Localization and light-dependent phosphorylation of white collar 1 and 2, the two central components of blue light signaling in Neurospora crassa

Transcriptome Analysis Reveals Candidate Genes for Light Regulation of Elsinochrome Biosynthesis in Elsinoë arachidis

Light regulation is critical in fungal growth, development, morphogenesis, secondary metabolism, and the biological clock. The fungus Elsinoë arachidis is known to produce the mycotoxin Elsinochrome (ESC), a key factor contributing to its pathogenicity, under light conditions. Although previous studies have predominantly focused on the light-induced production of ESC and its biosynthetic pathways, the detailed mechanisms underlying this process remain largely unexplored. This study explores the influence of light on ESC production and gene expression in E. arachidis. Under white light exposure for 28 days, the ESC yield was observed to reach 33.22 nmol/plug. Through transcriptome analysis, 5925 genes were identified as differentially expressed between dark and white light conditions, highlighting the significant impact of light on gene expression. Bioinformatics identified specific light-regulated genes, including eight photoreceptor genes, five global regulatory factors, and a cluster of 12 genes directly involved in the ESC biosynthesis, with expression trends confirmed by RT-qPCR. In conclusion, the study reveals the substantial alteration in gene expression associated with ESC biosynthesis under white light and identifies potential candidates for in-depth functional analysis. These findings advance understanding of ESC biosynthesis regulation and suggest new strategies for fungal pathogenicity control.

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.

Optimized fluorescent proteins for 4-color and photoconvertible live-cell imaging in Neurospora crassa

Fungal cells are quite unique among life in their organization and structure, and yet implementation of many tools recently developed for fluorescence imaging in animal systems and yeast has been slow in filamentous fungi. Here we present analysis of properties of fluorescent proteins in Neurospora crassa as well as describing genetic tools for the expression of these proteins that may be useful beyond cell biology applications. The brightness and photostability of ten different fluorescent protein tags were compared in a well-controlled system; six different promoters are described for the assessment of the fluorescent proteins and varying levels of expression, as well as a customizable bidirectional promoter system. We present an array of fluorescent proteins suitable for use across the visible light spectrum to allow for 4-color imaging, in addition to a photoconvertible fluorescent protein that enables a change in the color of a small subset of proteins in the cell. These tools build on the rich history of cell biology research in filamentous fungi and provide new tools to help expand research capabilities.

Transcriptional Regulation by the Velvet Protein VE-1 during Asexual Development in the Fungus Neurospora crassa

Asexual reproduction in fungi facilitates the dispersal and colonization of new substrates and, in pathogenic fungi, allows infection of plants and animals. The velvet complex is a fungus-specific protein complex that participates in the regulation of gene expression in response to environmental signals like light, as well as developmental processes, pathogenesis, and secondary metabolism. The velvet complex in the fungus Neurospora crassa is composed of three proteins, VE-1, VE-2, and LAE-1. Mutations in ve-1 or ve-2, but not in lae-1, led to shorter heights of aerial tissue, a mixture of aerial hyphae and developing macroconidia, and increased microconidiation when they were combined with mutations in the transcription factor gene fl. VE-2 and LAE-1 were detected during vegetative growth and conidiation, unlike VE-1, which was mostly observed in samples obtained from submerged vegetative hyphae. We propose that VE-1 is the limiting component of the velvet complex during conidiation and has a major role in the transcriptional regulation of conidiation. Characterization of the role of VE-1 during mycelial growth and asexual development (conidiation) by transcriptome sequencing (RNA-seq) experiments allowed the identification of a set of genes regulated by VE-1 that participate in the regulation of conidiation, most notably the transcription factor genes vib-1 and fl. We propose that VE-1 and VE-2 regulate the development of aerial tissue and the balance between macro- and microconidiation in coordination with FL and VIB-1. IMPORTANCE Most fungi disperse in nature and infect new hosts by producing vegetative spores or conidia during asexual development. This is a process that is regulated by environmental signals like light and the availability of nutrients. A protein complex, the velvet complex, participates in the integration of environmental signals to regulate conidiation. We have found that a key component of this complex in the fungus Neurospora crassa, VE-1, has a major role in the regulation of transcription during conidiation. VE-1 regulates a large number of genes, including the genes for the transcription factors FL and VIB-1. Our results will help to understand how environmental signals are integrated in the fungal cell to regulate development.

Light regulates the degradation of the regulatory protein VE-1 in the fungus Neurospora crassa

BACKGROUND

Fungi use light as an environmental signal to regulate developmental transitions that are key aspects of their biological cycles and that are also relevant for their dispersal and infectivity as plant or animal pathogens. In addition, light regulates the accumulation of photoprotective pigments, like carotenoids, and other secondary metabolites. Most fungal light responses occur after changes in gene transcription and we describe here a novel effect of light in the regulation of degradation of VE-1, a key component of the velvet complex, in the model fungus Neurospora crassa. The velvet complex is a fungal-specific protein complex that coordinates fungal development, secondary metabolism, and light regulation by interacting with other regulators and photoreceptors and modifying gene expression.

