shaggy and Clock showed significant cycling in Nasonia, highlighting the potential diversity in molecular clock mechanisms across insect species.

Transcriptional rewiring of an evolutionarily conserved circadian clock

Circadian clocks temporally coordinate daily organismal biology over the 24-h cycle. Their molecular design, preserved between fungi and animals, is based on a core-oscillator composed of a one-step transcriptional-translational-negative-feedback-loop (TTFL). To test whether this evolutionarily conserved TTFL architecture is the only plausible way for achieving a functional circadian clock, we adopted a transcriptional rewiring approach, artificially co-opting regulators of the circadian output pathways into the core-oscillator. Herein we describe one of these semi-synthetic clocks which maintains all basic circadian features but, notably, it also exhibits new attributes such as a "lights-on timer" logic, where clock phase is fixed at the end of the night. Our findings indicate that fundamental circadian properties such as period, phase and temperature compensation are differentially regulated by transcriptional and posttranslational aspects of the clockworks.

Uncoupling of behavioral and metabolic 24-h rhythms in reindeer

Reindeer in the Arctic seasonally suppress daily circadian patterns of behavior present in most animals.1 In humans and mice, even when all daily behavioral and environmental influences are artificially suppressed, robust endogenous rhythms of metabolism governed by the circadian clock persist and are essential to health.2,3 Disrupted rhythms foster metabolic disorders and weight gain.4 To understand circadian metabolic organization in reindeer, we performed behavioral measurements and untargeted metabolomics from blood plasma samples taken from Eurasian tundra reindeer (Rangifer tarandus tarandus) across 24 h at 2-h intervals in four seasons. Our study confirmed the absence of circadian rhythms of behavior under constant darkness in the Arctic winter and constant daylight in the Arctic summer, as reported by others.1 We detected and measured the intensity of 893 metabolic features in all plasma samples using untargeted ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS). A core group of metabolites (66/893 metabolic features) consistently displayed 24-h rhythmicity. Most metabolites displayed a robust 24-h rhythm in winter and spring but were arrhythmic in summer and fall. Half of all measured metabolites displayed ultradian sleep-wake dependence in summer. Irrespective of the arrhythmic behavior, metabolism is rhythmic (24 h) in seasons of low food availability, potentially favoring energy efficiency. In seasons of food abundance, 24-h rhythmicity in metabolism is drastically reduced, again irrespective of behavioral rhythms, potentially fostering weight gain.

Syncytial Assembly Lines: Consequences of Multinucleate Cellular Compartments for Fungal Protein Synthesis

Fast growth and prodigious cellular outputs make fungi powerful tools in biotechnology. Recent modeling work has exposed efficiency gains associated with dividing the labor of transcription over multiple nuclei, and experimental innovations are opening new windows on the capacities and adaptations that allow nuclei to behave autonomously or in coordination while sharing a single, common cytoplasm. Although the motivation of our review is to motivate and connect recent work toward a greater understanding of fungal factories, we use the analogy of the assembly line as an organizing idea for studying coordinated gene expression, generally.

Circadian regulation of metabolism across photosynthetic organisms

Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.

Circadian clock control of tRNA synthetases in Neurospora crassa

Background: In Neurospora crassa, the circadian clock controls rhythmic mRNA translation initiation through regulation of the eIF2α kinase CPC-3 (the homolog of yeast and mammalian GCN2). Active CPC-3 phosphorylates and inactivates eIF2α, leading to higher phosphorylated eIF2α (P-eIF2α) levels and reduced translation initiation during the subjective day. This daytime activation of CPC-3 is driven by its binding to uncharged tRNA, and uncharged tRNA levels peak during the day under control of the circadian clock. The daily rhythm in uncharged tRNA levels could arise from rhythmic amino acid levels or aminoacyl-tRNA synthetase (aaRSs) levels. Methods: To determine if and how the clock potentially controls rhythms in aspartyl-tRNA synthetase (AspRS) and glutaminyl-tRNA synthetase (GlnRS), both observed to be rhythmic in circadian genomic datasets, transcriptional and translational fusions to luciferase were generated. These luciferase reporter fusions were examined in wild type (WT), clock mutant Δ frq, and clock-controlled transcription factor deletion strains. Results: Translational and transcriptional fusions of AspRS and GlnRS to luciferase confirmed that their protein levels are clock-controlled with peak levels at night. Moreover, clock-controlled transcription factors NCU00275 and ADV-1 drive robust rhythmic protein expression of AspRS and GlnRS, respectively. Conclusions: These data support a model whereby coordinate clock control of select aaRSs drives rhythms in uncharged tRNAs, leading to rhythmic CPC-3 activation, and rhythms in translation of specific mRNAs.

The genomic basis of temporal niche evolution in a diurnal rodent

Patterns of diel activity-how animals allocate their activity throughout the 24-h daily cycle-play key roles in shaping the internal physiology of an animal and its relationship with the external environment.1,2,3,4,5 Although shifts in diel activity patterns have occurred numerous times over the course of vertebrate evolution,6 the genomic correlates of such transitions remain unknown. Here, we use the African striped mouse (Rhabdomys pumilio), a species that transitioned from the ancestrally nocturnal diel niche of its close relatives to a diurnal one,7,8,9,10,11 to define patterns of naturally occurring molecular variation in diel niche traits. First, to facilitate genomic analyses, we generate a chromosome-level genome assembly of the striped mouse. Next, using transcriptomics, we show that the switch to daytime activity in this species is associated with a realignment of daily rhythms in peripheral tissues with respect to the light:dark cycle and the central circadian clock. To uncover selection pressures associated with this temporal niche shift, we perform comparative genomic analyses with closely related rodent species and find evidence of relaxation of purifying selection on striped mouse genes in the rod phototransduction pathway. In agreement with this, electroretinogram measurements demonstrate that striped mice have functional differences in dim-light visual responses compared with nocturnal rodents. Taken together, our results show that striped mice have undergone a drastic change in circadian organization and provide evidence that the visual system has been a major target of selection as this species transitioned to a novel temporal niche.

Transcription activator WCC recruits deacetylase HDA3 to control transcription dynamics and bursting in Neurospora

RNA polymerase II initiates transcription either randomly or in bursts. We examined the light-dependent transcriptional activator White Collar Complex (WCC) of Neurospora to characterize the transcriptional dynamics of the strong vivid (vvd) promoter and the weaker frequency (frq) promoter. We show that WCC is not only an activator but also represses transcription by recruiting histone deacetylase 3 (HDA3). Our data suggest that bursts of frq transcription are governed by a long-lived refractory state established and maintained by WCC and HDA3 at the core promoter, whereas transcription of vvd is determined by WCC binding dynamics at an upstream activating sequence. Thus, in addition to stochastic binding of transcription factors, transcription factor-mediated repression may also influence transcriptional bursting.