RESULTS

We have characterized the role of VE-1 during conidiation in N. crassa. In vegetative mycelia, VE-1 is localized in the cytoplasm and nuclei and is required for light-dependent transcription but does not interact with the photoreceptor and transcription factor WC-1. VE-1 is more stable in light than in darkness during asexual development (conidiation). We have shown that this light effect requires the blue-light photoreceptor WC-1. We have characterized the role of the proteasome, the COP9 signalosome (CSN), and the adaptor component of cullin-RING ubiquitin ligases, FWD-1, in the degradation of VE-1.

CONCLUSIONS

We propose that this new effect of light allows the fungal cell to adapt quickly to changes in light exposure by promoting the accumulation of VE-1 for the regulation of genes that participate in the biosynthesis of photoprotective pigments.

Cellular Calcium Levels Influenced by NCA-2 Impact Circadian Period Determination in Neurospora

Intracellular calcium signaling has been implicated in the control of a variety of circadian processes in animals and plants, but its role in microbial clocks has remained largely cryptic. To examine the role of intracellular Ca²⁺ in the Neurospora clock, we screened mutants with knockouts of calcium transporter genes and identified a gene encoding a calcium exporter, nca-2, uniquely as having significant period effects. The loss of NCA-2 results in an increase in the cytosolic calcium level, and this leads to hyper-phosphorylation of core clock components, FRQ and WC-1, and a short period, as measured by both the core oscillator and the overt clock. Genetic analyses showed that mutations in certain frq phospho-sites and in Ca²⁺-calmodulin-dependent kinase 2 (camk-2) are epistatic to nca-2 in controlling the pace of the oscillator. These data are consistent with a model in which elevated intracellular Ca²⁺ leads to the increased activity of CAMK-2, leading to enhanced FRQ phosphorylation, accelerated closure of the circadian feedback loop, and a shortened circadian period length. At a mechanistic level, some CAMKs undergo more auto-phosphorylations in the Δnca-2 mutant, consistent with high calcium levels in the Δnca-2 mutant influencing the enzymatic activities of CAMKs. NCA-2 interacts with multiple proteins, including CSP-6, a protein known to be required for circadian output. Most importantly, the expression of nca-2 is circadian clock-controlled at both the transcriptional and translational levels, and this in combination with the period effects seen in strains lacking NCA-2 firmly places calcium signaling within the larger circadian system, where it acts as both an input to and an output from the core clock.

Blakeslea trispora Photoreceptors: Identification and Functional Analysis

Blakeslea trispora is an industrial fungal species used for large-scale production of carotenoids. However, B. trispora light-regulated physiological processes, such as carotenoid biosynthesis and phototropism, are not fully understood. In this study, we isolated and characterized three photoreceptor genes, btwc-1a, btwc-1b, and btwc-1c, in B. trispora Bioinformatics analyses of these genes and their protein sequences revealed that the functional domains (PAS/LOV [Per-ARNT-Sim/light-oxygen-voltage] domain and zinc finger structure) of the proteins have significant homology to those of other fungal blue-light regulator proteins expressed by Mucor circinelloides and Neurospora crassa The photoreceptor proteins were synthesized by heterologous expression in Escherichia coli The chromogenic groups consisting of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) were detected to accompany BTWC-1 proteins by using high-performance liquid chromatography (HPLC) and fluorescence spectrometry, demonstrating that the proteins may be photosensitive. The absorbance changes of the purified BTWC-1 proteins seen under dark and light conditions indicated that they were light responsive and underwent a characteristic photocycle by light induction. Site-directed mutagenesis of the cysteine residual (Cys) in BTWC-1 did not affect the normal expression of the protein in E. coli but did lead to the loss of photocycle response, indicating that Cys represents a flavin-binding domain for photon detection. We then analyzed the functions of BTWC-1 proteins by complementing btwc-1a, btwc-1b, and btwc-1c into the counterpart knockout strains of M. circinelloides for each mcwc-1 gene. Transformation of the btwc-1a complement into mcwc-1a knockout strains restored the positive phototropism, while the addition of btwc-1c complement remedied the deficiency of carotene biosynthesis in the mcwc-1c knockout strains under conditions of illumination. These results indicate that btwc-1a and btwc-1c are involved in phototropism and light-inducible carotenogenesis. Thus, btwc-1 genes share a conserved flavin-binding domain and act as photoreceptors for control of different light transduction pathways in B. trispora IMPORTANCE Studies have confirmed that light-regulated carotenogenesis is prevalent in filamentous fungi, especially in mucorales. However, few investigations have been done to understand photoinduced synthesis of carotenoids and related mechanisms in B. trispora, a well-known industrial microbial strains. In the present study, three photoreceptor genes in B. trispora were cloned, expressed, and characterized by bioinformatics and photoreception analyses, and then in vivo functional analyses of these genes were constructed in M. circinelloides The results of this study will lead to a better understanding of photoreception and light-regulated carotenoid synthesis and other physiological responses in B. trispora.