Antisense Transcription of the Neurospora Frequency Gene Is Rhythmically Regulated by CSP-1 Repressor but Dispensable for Clock Function

The circadian clock of Neurospora crassa is based on a negative transcriptional/translational feedback loops. The frequency (frq) gene controls the morning-specific rhythmic transcription of a sense RNA encoding FRQ, the negative element of the core circadian feedback loop. In addition, a long noncoding antisense RNA, qrf, is rhythmically transcribed in an evening-specific manner. It has been reported that the qrf rhythm relies on transcriptional interference with frq transcription and that complete suppression of qrf transcription impairs the circadian clock. We show here that qrf transcription is dispensable for circadian clock function. Rather, the evening-specific transcriptional rhythm of qrf is mediated by the morning-specific repressor CSP-1. Since CSP-1 expression is induced by light and glucose, this suggests a rhythmic coordination of qrf transcription with metabolism. However, a possible physiological significance for the circadian clock remains unclear, as suitable assays are not available.

Adaptation to glucose starvation is associated with molecular reorganization of the circadian clock in Neurospora crassa

The circadian clock governs rhythmic cellular functions by driving the expression of a substantial fraction of the genome and thereby significantly contributes to the adaptation to changing environmental conditions. Using the circadian model organism Neurospora crassa, we show that molecular timekeeping is robust even under severe limitation of carbon sources, however, stoichiometry, phosphorylation and subcellular distribution of the key clock components display drastic alterations. Protein kinase A, protein phosphatase 2 A and glycogen synthase kinase are involved in the molecular reorganization of the clock. RNA-seq analysis reveals that the transcriptomic response of metabolism to starvation is highly dependent on the positive clock component WC-1. Moreover, our molecular and phenotypic data indicate that a functional clock facilitates recovery from starvation. We suggest that the molecular clock is a flexible network that allows the organism to maintain rhythmic physiology and preserve fitness even under long-term nutritional stress.

A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules

Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.

Dawn-to-dusk dry fasting induces anti-atherosclerotic, anti-inflammatory, and anti-tumorigenic proteome in peripheral blood mononuclear cells in subjects with metabolic syndrome

BACKGROUND

Metabolic syndrome characterized by abdominal obesity, high blood pressure, elevated fasting glucose and triglyceride levels and low high-density lipoprotein cholesterol level is associated with pro-inflammatory state, increased risk for atherosclerosis, and multiple cancers. Our previous results on subjects with metabolic syndrome showed that 4-week dawn-to-dusk (sunset) dry fasting resulted in significant changes in the serum proteome and improvement in several metabolic risk factors. Peripheral blood mononuclear cells (PBMC) proteomics is a powerful tool that can provide mechanistic insights into how dawn-to-dusk dry fasting affects protein expression in metabolic pathways at cellular level. In this study, we determined whether dawn-to-dusk dry fasting would induce favorable changes in PBMC proteome in subjects with metabolic syndrome, similar to the changes induced by dawn-to-dusk dry fasting in the same subjects' serum proteome.

METHODS

We conducted a prospective study on subjects with metabolic syndrome and collected blood specimens before 4-week dawn-to-dusk dry fasting, at the end of 4-week dawn-to-dusk dry fasting, and one week after 4-week dawn-to-dusk dry fasting. We performed untargeted proteomics using nano ultra-high performance liquid chromatography-tandem mass spectrometry to assess the impact of 4-week dawn-to-dusk dry fasting on PBMC proteome.

RESULTS

There were 14 subjects with metabolic syndrome with a mean age of 59 who fasted from dawn to dusk (strict dry fasting without any liquid or food intake) for more than 14 h daily for 29 days. The quantitative proteome analysis showed that apolipoprotein B (APOB) gene protein products (GP) levels were downregulated and had the most statistical significance of the observed difference at the end of 4-week dawn-to-dusk dry fasting (P = 0.008) and one week after 4-week dawn-to-dusk dry fasting (P = 0.0004) compared with the levels before 4-week dawn-to-dusk dry fasting. The comparison between GP levels before and at the end of 4-week dawn-to-dusk dry fasting showed an alteration in the expression of genes associated with lipid and atherosclerosis pathway (P = 6.014e-4) and C-type lectin receptor signaling pathway (P = 1.064e-5). The genes that were differentially expressed in the lipid and atherosclerosis pathway were APOB (P = 0.008), CD36 (P = 0.040), CALM1, CALM2, CALM3 (P = 0.015), and HSPA8 (P = 0.047). One of the differentially expressed genes in the C-type lectin receptor signaling pathway was lymphocyte-specific protein 1 (LSP1), which showed an average of 19-fold increase at the end of 4-week dawn-to-dusk dry fasting compared with the GP levels before fasting (P = 0.004). Several GPs associated with tumor-suppressor effect (TUBB4B, LSP1, ACTR3B) were upregulated, and GPs associated with tumor-promoter effect (CD36, CALM1, CALM2, CALM3, FLOT2, PPIF) were downregulated at the end of 4-week dawn-to-dusk dry fasting or one week after 4-week dawn-to-dusk dry fasting compared with the GP levels before 4-week dawn-to-dusk dry fasting.

CONCLUSION

Based on our results, we conclude that in subjects with metabolic syndrome, 4-week dawn-to-dusk dry fasting induced anti-atherosclerotic, anti-inflammatory, and anti-tumorigenic PMBC proteome. Randomized, controlled clinical trials are needed to further investigate the effect of dawn-to-dusk dry fasting on subjects with chronic metabolic diseases and metabolic syndrome-induced cancers.

Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa

Eukaryotic circadian clocks are based on self-sustaining, cell-autonomous oscillatory feedback loops that can synchronize with the environment via recurrent stimuli (zeitgebers) such as light. The components of biological clocks and their network interactions are becoming increasingly known, calling for a quantitative understanding of their role for clock function. However, the development of data-driven mathematical clock models has remained limited by the lack of sufficiently accurate data. Here we present a comprehensive model of the circadian clock of Neurospora crassa that describe free-running oscillations in constant darkness and entrainment in light-dark cycles. To parameterize the model, we measured high-resolution time courses of luciferase reporters of morning and evening specific clock genes in WT and a mutant strain. Fitting the model to such comprehensive data allowed estimating parameters governing circadian phase, period length and amplitude, and the response of genes to light cues. Our model suggests that functional maturation of the core clock protein Frequency causes a delay in negative feedback that is critical for generating circadian rhythms.