Light in the Fungal World: From Photoreception to Gene Transcription and Beyond

Fungi see light of different colors by using photoreceptors such as the White Collar proteins and cryptochromes for blue light, opsins for green light, and phytochromes for red light. Light regulates fungal development, promotes the accumulation of protective pigments and proteins, and regulates tropic growth. The White Collar complex (WCC) is a photoreceptor and a transcription factor that is responsible for regulating transcription after exposure to blue light. In Neurospora crassa, light promotes the interaction of WCCs and their binding to the promoters to activate transcription. In Aspergillus nidulans, the WCC and the phytochrome interact to coordinate gene transcription and other responses, but the contribution of these photoreceptors to fungal photobiology varies across fungal species. Ultimately, the effect of light on fungal biology is the result of the coordinated transcriptional regulation and activation of signal transduction pathways.

Identification of two Pleurotus ostreatus blue light receptor genes (PoWC-1 and PoWC-2) and in vivo confirmation of complex PoWC-12 formation through yeast two hybrid system

Blue light is necessary for initiation of mushroom formation of Pleurotus ostreatus. In this study, we isolated homologues of the blue light receptor genes wc-1 and wc-2 from P. ostreatus, PoWC-1 and PoWC-2. The PoWC-1 contained three typical PAS domains and one PAS domain exhibited significant similarity to the LOV domain of known blue light receptors. The PoWC-2 had one typical PAS domain and one ZnF domain. The qRT-PCR analysis showed that PoWC-1 and PoWC-2 expression increased in a short time, and the final level tended to be stable along with the light illumination. The PoWC-1 and PoWC-2 expression levels of the primordium period was higher than that of mature fruiting-body period; and in the pileus were the highest, followed by the stipe and the gills. The expression of PoWC-1 and PoWC-2 in pre-primordial mycelia was induced by light exposure. In vivo analysis through yeast two-hybrid experiment disclosed that PoWC-1 and PoWC-2 could form heterologous complex to activate the reporter genes and the complex perform the transcription factor function requiring the addition of FAD.

The Effect of Blue Light on the Production of Citrinin in Monascus purpureus M9 by Regulating the mraox Gene through lncRNA AOANCR

Blue light, as an important environmental factor, can regulate the production of various secondary metabolites of Monascus purpureus M9, including mycotoxin-citrinin, pigments, and monacolin K. The analysis of citrinin in Monascus M9 exposed to blue light for 0 min./d, 15 min./d, and 60 min./d showed that 15 min./d of blue light illumination could significantly increase citrinin production, while 60 min./d of blue light illumination decreased citrinin production. Analysis of long non-coding RNA (LncRNA) was performed on the transcripts of Monascus M9 under three culture conditions, and this analysis identified an lncRNA named AOANCR that can negatively regulate the mraox gene. Fermentation studies suggested that alternate respiratory pathways could be among the pathways that are involved in the regulation of the synthesis of citrinin by environmental factors. Aminophylline and citric acid were added to the culture medium to simulate the process of generating cyclic adenosine monophosphate (cAMP) in cells under illumination conditions. The results of the fermentation showed that aminophylline and citric acid could increase the expression of the mraox gene, decrease the expression of lncRNA AOANCR, and reduce the yield of citrinin. This result also indicates a reverse regulation relationship between lncRNA AOANCR and the mraox gene. A blue light signal might regulate the mraox gene at least partially through lncRNA AOANCR, thereby regulating citrinin production. Citrinin has severe nephrotoxicity in mammals, and it is important to control the residual amout of citrinin in red yeast products during fermentation. LncRNA AOANCR and mraox can potentially be used as new targets for the control of citrinin production.

Control of Development, Secondary Metabolism and Light-Dependent Carotenoid Biosynthesis by the Velvet Complex of Neurospora crassa

Neurospora crassa is an established reference organism to investigate carotene biosynthesis and light regulation. However, there is little evidence of its capacity to produce secondary metabolites. Here, we report the role of the fungal-specific regulatory velvet complexes in development and secondary metabolism (SM) in N. crassa Three velvet proteins VE-1, VE-2, VOS-1, and a putative methyltransferase LAE-1 show light-independent nucleocytoplasmic localization. Two distinct velvet complexes, a heterotrimeric VE-1/VE-2/LAE-1 and a heterodimeric VE-2/VOS-1 are found in vivo The heterotrimer-complex, which positively regulates sexual development and represses asexual sporulation, suppresses siderophore coprogen production under iron starvation conditions. The VE-1/VE-2 heterodimer controls carotene production. VE-1 regulates the expression of >15% of the whole genome, comprising mainly regulatory and developmental features. We also studied intergenera functions of the velvet complex through complementation of Aspergillus nidulans veA, velB, laeA, vosA mutants with their N. crassa orthologs ve-1, ve-2, lae-1, and vos-1, respectively. Expression of VE-1 and VE-2 in A. nidulans successfully substitutes the developmental and SM functions of VeA and VelB by forming two functional chimeric velvet complexes in vivo, VelB/VE-1/LaeA and VE-2/VeA/LaeA, respectively. Reciprocally, expression of veA restores the phenotypes of the N. crassa ve-1 mutant. All N. crassa velvet proteins heterologously expressed in A. nidulans are localized to the nuclear fraction independent of light. These data highlight the conservation of the complex formation in N. crassa and A. nidulans However, they also underline the intergenera similarities and differences of velvet roles according to different life styles, niches and ontogenetic processes.

The Blue-Light Photoreceptor Sfwc-1 Gene Regulates the Phototropic Response and Fruiting-Body Development in the Homothallic Ascomycete Sordaria fimicola

Sordaria fimicola, a coprophilous ascomycete, is a homothallic fungus that can undergo sexual differentiation with cellular and morphological changes followed by multicellular tissue development to complete its sexual cycle. In this study, we identified and characterized the blue-light photoreceptor gene in S. fimicola The S. fimicola white collar-1 photoreceptor (SfWC-1) contains light-oxygen-voltage-sensing (LOV), Per-Arnt-Sim (PAS), and other conserved domains and is homologous to the WC-1 blue-light photoreceptor of Neurospora crassa The LOV domain of Sfwc-1 was deleted by homologous recombination using Agrobacterium-mediated protoplast transformation. The Sfwc-1(Δlov) mutant showed normal vegetative growth but produced less carotenoid pigment under illumination. The mutant showed delayed and less-pronounced fruiting-body formation, was defective in phototropism of the perithecial beaks, and lacked the fruiting-body zonation pattern compared with the wild type under the illumination condition. Gene expression analyses supported the light-induced functions of the Sfwc-1 gene in the physiology and developmental process of perithecial formation in S. fimicola Moreover, green fluorescent protein (GFP)-tagged SfWC-1 fluorescence signals were transiently strong upon light induction and prominently located inside the nuclei of living hyphae. Our studies focused on the putative blue-light photoreceptor in a model ascomycete and contribute to a better understanding of the photoregulatory functions and networks mediated by the evolutionarily conserved blue-light photoreceptors across diverse fungal phyla.IMPORTANCESordaria sp. has been a model for study of fruiting-body differentiation in fungi. Several environmental factors, including light, affect cellular and morphological changes during multicellular tissue development. Here, we created a light-oxygen-voltage-sensing (LOV) domain-deleted Sfwc-1 mutant to study blue-light photoresponses in Sordaria fimicola Phototropism and rhythmic zonation of perithecia were defective in the Sfwc-1(Δlov) mutant. Moreover, fruiting-body development in the mutant was reduced and also significantly delayed. Gene expression analysis and subcellular localization study further revealed the light-induced differential gene expression and cellular responses upon light stimulation in S. fimicola.

Light-Irradiation Wavelength and Intensity Changes Influence Aflatoxin Synthesis in Fungi

Fungi respond to light irradiation by forming conidia and occasionally synthesizing mycotoxins. Several light wavelengths, such as blue and red, affect the latter. However, the relationship between light irradiation and mycotoxin synthesis varies depending on the fungal species or strain. This study focused on aflatoxin (AF), which is a mycotoxin, and the types of light irradiation that increase AF synthesis. Light-irradiation tests using the visible region indicated that blue wavelengths in the lower 500 nm region promoted AF synthesis. In contrast, red wavelengths of 660 nm resulted in limited significant changes compared with dark conditions. Irradiation tests with different intensity levels indicated that a low light intensity increased AF synthesis. For one fungal strain, light irradiation decreased the AF synthesis under all wavelength conditions. However, the decrease was mitigated by 525 nm low intensity irradiation. Thus, blue-green low intensity irradiation may increase AF synthesis in fungi.