Circadian rhythms are endogenous autonomous clocks that emancipate daily rhythms in physiology and behavior. Lately, a large body of research has contributed to our understanding of clocks’ genetic and mechanistic basis across kingdoms of life, i.e., mammals, fungi, plants, and bacteria. Several mathematical models have made key contributions to our current understanding of the design principles of the Neurospora crassa circadian clock and conditions for self-sustained oscillations. However, previous models uncovered and described the principle properties of the clock in generic manner due to a lack of experimental data. In this study, we developed a mathematical model based on systems of differential equations to describe the core clock components and estimated model parameters from luciferase data that capture experimental observations. We demonstrate the model predictive control simulation emphasizing the importance of functional maturation of the core clock protein Frequency in generating circadian rhythms.

Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea

Circadian clocks are important for an individual’s fitness, and recent studies have underlined their role in the outcome of biological interactions. However, the relevance of circadian clocks in fungal–fungal interactions remains largely unexplored. We sought to characterize a functional clock in the biocontrol agent Trichoderma atroviride to assess its importance in the mycoparasitic interaction against the phytopathogen Botrytis cinerea. Thus, we confirmed the existence of circadian rhythms in T. atroviride, which are temperature-compensated and modulated by environmental cues such as light and temperature. Nevertheless, the presence of such molecular rhythms appears to be highly dependent on the nutritional composition of the media. Complementation of a clock null (Δfrq) Neurospora crassa strain with the T. atroviride-negative clock component (tafrq) restored core clock function, with the same period observed in the latter fungus, confirming the role of tafrq as a bona fide core clock component. Confrontation assays between wild-type and clock mutant strains of T. atroviride and B. cinerea, in constant light or darkness, revealed an inhibitory effect of light on T. atroviride’s mycoparasitic capabilities. Interestingly, when confrontation assays were performed under light/dark cycles, T. atroviride’s overgrowth capacity was enhanced when inoculations were at dawn compared to dusk. Deleting the core clock-negative element FRQ in B. cinerea, but not in T. atroviride, was vital for the daily differential phenotype, suggesting that the B. cinerea clock has a more significant influence on the result of this interaction. Additionally, we observed that T. atroviride clock components largely modulate development and secondary metabolism in this fungus, including the rhythmic production of distinct volatile organic compounds (VOCs). Thus, this study provides evidence on how clock components impact diverse aspects of T. atroviride lifestyle and how daily changes modulate fungal interactions and dynamics.

Casein kinase 1 and disordered clock proteins form functionally equivalent, phospho-based circadian modules in fungi and mammals

Circadian clocks rely on negative feedback loops. The core circadian inhibitors, FRQ in Neurospora and PERs in animals, are progressively hyperphosphorylated, inactivated, and degraded. CK1 is essential for these clocks. Despite our knowledge of the role of CK1, it is not known how many other kinases are required and how multisite phosphorylation might contribute to circadian timekeeping. We show here that CK1 alone is sufficient to slowly phosphorylate low-affinity sites in FRQ or PER2. The reaction is nearly temperature compensated, and the phosphorylation state of FRQ or PER2 corresponds to the time elapsed since the start of the reaction. Thus, CK1 and FRQ or PER2 form equivalent modules that are in principle capable of measuring time on a circadian scale.

Circadian clocks are timing systems that rhythmically adjust physiology and metabolism to the 24-h day–night cycle. Eukaryotic circadian clocks are based on transcriptional–translational feedback loops (TTFLs). Yet TTFL-core components such as Frequency (FRQ) in Neurospora and Periods (PERs) in animals are not conserved, leaving unclear how a 24-h period is measured on the molecular level. Here, we show that CK1 is sufficient to promote FRQ and mouse PER2 (mPER2) hyperphosphorylation on a circadian timescale by targeting a large number of low-affinity phosphorylation sites. Slow phosphorylation kinetics rely on site-specific recruitment of Casein Kinase 1 (CK1) and access of intrinsically disordered segments of FRQ or mPER2 to bound CK1 and on CK1 autoinhibition. Compromising CK1 activity and substrate binding affects the circadian clock in Neurospora and mammalian cells, respectively. We propose that CK1 and the clock proteins FRQ and PERs form functionally equivalent, phospho-based timing modules in the core of the circadian clocks of fungi and animals.

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor

Background

Circadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. Brood-tending nurse ants are usually younger individuals and show “around-the-clock” activity. With age or in the absence of brood, nurses transition into foraging ants that show daily rhythms in activity. Ants can adaptively shift between these behavioral castes and caste-associated chronotypes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity in Camponotus floridanus carpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains.

Results

We found that nurse brains have three times fewer 24 h oscillating genes than foragers. However, several hundred genes that oscillated every 24 h in forager brains showed robust 8 h oscillations in nurses, including the core clock genes Period and Shaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment and output pathway, including genes said to be involved in regulating insect locomotory behavior. We also found that Vitellogenin, known to regulate division of labor in social insects, showed robust 24 h oscillations in nurse brains but not in foragers. Finally, we found significant overlap between genes differentially expressed between the two ant castes and genes that show ultradian rhythms in daily expression.

Conclusion

This study provides a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify a putative molecular mechanism underlying plastic timekeeping: several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found in C. floridanus, thus, likely represent a more general phenomenon that warrants further investigation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08282-x.

Inoculation of Neurospora sp. for improving ammonia production during thermophilic composting of organic sludge

Recent attempts have been made to develop a thermophilic composting process for organic sludge to not only produce organic fertilizers and soil conditioners, but to also utilize the generated ammonia gas to produce high value-added algae. The hydrolysis of organic nitrogen in sludge is a bottleneck in ammonia conversion, and its improvement is a major challenge. The present study aimed to elucidate the effects of inoculated Neurospora sp. on organic matter decomposition and ammonia conversion during thermophilic composting of two organic sludge types: anaerobic digestion sludge and shrimp pond sludge. A laboratory-scale sludge composting experiment was conducted with a 6-day pretreatment period at 30 °C with Neurospora sp., followed by a 10-day thermophilic composting period at 50 °C by inoculating the bacterial community. The final organic matter decomposition was significantly higher in the sludge pretreated with Neurospora sp. than in the untreated sludge. Correspondingly, the amount of non-dissolved nitrogen was also markedly reduced by pretreatment, and the ammonia conversion rate was notably improved. Five enzymes exhibiting high activity only during the pretreatment period were identified, while no or low activity was observed during the subsequent thermophilic composting period, suggesting the involvement of these enzymes in the degradation of hardly degradable fractions, such as bacterial cells. The bacterial community analysis and its function prediction suggested the contribution of Bacillaceae in the degradation of easily degradable organic matter, but the entire bacterial community was highly incapable in degrading the hardly degradable fraction. To conclude, this study is the first to demonstrate that Neurospora sp. decomposes those organic nitrogen fractions that require a long time to be decomposed by the bacterial community during thermophilic composting.

A global search for novel transcription factors impacting the Neurospora crassa circadian clock

Eukaryotic circadian oscillators share a common circuit architecture, a negative feedback loop in which a positive element activates the transcription of a negative one that then represses the action of the former, inhibiting its own expression. While studies in mammals and insects have revealed additional transcriptional inputs modulating the expression of core clock components, this has been less characterized in the model Neurospora crassa, where the participation of other transcriptional components impacting circadian clock dynamics remains rather unexplored. Thus, we sought to identify additional transcriptional regulators modulating the N. crassa clock, following a reverse genetic screen based on luminescent circadian reporters and a collection of transcription factors (TFs) knockouts, successfully covering close to 60% of them. Besides the canonical core clock components WC-1 and -2, none of the tested transcriptional regulators proved to be essential for rhythmicity. Nevertheless, we identified a set of 23 TFs that when absent lead to discrete, but significant, changes in circadian period. While the current level of analysis does not provide mechanistic information about how these new players modulate circadian parameters, the results of this screen reveal that an important number of light and clock-regulated TFs, involved in a plethora of processes, are capable of modulating the clockworks. This partial reverse genetic clock screen also exemplifies how the N. crassa knockout collection continues to serve as an expedite platform to address broad biological questions.

Circadian Interactomics: How Research Into Protein-Protein Interactions Beyond the Core Clock Has Influenced the Model of Circadian Timekeeping

The circadian clock is the broadly conserved, protein-based, timekeeping mechanism that synchronizes biology to the Earth's 24-h light-dark cycle. Studies of the mechanisms of circadian timekeeping have placed great focus on the role that individual protein-protein interactions play in the creation of the timekeeping loop. However, research has shown that clock proteins most commonly act as part of large macromolecular protein complexes to facilitate circadian control over physiology. The formation of these complexes has led to the large-scale study of the proteins that comprise these complexes, termed here "circadian interactomics." Circadian interactomic studies of the macromolecular protein complexes that comprise the circadian clock have uncovered many basic principles of circadian timekeeping as well as mechanisms of circadian control over cellular physiology. In this review, we examine the wealth of knowledge accumulated using circadian interactomics approaches to investigate the macromolecular complexes of the core circadian clock, including insights into the core mechanisms that impart circadian timing and the clock's regulation of many physiological processes. We examine data acquired from the investigation of the macromolecular complexes centered on both the activating and repressing arm of the circadian clock and from many circadian model organisms.

Impact of the White Collar Photoreceptor WcoA on the Fusarium fujikuroi Transcriptome

The proteins of the White Collar 1 family (WC) constitute a major class of flavin photoreceptors, widely distributed in fungi, that work in cooperation with a WC 2 protein forming a regulatory complex. The WC complex was investigated in great detail in Neurospora crassa, a model fungus in photobiology studies, where it controls all its major photoresponses. The fungus Fusarium fujikuroi, a model system in the production of secondary metabolites, contains a single WC-1 gene called wcoA. The best-known light response in this fungus is the photoinduction of the synthesis of carotenoids, terpenoid pigments with antioxidant properties. Loss of WcoA in F. fujikuroi results in a drastic reduction in the mRNA levels of the carotenoid genes, and a diversity of morphological and metabolic changes, including alterations in the synthesis of several secondary metabolites, suggesting a complex regulatory role. To investigate the function of WcoA, the transcriptome of F. fujikuroi was analyzed in the dark and after 15-, 60- or 240-min illumination in a wild strain and in a formerly investigated wcoA insertional mutant. Using a threshold of four-fold change in transcript levels, 298 genes were activated and 160 were repressed in the wild strain under at least one of the light exposures. Different response patterns were observed among them, with genes exhibiting either fast, intermediate, and slow photoinduction, or intermediate or slow repression. All the fast and intermediate photoresponses, and most of the slow ones, were lost in the wcoA mutant. However, the wcoA mutation altered the expression of a much larger number of genes irrespective of illumination, reaching at least 16% of the annotated genes in this fungus. Such genes include many related to secondary metabolism, as well as others related to photobiology and other cellular functions, including the production of hydrophobins. As judged by the massive transcriptomic changes exhibited by the wcoA mutant in the dark, the results point to WcoA as a master regulatory protein in F. fujikuroi, in addition to a central function as the photoreceptor responsible for most of the transcriptional responses to light in this fungus.

The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in Mammals

The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.

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

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

Coupling protocol of interlocked feedback oscillators in circadian clocks

Circadian rhythms (approx. 24 h) show the robustness of key oscillatory features such as phase, period and amplitude against external and internal variations. The robustness of Drosophila circadian clocks can be generated by interlocked transcriptional-translational feedback loops, where two negative feedback loops are coupled through mutual activations. The mechanisms by which such coupling protocols have survived out of many possible protocols remain to be revealed. To address this question, we investigated two distinct coupling protocols: activator-coupled oscillators (ACO) and repressor-coupled oscillators (RCO). We focused on the two coupling parameters: coupling dissociation constant and coupling time-delay. Interestingly, the ACO was able to produce anti-phase or morning-evening cycles, whereas the RCO produced in-phase ones. Deterministic and stochastic analyses demonstrated that the anti-phase ACO provided greater fluctuations in amplitude not only with respect to changes in coupling parameters but also to random parameter perturbations than the in-phase RCO. Moreover, the ACO deteriorated the entrainability to the day-night master clock, whereas the RCO produced high entrainability. Considering that the real, interlocked feedback loops have evolved as the ACO, instead of the RCO, we first proposed a hypothesis that the morning-evening or anti-phase cycle is more essential for Drosophila than achieving robustness and entrainability.