Photoreceptors mapping from past history till date

The critical source of information in plants is light, which is perceived by receptors present in plants and animals. Receptors present in plant and animal system regulate important processes, and knowing the chromophores and signalling domains for each receptor could pave a way to trace out links between these receptors. The signalling mechanism for each receptor will give insight knowledge. This review has focussed on the photoreceptors from past history till date, that have evolved in the plant as well as in the animal system (to lesser extent). We have also focussed our attention on finding the links between the receptors by showing the commonalities as well as the differences between them, and also tried to trace out the links with the help of chromophores and signalling domain. Several photoreceptors have been traced out, which share similarity in the chromophore as well as in the signalling domain, which indicate towards the evolution of photoreceptors from one another. For instance, cryptochrome has been found to evolve three times from CPD photolyase as well as evolution of different types of phytochrome is a result of duplication and divergence. In addition, similarity between the photoreceptors suggested towards evolution from one another. This review has also discussed possible mechanism for each receptor i.e. how they regulate developmental processes and involve what kinds of regulators and also gives an insight on signalling mechanisms by these receptors. This review could also be a new initiative in the study of UVR8 associated studies.

Alternative Use of DNA Binding Domains by the Neurospora White Collar Complex Dictates Circadian Regulation and Light Responses

In the Neurospora circadian system, the White Collar complex (WCC) of WC-1 and WC-2 drives transcription of the circadian pacemaker gene frequency (frq), whose gene product, FRQ, as a part of the FRQ-FRH complex (FFC), inhibits its own expression. The WCC is also the principal Neurospora photoreceptor; WCC-mediated light induction of frq resets the clock, and all acute light induction is triggered by WCC binding to promoters of light-induced genes. However, not all acutely light-induced genes are also clock regulated, and conversely, not all clock-regulated direct targets of WCC are light induced; the structural determinants governing the shift from WCC's dark circadian role to its light activation role are poorly described. We report that the DBD region (named for being defective in binding DNA), a basic region in WC-1 proximal to the DNA-binding zinc finger (ZnF) whose function was previously ascribed to nuclear localization, instead plays multiple essential roles assisting in DNA binding and mediating interactions with the FFC. DNA binding for light induction by the WCC requires only WC-2, whereas DNA binding for circadian functions requires WC-2 as well as the ZnF and DBD motif of WC-1. The data suggest a means by which alterations in the tertiary and quaternary structures of the WCC can lead to its distinct functions in the dark and in the light.

Epigenetic and Posttranslational Modifications in Light Signal Transduction and the Circadian Clock in Neurospora crassa

Blue light, a key abiotic signal, regulates a wide variety of physiological processes in many organisms. One of these phenomena is the circadian rhythm presents in organisms sensitive to the phase-setting effects of blue light and under control of the daily alternation of light and dark. Circadian clocks consist of autoregulatory alternating negative and positive feedback loops intimately connected with the cellular metabolism and biochemical processes. Neurospora crassa provides an excellent model for studying the molecular mechanisms involved in these phenomena. The White Collar Complex (WCC), a blue-light receptor and transcription factor of the circadian oscillator, and Frequency (FRQ), the circadian clock pacemaker, are at the core of the Neurospora circadian system. The eukaryotic circadian clock relies on transcriptional/translational feedback loops: some proteins rhythmically repress their own synthesis by inhibiting the activity of their transcriptional factors, generating self-sustained oscillations over a period of about 24 h. One of the basic mechanisms that perpetuate self-sustained oscillations is post translation modification (PTM). The acronym PTM generically indicates the addition of acetyl, methyl, sumoyl, or phosphoric groups to various types of proteins. The protein can be regulatory or enzymatic or a component of the chromatin. PTMs influence protein stability, interaction, localization, activity, and chromatin packaging. Chromatin modification and PTMs have been implicated in regulating circadian clock function in Neurospora. Research into the epigenetic control of transcription factors such as WCC has yielded new insights into the temporal modulation of light-dependent gene transcription. Here we report on epigenetic and protein PTMs in the regulation of the Neurospora crassa circadian clock. We also present a model that illustrates the molecular mechanisms at the basis of the blue light control of the circadian clock.

The histone H3 lysine 9 methyltransferase DIM-5 modifies chromatin at frequency and represses light-activated gene expression

The transcriptional program controlling the circadian rhythm requires coordinated regulation of chromatin. Characterization of the chromodomain helicase DNA-binding enzyme CHD1 revealed DNA methylation in the promoter of the central clock gene frequency (frq) in Neurospora crassa. In this report, we show that the DNA methylation at frq is not only dependent on the DNA methyltransferase DIM-2 but also on the H3K9 methyltransferase DIM-5 and HP1. Histone H3 lysine 9 trimethylation (H3K9me3) occurs at frq and is most prominent 30 min after light-activated expression. Strains lacking dim-5 have an increase in light-induced transcription, and more White Collar-2 is found associated with the frq promoter. Consistent with the notion that DNA methylation assists in establishing the proper circadian phase, loss of H3K9 methylation results in a phase advance suggesting it delays the onset of frq expression. The dim-5 deletion strain displays an increase in circadian-regulated conidia formation on race tubes and there is a synthetic genetic interaction between dim-5 and ras-1(bd). These results indicate DIM-5 has a regulatory role in muting circadian output. Overall, the data support a model where facultative heterochromatic at frq serves to establish the appropriate phase, mute the light response, and repress circadian output.