A circadian clock in Neurospora crassa functions during plant cell wall deconstruction

Circadian clocks are autonomous timers that are believed to confer organisms a selective advantage by enabling processes to occur at appropriate times of the day. In the model fungus Neurospora crassa, 20-40 % of its genes are reported to be under circadian regulation, as assayed in simple sugar media. Although it has been well-described that Neurospora efficiently deconstructs plant cell wall components, little is known regarding the status of the clock when Neurospora grows on cellulosic material, or whether such a clock has an impact on any of the genes involved in this process. Through luciferase-based reporters and fluorescent detection assays, we show that a clock is functioning when Neurospora grows on cellulose-containing wheat straw as the only carbon and nitrogen source. Additionally, we found that the major cellobiohydrolase encoding gene involved in plant cell wall deconstruction, cbh-1, is rhythmically regulated by the Neurospora clock, in a manner that depends on cellulose concentration and on the transcription factor CRE-1, known as a key player in carbon-catabolite repression in this fungus. Our findings are a step towards a more comprehensive understanding on how clock regulation modulates cellulose degradation, and thus Neurospora's physiology.

Circadian clock control of eIF2α phosphorylation is necessary for rhythmic translation initiation

Circadian clock control of mRNA translation, which contributes to the daily cycling of at least 50% of the proteins synthesized in eukaryotic cells, is understudied. We show that the circadian clock in the model fungus Neurospora crassa regulates rhythms in phosphorylation and activity of the conserved translation initiation factor eIF2α, with a peak in phosphorylated eIF2α levels during the daytime. This leads to reduced mRNA translation of select messages during the day and increased translation at night. We demonstrate that rhythmic accumulation of phosphorylated eIF2α requires increased uncharged tRNA levels during the day to activate the eIF2α kinase, coordinating rhythmic translation initiation and protein production with nutrient and energy metabolism.

The circadian clock in eukaryotes controls transcriptional and posttranscriptional events, including regulation of the levels and phosphorylation state of translation factors. However, the mechanisms underlying clock control of translation initiation, and the impact of this potential regulation on rhythmic protein synthesis, were not known. We show that inhibitory phosphorylation of eIF2α (P-eIF2α), a conserved translation initiation factor, is clock controlled in Neurospora crassa, peaking during the subjective day. Cycling P-eIF2α levels required rhythmic activation of the eIF2α kinase CPC-3 (the homolog of yeast and mammalian GCN2), and rhythmic activation of CPC-3 was abolished under conditions in which the levels of charged tRNAs were altered. Clock-controlled accumulation of P-eIF2α led to reduced translation during the day in vitro and was necessary for the rhythmic synthesis of select proteins in vivo. Finally, loss of rhythmic P-eIF2α levels led to reduced linear growth rates, supporting the idea that partitioning translation to specific times of day provides a growth advantage to the organism. Together, these results reveal a fundamental mechanism by which the clock regulates rhythmic protein production, and provide key insights into how rhythmic translation, cellular energy, stress, and nutrient metabolism are linked through the levels of charged versus uncharged tRNAs.

Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain

The Eastern North American monarch butterfly, Danaus plexippus, is famous for its spectacular seasonal long-distance migration. In recent years, it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and seasonal behavioral outputs. However, unlike in Drosophila and the mouse, little work has been undertaken in the monarch to identify rhythmic genes at the genome-wide level and elucidate the regulation of their diurnal expression. Here, we used RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing to profile the diurnal transcriptome, open chromatin regions, and transcription factor (TF) footprints in the brain of wild-type monarchs and of monarchs with impaired clock function, including Cryptochrome 2 (Cry2), Clock (Clk), and Cycle-like loss-of-function mutants. We identified 217 rhythmically expressed genes in the monarch brain; many of them were involved in the regulation of biological processes key to brain function, such as glucose metabolism and neurotransmission. Surprisingly, we found no significant time-of-day and genotype-dependent changes in chromatin accessibility in the brain. Instead, we found the existence of a temporal regulation of TF occupancy within open chromatin regions in the vicinity of rhythmic genes in the brains of wild-type monarchs, which is disrupted in clock deficient mutants. Together, this work identifies for the first time the rhythmic genes and modes of regulation by which diurnal transcription rhythms are regulated in the monarch brain. It also illustrates the power of ATAC-sequencing to profile genome-wide regulatory elements and TF binding in a non-model organism for which TF-specific antibodies are not yet available.

With a rich biology that includes a clock-regulated migratory behavior and a circadian clock possessing mammalian clock orthologues, the monarch butterfly is an unconventional system with broad appeal to study circadian and seasonal rhythms. While clockwork mechanisms and rhythmic behavioral outputs have been studied in this species, the rhythmic genes that regulate rhythmic daily and seasonal activities remain largely unknown. Likewise, the mechanisms regulating rhythmic gene expression have not been explored in the monarch. Here, we applied genome-wide sequencing approaches to identify genes with rhythmic diurnal expression in the monarch brain, revealing the coordination of key pathways for brain function. We also identified the monarch brain open chromatin regions and provide evidence that regulation of rhythmic gene expression does not occur through temporal regulation of chromatin opening but rather by the time-of-day dependent binding of transcription factors in cis-regulatory elements. Together, our data extend our knowledge of the molecular rhythmic pathways, which may prove important in understanding the mechanisms underlying the daily and seasonal biology of the migratory monarch butterflies.

Circadian clock regulation of the glycogen synthase (gsn) gene by WCC is critical for rhythmic glycogen metabolism in Neurospora crassa

Circadian rhythms enable organisms to anticipate daily environmental cycles and control the timing of numerous biological processes, including metabolism, to optimize the health and survival of organisms. Glycogen metabolism is a conserved glucose homeostatic process; however, the molecular mechanisms linking the circadian clock and glycogen metabolism remain largely unknown. In this report, we demonstrate that circadian clock-dependent transcriptional regulation of glycogen synthase, gsn, regulates circadian oscillations of GSN protein and glycogen accumulation in the model filamentous fungus, Neurospora crassa.

Circadian clocks generate rhythms in cellular functions, including metabolism, to align biological processes with the 24-hour environment. Disruption of this alignment by shift work alters glucose homeostasis. Glucose homeostasis depends on signaling and allosteric control; however, the molecular mechanisms linking the clock to glucose homeostasis remain largely unknown. We investigated the molecular links between the clock and glycogen metabolism, a conserved glucose homeostatic process, in Neurospora crassa. We find that glycogen synthase (gsn) mRNA, glycogen phosphorylase (gpn) mRNA, and glycogen levels, accumulate with a daily rhythm controlled by the circadian clock. Because the synthase and phosphorylase are critical to homeostasis, their roles in generating glycogen rhythms were investigated. We demonstrate that while gsn was necessary for glycogen production, constitutive gsn expression resulted in high and arrhythmic glycogen levels, and deletion of gpn abolished gsn mRNA rhythms and rhythmic glycogen accumulation. Furthermore, we show that gsn promoter activity is rhythmic and is directly controlled by core clock component white collar complex (WCC). We also discovered that WCC-regulated transcription factors, VOS-1 and CSP-1, modulate the phase and amplitude of rhythmic gsn mRNA, and these changes are similarly reflected in glycogen oscillations. Together, these data indicate the importance of clock-regulated gsn transcription over signaling or allosteric control of glycogen rhythms, a mechanism that is potentially conserved in mammals and critical to metabolic homeostasis.