Genome-wide characterization of light-regulated genes in Neurospora crassa

The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 hr in the dark and then exposed to light for 0 (control) 15, 60, 120, and 240 min. More than three-quarters of all defined protein coding genes (79%) were expressed in these cells. The increased sensitivity of RNA-seq compared with previous microarray studies revealed that the RNA levels for 31% of expressed genes were affected two-fold or more by exposure to light. Additionally, a large class of mRNAs, enriched for transcripts specifying products involved in rRNA metabolism, showed decreased expression in response to light, indicating a heretofore undocumented effect of light on this pathway. Based on measured changes in mRNA levels, light generally increases cellular metabolism and at the same time causes significant oxidative stress to the organism. To deal with this stress, protective photopigments are made, antioxidants are produced, and genes involved in ribosome biogenesis are transiently repressed.

Alteration of light-dependent gene regulation by the absence of the RCO-1/RCM-1 repressor complex in the fungus Neurospora crassa

The activation of transcription by light in the fungus Neurospora crassa requires the White Collar Complex (WCC), a photoreceptor and transcription factor complex. After light reception two WCCs interact and bind the promoters of light-regulated genes to activate transcription. This process is regulated by VVD, a small photoreceptor that disrupts the interaction between WCCs and leads to a reduction in transcription after long exposures to light. The N. crassa RCO-1/RCM-1 repressor complex is the homolog of the Tup1-Ssn6 repressor complex in yeast, and its absence modifies photoadaptation. We show that the absence of the RCO-1/RCM-1 repressor complex leads to several alterations in transcription that are gene-specific: an increase in the accumulation of mRNAs in the dark, a repression of transcription, and a derepression of transcription after long exposures to light. The absence of the RCO-1/RCM-1 repressor complex leads to lower VVD levels that are available for the regulation of the activity of the WCC. The reduction in the amount of VVD results in increased WCC binding to the promoters of light-regulated genes in the dark and after long exposures to light, leading to the modification of photoadaptation that has been observed in rco-1 and rcm-1 mutants. Our results show that the photoadaptation phenotype of mutants in the RCO-1/RCM-1 repressor complex is, at least in part, an indirect consequence of the reduction of vvd transcription, and the resulting modification in the regulation of transcription by the WCC.

Consistent mutational paths predict eukaryotic thermostability

BACKGROUND

Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published.

RESULTS

Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1), we could also characterise the molecular consequences of some of these mutations.

CONCLUSIONS

The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.

The blue light receptor complex WC-1/2 of Schizophyllum commune is involved in mushroom formation and protection against phototoxicity

Blue light is necessary for initiation of mushroom formation in Schizophyllum commune. The genome of this basidiomycete contains homologues of the blue light receptor genes wc-1 and wc-2 of Neurospora crassa. Here, it is shown that inactivation of either or both of these genes in S. commune results in a blind phenotype. Mushroom formation was abolished in dikaryons and they formed symmetrical instead of asymmetrical colonies. Development was restored in a temperature dependent way in a Δwc-2Δwc-2 strain by introducing a construct encompassing the wc-2 gene under control of the promoter of the heat shock gene hsp3. A genome-wide expression analysis showed that the transcription factor genes c2h2 and hom1 as well as many hydrophobin genes are downregulated in light-grown colonies of the Δwc-2Δwc-2 mutant when compared with the wild-type dikaryon. Inactivation of wc-1 and/or wc-2 also resulted in sensitivity of the mycelium to intense light. Monokaryotic mutant strains only survived exposure to 6500 lux of light by growing into the agar. Expression analysis indicates that the photosensitivity of the Δwc-1 and Δwc-2 strains is due to lower levels of photolyase and ferrochelatase.

Time for a nuclear meeting: protein trafficking and chromatin dynamics intersect in the plant circadian system

Circadian clocks mediate adaptation to the 24-h world. In Arabidopsis, most circadian-clock components act in the nucleus as transcriptional regulators and generate rhythmic oscillations of transcript accumulation. In this review, we focus on post-transcriptional events that modulate the activity of circadian-clock components, such as phosphorylation, ubiquitination and proteasome-mediated degradation, changes in cellular localization, and protein-protein interactions. These processes have been found to be essential for circadian function, not only in plants, but also in other circadian systems. Moreover, light and clock signaling networks are highly interconnected. In the nucleus, light and clock components work together to generate transcriptional rhythms, leading to a general control of the timing of plant physiological processes.

Neurospora crassa Light Signal Transduction Is Affected by ROS

In the ascomycete fungus Neurospora crassa blue-violet light controls the expression of genes responsible for differentiation of reproductive structures, synthesis of secondary metabolites, and the circadian oscillator activity. A major photoreceptor in Neurospora cells is WCC, a heterodimeric complex formed by the PAS-domain-containing polypeptides WC-1 and WC-2, the products of genes white collar-1 and white collar-2. The photosignal transduction is started by photochemical activity of an excited FAD molecule noncovalently bound by the LOV domain (a specialized variant of the PAS domain). The presence of zinc fingers (the GATA-recognizing sequences) in both WC-1 and WC-2 proteins suggests that they might function as transcription factors. However, a critical analysis of the phototransduction mechanism considers the existence of residual light responses upon absence of WCC or its homologs in fungi. The data presented point at endogenous ROS generated by a photon stimulus as an alternative input to pass on light signals to downstream targets.

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

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

The genetics of circadian rhythms in Neurospora

This chapter describes our current understanding of the genetics of the Neurospora clock and summarizes the important findings in this area in the past decade. Neurospora is the most intensively studied clock system, and the reasons for this are listed. A discussion of the genetic interactions between clock mutants is included, highlighting the utility of dissecting complex mechanisms by genetic means. The molecular details of the Neurospora circadian clock mechanism are described, as well as the mutations that affect the key clock proteins, FRQ, WC-1, and WC-2, with an emphasis on the roles of protein phosphorylation. Studies on additional genes affecting clock properties are described and place these genes into two categories: those that affect the FRQ/WCC oscillator and those that do not. A discussion of temperature compensation and the mutants affecting this property is included. A section is devoted to the observations pertinent to the existence of other oscillators in this organism with respect to their properties, their effects, and their preliminary characterization. The output of the clock and the control of clock-controlled genes are discussed, emphasizing the phasing of these genes and the layers of control. In conclusion, the authors provide an outlook summarizing their suggestions for areas that would be fruitful for further exploration.

Fungi, hidden in soil or up in the air: light makes a difference

Light is one of the most important environmental factors for orientation of almost all organisms on Earth. Whereas light sensing is of crucial importance in plants to optimize light-dependent energy conservation, in nonphotosynthetic organisms, the synchronization of biological clocks to the length of a day is an important function. Filamentous fungi may use the light signal as an indicator for the exposure of hyphae to air and adapt their physiology to this situation or induce morphogenetic pathways. Although a yes/no decision appears to be sufficient for the light-sensing function in fungi, most species apply a number of different, wavelength-specific receptors. The core of all receptor types is a chromophore, a low-molecular-weight organic molecule, such as flavin, retinal, or linear tetrapyrrols for blue-, green-, or red-light sensing, respectively. Whereas the blue-light response in fungi is one of the best-studied light responses, all other light-sensing mechanisms are less well studied or largely unknown. The discovery of phytochrome in bacteria and fungi in recent years not only advanced the scientific field significantly, but also had great impact on our view of the evolution of phytochrome-like photoreceptors.

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

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

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

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

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

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

Circadian activity and abundance rhythms of the Neurospora clock transcription factor WCC associated with rapid nucleo-cytoplasmic shuttling

The Neurospora clock protein FREQUENCY (FRQ) inhibits its transcriptional activator WHITE COLLAR COMPLEX (WCC) in a negative feedback loop and supports its accumulation in a positive loop. We show that positive feedback is a delayed effect of negative feedback underlying the same post-translational mechanisms: DNA-binding-competent active WCC commits rapidly to degradation. FRQ-dependent phosphorylation of WCC, which interferes with DNA binding (negative feedback), leads to reduced turnover and slow accumulation of newly expressed WCC (positive feedback). When DNA binding of WCC is compromised by mutation, its accumulation is independent of FRQ. Cycles of FRQ-dependent inactivation and PP2A-dependent reactivation of WCC occur in the minute range and are coupled to obligate rapid cycles of nucleo-cytoplasmic shuttling. WCC shuttling and activity cycles are modulated by FRQ in circadian fashion.

Analysis of posttranslational regulations in the Neurospora circadian clock

Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinases and phosphatases, and the phosphorylation is important for regulating FRQ stability and its function in the circadian negative feedback loop. The degradation of FRQ is mediated by the ubiquitin/proteasome pathway. This article discusses posttranslational regulations of the Neurospora clock and describes the methods used in the studies of FRQ phosphorylation, FRQ kinases and phosphatases, and FRQ degradation.