Memory in Fungal Pathogens Promotes Immune Evasion, Colonisation, and Infection

By analogy with Pavlov's dogs, certain pathogens have evolved anticipatory behaviours that exploit specific signals in the human host to prepare themselves against imminent host challenges. This adaptive prediction, a type of history-dependent microbial behaviour, represents a primitive form of microbial memory. For fungal pathogens, adaptive prediction helps them circumvent nutritional immunity, protects them against phagocytic killing, and activates immune evasion strategies. We describe how these anticipatory responses, and the contrasting lifestyles and evolutionary trajectories of fungal pathogens, have influenced the evolution of such adaptive behaviours, and how these behaviours affect host colonisation and infection.

Metabolic rhythms: A framework for coordinating cellular function

Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.

Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways

Transcriptional and translational feedback loops in fungi and animals drive circadian rhythms in transcript levels that provide output from the clock, but post-transcriptional mechanisms also contribute. To determine the extent and underlying source of this regulation, we applied newly developed analytical tools to a long-duration, deeply sampled, circadian proteomics time course comprising half of the proteome. We found a quarter of expressed proteins are clock regulated, but >40% of these do not arise from clock-regulated transcripts, and our analysis predicts that these protein rhythms arise from oscillations in translational rates. Our data highlighted the impact of the clock on metabolic regulation, with central carbon metabolism reflecting both transcriptional and post-transcriptional control and opposing metabolic pathways showing peak activities at different times of day. The transcription factor CSP-1 plays a role in this metabolic regulation, contributing to the rhythmicity and phase of clock-regulated proteins.

Waveforms of molecular oscillations reveal circadian timekeeping mechanisms

Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian clocks. We derive a mathematical framework where waveforms do reveal hidden biochemical mechanisms of circadian timekeeping. We find that the cost of synthesizing proteins with particular waveforms can be substantially reduced by rhythmic protein half-lives over time, as supported by previous plant and mammalian data, as well as our own seedling experiment. We also find that previously enigmatic, cyclic expression of positive arm components within the mammalian and insect clocks allows both a broad range of peak time differences between protein waveforms and the symmetries of the waveforms about the peak times. Such various peak-time differences may facilitate tissue-specific or developmental stage-specific multicellular processes. Our waveform-guided approach can be extended to various biological oscillators, including cell-cycle and synthetic genetic oscillators.

Hang-Hyun Jo et al. derive a mathematical framework for analyzing circadian clock waveforms. Using data from plants and animals, they find that waveforms of clock protein profiles provide important information about the biochemical mechanisms of circadian timekeeping.

Ultradian Rhythms in the Transcriptome of Neurospora crassa

In many organisms, the circadian clock drives rhythms in the transcription of clock-controlled genes that can be either circadian (∼24-hr period) or ultradian (<24-hr period). Ultradian rhythms with periods that are a fraction of 24 hr are termed harmonics. Several harmonic transcripts were discovered in the mouse liver, but their functional significance remains unclear. Using a model-based analysis, we report for the first time ∼7-hr third harmonic transcripts in Neurospora crassa, a well-established fungal circadian model organism. Several third harmonic genes are regulated by female fertility 7 (FF-7), whose transcript itself is third harmonic. The knockout of circadian output regulator CSP1 superimposes circadian rhythms on the third harmonic genes, whereas the knockout of stress response regulator MSN1 converts third harmonic rhythms to second harmonic rhythms. The 460 ∼7-hr genes are co-regulated in two anti-phasic groups in multiple genotypes and include kinases, chromatin remodelers, and homologs of harmonic genes in the mouse liver.

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Coexisting harmonic ∼7-hr and circadian rhythms in fungal clock model organism

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Knockout of output regulator CSP1 imposes circadian rhythms over ∼7-hr rhythms

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Third harmonic rhythms are a part of key cellular processes and mediated by FF-7

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7-hr genes are co-regulated in two anti-phasic clusters across genotypes and laboratories

Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes

In living organisms, biological clocks regulate 24 h (circadian) molecular, physiological, and behavioral rhythms to maintain homeostasis and synchrony with predictable environmental changes, in particular with those induced by Earth’s rotation on its axis. Harmonics of these circadian rhythms having periods of 8 and 12 h (ultradian) have been documented in several species. In mouse liver, harmonics of the 24-h period of gene transcription hallmarked genes oscillating with a frequency two or three times faster than circadian periodicity. Many of these harmonic transcripts enriched pathways regulating responses to environmental stress and coinciding preferentially with subjective dawn and dusk. At this time, the evolutionary history of genes with rhythmic expression is still poorly known and the role of length-of-day changes due to Earth’s rotation speed decrease over the last four billion years is totally ignored. We hypothesized that ultradian and stress anticipatory genes would be more evolutionarily conserved than circadian genes and background non-oscillating genes. To investigate this issue, we performed broad computational analyses of genes/proteins oscillating at different frequency ranges across several species and showed that ultradian genes/proteins, especially those oscillating with a 12-h periodicity, are more likely to be of ancient origin and essential in mice. In summary, our results show that genes with ultradian transcriptional patterns are more likely to be phylogenetically conserved and associated with the primeval and inevitable dawn/dusk transitions.

A component of the TOR (Target Of Rapamycin) nutrient-sensing pathway plays a role in circadian rhythmicity in Neurospora crassa

The TOR (Target of Rapamycin) pathway is a highly-conserved signaling pathway in eukaryotes that regulates cellular growth and stress responses. The cellular response to amino acids or carbon sources such as glucose requires anchoring of the TOR kinase complex to the lysosomal/vacuolar membrane by the Ragulator (mammals) or EGO (yeast) protein complex. Here we report a connection between the TOR pathway and circadian (daily) rhythmicity. The molecular mechanism of circadian rhythmicity in all eukaryotes has long been thought to be transcription/translation feedback loops (TTFLs). In the model eukaryote Neurospora crassa, a TTFL including FRQ (frequency) and WCC (white collar complex) has been intensively studied. However, it is also well-known that rhythmicity can be seen in the absence of TTFL functioning. We previously isolated uv90 as a mutation that compromises FRQ-less rhythms and also damps the circadian oscillator when FRQ is present. We have now mapped the uv90 gene and identified it as NCU05950, homologous to the TOR pathway proteins EGO1 (yeast) and LAMTOR1 (mammals), and we have named the N. crassa protein VTA (vacuolar TOR-associated protein). The protein is anchored to the outer vacuolar membrane and deletion of putative acylation sites destroys this localization as well as the protein’s function in rhythmicity. A deletion of VTA is compromised in its growth responses to amino acids and glucose. We conclude that a key protein in the complex that anchors TOR to the vacuole plays a role in maintaining circadian (daily) rhythmicity. Our results establish a connection between the TOR pathway and circadian rhythms and point towards a network integrating metabolism and the circadian system.

Circadian clocks drive 24-hour rhythms in living things at all levels of organization, from single cells to whole organisms. In spite of the importance of daily clocks for organizing the activities and internal functions of organisms, there are still many unsolved problems concerning the molecular mechanisms. In eukaryotes, a set of “clock proteins” turns on and off specific genes in a 24-hour feedback loop. This “clock gene feedback loop” has been the dominant idea about how clocks work for many years. However, some rhythms can still be seen when these feedback loops are not functioning. Using the fungus Neurospora crassa as a model organism, we have discovered a gene that is important for maintaining rhythms that continue without the known feedback loop. We have found that this gene codes for a protein that was already known to be important in helping cells to adjust their growth rate to adapt to varying availability of nutrients. Because the same gene is found in all eukaryotes, including mammals, this finding may point towards a universal clock mechanism that integrates nutritional needs with daily rhythms.

Regulation of plant cell wall degradation by light in Trichoderma

Trichoderma reesei (syn. Hypocrea jecorina) is the model organism for industrial production of plant cell wall degradating enzymes. The integration of light and nutrient signals for adaptation of enzyme production in T. reesei emerged as an important regulatory mechanism to be tackled for strain improvement. Gene regulation specific for cellulase inducing conditions is different in light and darkness with substantial regulation by photoreceptors. Genes regulated by light are clustered in the genome, with several of the clusters overlapping with CAZyme clusters. Major cellulase transcription factor genes and at least 75% of glycoside hydrolase encoding genes show the potential of light dependent regulation. Accordingly, light dependent protein complex formation occurs within the promoters of cellulases and their regulators. Additionally growth on diverse carbon sources is different between light and darkness and dependent on the presence of photoreceptors in several cases. Thereby, also light intensity plays a regulatory role, with cellulase levels dropping at higher light intensities dependent in the strain background. The heterotrimeric G-protein pathway is the most important nutrient signaling pathway in the connection with light response and triggers posttranscriptional regulation of cellulase expression. All G-protein alpha subunits impact cellulase regulation in a light dependent manner. The downstream cAMP pathway is involved in light dependent regulation as well. Connections between the regulatory pathways are mainly established via the photoreceptor ENV1. The effect of photoreceptors on plant cell wall degradation also occurs in the model filamentous fungus Neurospora crassa. In the currently proposed model, T. reesei senses the presence of plant biomass in its environment by detection of building blocks of cellulose and hemicellulose. Interpretation of the respective signals is subsequently adjusted to the requirements in light and darkness (or on the surface versus within the substrate) by an interconnection of nutrient signaling with light response. This review provides an overview on the importance of light, photoreceptors and related signaling pathways for formation of plant cell wall degrading enzymes in T. reesei. Additionally, the relevance of light dependent gene regulation for industrial fermentations with Trichoderma as well as strategies for exploitation of the observed effects are discussed.

The Clock Keeps on Ticking: Emerging Roles for Circadian Regulation in the Control of Fungal Physiology and Pathogenesis

Tic-tac, tic-tac, the sound of time is familiar to us, yet, it also silently shapes daily biological processes conferring 24-hour rhythms in, among others, cellular and systemic signaling, gene expression, and metabolism. Indeed, circadian clocks are molecular machines that permit temporal control of a variety of processes in individuals, with a close to 24-hour period, optimizing cellular dynamics in synchrony with daily environmental cycles. For over three decades, the molecular bases of these clocks have been extensively described in the filamentous fungus Neurospora crassa, yet, there have been few molecular studies in fungi other than Neurospora, despite evidence of rhythmic phenomena in many fungal species, including pathogenic ones. This chapter will revise the mechanisms underlying clock regulation in the model fungus N. crassa, as well as recent findings obtained in several fungi. In particular, this chapter will review the effect of circadian regulation of virulence and organismal interactions, focusing on the phytopathogen Botrytis cinerea, as well as several entomopathogenic fungi, including the behavior-manipulating species Ophiocordyceps kimflemingiae and Entomophthora muscae. Finally, this review will comment current efforts in the study of mammalian pathogenic fungi, while highlighting recent circadian lessons from parasites such as Trypanosoma and Plasmodium. The clock keeps on ticking, whether we can hear it or not.

The coding and noncoding transcriptome of Neurospora crassa

Background

Long non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete.

Results

We have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 natural antisense transcripts, indicating that 20% of the RNA Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncRNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. Our analysis showed that the vast majority of lincRNAs and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincRNA genes. We show furthermore most lincRNA sequences evolve rapidly, even between phylogenetically close species.

Conclusions

Our transcriptome analyses revealed distinct features of Neurospora lincRNAs and antisense transcripts in comparison to mRNAs and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncRNAs.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4360-8) contains supplementary material, which is available to authorized users.

Daily rhythms and enrichment patterns in the transcriptome of the behavior-manipulating parasite Ophiocordyceps kimflemingiae

Various parasite-host interactions that involve adaptive manipulation of host behavior display time-of-day synchronization of certain events. One example is the manipulated biting behavior observed in Carpenter ants infected with Ophiocordyceps unilateralis sensu lato. We hypothesized that biological clocks play an important role in this and other parasite-host interactions. In order to identify candidate molecular clock components, we used two general strategies: bioinformatics and transcriptional profiling. The bioinformatics approach was used to identify putative homologs of known clock genes. For transcriptional profiling, RNA-Seq was performed on 48 h time courses of Ophiocordyceps kimflemingiae (a recently named species of the O. unilateralis complex), whose genome has recently been sequenced. Fungal blastospores were entrained in liquid media under 24 h light-dark (LD) cycles and were harvested at 4 h intervals either under LD or continuous darkness. Of all O. kimflemingiae genes, 5.3% had rhythmic mRNAs under these conditions (JTK Cycle, ≤ 0.057 statistical cutoff). Our data further indicates that a significant number of transcription factors have a peaked activity during the light phase (day time). The expression levels of a significant number of secreted enzymes, proteases, toxins and small bioactive compounds peaked during the dark phase or subjective night. These findings support a model whereby this fungal parasite uses its biological clock for phase-specific activity. We further suggest that this may be a general mechanism involved in parasite-host interactions.

A CRE1- regulated cluster is responsible for light dependent production of dihydrotrichotetronin in Trichoderma reesei

Changing light conditions, caused by the rotation of earth resulting in day and night or growth on the surface or within a substrate, result in considerably altered physiological processes in fungi. For the biotechnological workhorse Trichoderma reesei, regulation of glycoside hydrolase gene expression, especially cellulase expression was shown to be a target of light dependent gene regulation. Analysis of regulatory targets of the carbon catabolite repressor CRE1 under cellulase inducing conditions revealed a secondary metabolite cluster to be differentially regulated in light and darkness and by photoreceptors. We found that this cluster is involved in production of trichodimerol and that the two polyketide synthases of the cluster are essential for biosynthesis of dihydrotrichotetronine (syn. bislongiquinolide or bisorbibutenolide). Additionally, an indirect influence on production of the peptaibol antibiotic paracelsin was observed. The two polyketide synthetase genes as well as the monooxygenase gene of the cluster were found to be connected at the level of transcription in a positive feedback cycle in darkness, but negative feedback in light, indicating a cellular sensing and response mechanism for the products of these enzymes. The transcription factor TR_102497/YPR2 residing within the cluster regulates the cluster genes in a light dependent manner. Additionally, an interrelationship of this cluster with regulation of cellulase gene expression was detected. Hence the regulatory connection between primary and secondary metabolism appears more widespread than previously assumed, indicating a sophisticated distribution of resources either to degradation of substrate (feed) or to antagonism of competitors (fight), which is influenced by light.

Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations

Circadian rhythms are endogenous cycles of approximately 24 hours reinforced by external cues such as light. These cycles are typically modeled as harmonic oscillators with fixed amplitude peaks. Using experimental data measuring global gene transcription in Neurospora crassa over 48 hours in the dark (i.e. with external queues removed), we demonstrate that many circadian genes frequently exhibit either damped harmonic oscillations, in which the peak amplitudes decrease each day, or driven harmonic oscillations, in which the peak amplitudes increase each day. By fitting extended harmonic oscillator models which include a damping ratio coefficient, we detected additional circadian genes that were not identified by the current standard tools that use fixed amplitude waves as reference, e.g. JTK_CYCLE. Functional Catalogue analysis confirms that our identified damped or driven genes exhibit distinct biological functions. The application of extended damped/driven harmonic oscillator models thus can elucidate, not only previously unidentified circadian genes, but also characterize gene subsets with expression patterns of biological relevance. Thus, expanded harmonic oscillators provide a powerful new tool for circadian system biology.

Analysis of Light- and Carbon-Specific Transcriptomes Implicates a Class of G-Protein-Coupled Receptors in Cellulose Sensing

In fungi, most metabolic processes are subject to regulation by light. Trichoderma reesei is adapted to degradation of plant cell walls and regulates production of the required enzymes in a manner dependent on the nutrient source and the light status. Here we investigated the interrelated relevance of two regulation levels of the transcriptome of T. reesei: light regulation and carbon source-dependent control. We show that the carbon source (cellulose, lactose, sophorose, glucose, or glycerol) is the major source of variation, with light having a modulating effect on transcript regulation. A total of 907 genes were regulated under cellulase-inducing conditions in light, and 947 genes were regulated in darkness, with 530 genes overlapping (1,324 in total). Only 218 of the 1,324 induction-specific genes were independent of light and not regulated by the BLR1, BLR2, and ENV1 photoreceptors. Analysis of the genomic distribution of genes regulated by light upon growth on cellulose revealed considerable overlap of light-regulated clusters with induction-specific clusters and carbohydrate-active enzyme (CAZyme) clusters. Further, we found evidence for the operation of a sensing mechanism for solid cellulosic substrates, with regulation of genes such as swo1, cip1, and cip2 or of genes encoding hydrophobins which is related to the cyclic AMP (cAMP)-dependent regulatory output of ENV1. We identified class XIII G-protein-coupled receptors (GPCRs) CSG1 and CSG2 in T. reesei as putative cellulose/glucose-sensing GPCRs. Our data indicate that the cellulase regulation pathway is bipartite, comprising a section corresponding to transcriptional regulation and one corresponding to posttranscriptional regulation, with the two connected by the function of CSG1. IMPORTANCE In fungi, most metabolic processes are subject to regulation by light. For Trichoderma reesei, light-dependent regulation of cellulase gene expression is specifically shown. Therefore, we intended to unravel the relationship between regulation of enzymes by the carbon source and regulation of enzymes by light. Our two-dimensional analysis included inducing and repressing carbon sources which we used to compare light-specific regulation to dark-specific regulation and to rule out effects specific for a single carbon source. We found close connections with respect to gene regulation as well as significant differences in dealing with carbon in the environment in light and darkness. Moreover, our analyses showed an intricate regulation mechanism for substrate degradation potentially involving surface sensing and provide a basis for knowledge-based screening for strain improvement.

Making Time: Conservation of Biological Clocks from Fungi to Animals

The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the fungi and the animals. Neurospora is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity, and sporulation, as well as much of metabolism; fungi use clocks to anticipate daily environmental changes. A negative feedback loop comprises the core of the circadian system in fungi and animals. In Neurospora, the best studied fungal model, it is driven by two transcription factors, WC-1 and WC-2, that form the White Collar Complex (WCC). WCC elicits expression of the frq gene. FRQ complexes with other proteins, physically interacts with the WCC, and reduces its activity; the kinetics of these processes is strongly influenced by progressive phosphorylation of FRQ. When FRQ becomes sufficiently phosphorylated that it loses the ability to influence WCC activity, the circadian cycle starts again. Environmental cycles of light and temperature influence frq and FRQ expression and thereby reset the internal circadian clocks. The molecular basis of circadian output is also becoming understood. Taken together, molecular explanations are emerging for all the canonical circadian properties, providing a molecular and regulatory framework that may be extended to many members of the fungal and animal kingdoms, including humans.