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

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

Functional and physical interaction of blue- and red-light sensors in Aspergillus nidulans

Light sensing is very important for organisms in all biological kingdoms to adapt to changing environmental conditions. It was discovered recently that plant-like phytochrome is involved in light sensing in the filamentous fungus Aspergillus nidulans[1]. Here, we show that phytochrome (FphA) is part of a protein complex containing LreA (WC-1) and LreB (WC-2) [2, 3], two central components of the Neurospora crassa blue-light-sensing system. We found that FphA represses sexual development and mycotoxin formation, whereas LreA and LreB stimulate both. Surprisingly, FphA interacted with LreB and with VeA, another regulator involved in light sensing and mycotoxin biosynthesis. LreB also interacted with LreA. All protein interactions occurred in the nucleus, despite cytoplasmic subfractions of the proteins. Whereas the FphA-VeA interaction was dependent on the presence of the linear tetrapyrrole in FphA, the interaction between FphA and LreB was chromophore independent. These results suggest that morphological and physiological differentiations in A. nidulans are mediated through a network consisting of FphA, LreA, LreB, and VeA acting in a large protein complex in the nucleus, sensing red and blue light.

Interlocked feedback loops of the circadian clock of Neurospora crassa

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

Impact of light on Hypocrea jecorina and the multiple cellular roles of ENVOY in this process

Background

In fungi, light is primarily known to influence general morphogenesis and both sexual and asexual sporulation. In order to expand the knowledge on the effect of light in fungi and to determine the role of the light regulatory protein ENVOY in the implementation of this effect, we performed a global screen for genes, which are specifically effected by light in the fungus Hypocrea jecorina (anamorph Trichoderma reesei) using Rapid Subtraction Hybridization (RaSH). Based on these data, we analyzed whether these genes are influenced by ENVOY and if overexpression of ENVOY in darkness would be sufficient to execute its function.

Results

The cellular functions of the detected light responsive genes comprised a variety of roles in transcription, translation, signal transduction, metabolism, and transport. Their response to light with respect to the involvement of ENVOY could be classified as follows: (i) ENVOY-mediated upregulation by light; (ii) ENVOY-independent upregulation by light; (iii) ENVOY-antagonized upregulation by light; ENVOY-dependent repression by light; (iv) ENVOY-independent repression by light; and (v) both positive and negative regulation by ENVOY of genes not responsive to light in the wild-type. ENVOY was found to be crucial for normal growth in light on various carbon sources and is not able to execute its regulatory function if overexpressed in the darkness.

Conclusion

The different responses indicate that light impacts fungi like H. jecorina at several cellular processes, and that it has both positive and negative effects. The data also emphasize that ENVOY has an apparently more widespread cellular role in this process than only in modulating the response to light.

The Neurospora crassa circadian clock

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

Looking through the eyes of fungi: molecular genetics of photoreception

Filamentous fungi respond to a variety of environmental signals. One of them is light, providing critical information about orientation, or impending stress. Cells of filamentous fungi appear to sense blue light through a unique transcription factor that has a flavin chromophore and activates its targets in a light-dependent manner, the white collar (WC) complex. Fungal photophysiology, though, predicted a greater complexity of responses to the whole visible spectrum. The rapidly growing fungal genome database provides candidates to explain how fungi see not only blue, but also near-UV, green and red light. At the same time, there are surprises in the genomes, including photoreceptors for which there are no obvious photoresponses. Linking these genes and their functions will help understand how a list of only a few biological chromophores accounts for such a diversity of responses. At the same time, deeper mechanistic understanding of how the WC complex functions will lead to fundamental insights at the point where the environment impinges, in this case in the form of photons, on the transcriptional machinery of the cell.

Novel light-regulated genes in Trichoderma atroviride: a dissection by cDNA microarrays

The influence of light on living organisms is critical, not only because of its importance as the main source of energy for the biosphere, but also due to its capacity to induce changes in the behaviour and morphology of nearly all forms of life. The common soil fungus Trichoderma atroviride responds to blue light in a synchronized manner, in time and space, by forming a ring of green conidia at what had been the colony perimeter at the time of exposure (photoconidiation). A putative complex formed by the BLR-1 and BLR-2 proteins in T. atroviride appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Expression analyses using microarrays containing 1438 unigenes were carried out in order to identify early light response genes. It was found that 2.8 % of the genes were light responsive: 2 % induced and 0.8 % repressed. Expression analysis in blr deletion mutants allowed the demonstration of the occurrence of two types of light responses, a blr-independent response in addition to the expected blr-dependent one, as well as a new role of the BLR proteins in repression of transcription. Exposure of T. atroviride to continuous light helped to establish that the light-responsive genes are subject to photoadaptation. Finally, evidence is provided of red-light-regulated gene expression and a possible crosstalk between the blue and red light signalling pathways.

Characterization of theBLR1gene encoding a putative blue-light regulator in the phytopathogenic fungusBipolaris oryzae

Bipolaris oryzae is a filamentous ascomycetous fungus that causes brown leaf spot disease in rice. We isolated and characterized BLR1, a gene that encodes a putative blue-light regulator similar to Neurospora crassa white-collar 1 (WC-1). The deduced amino acid sequence of BLR1 showed high degrees of similarity to other fungal blue-light regulator protein. Disruption of the BLR1 gene demonstrated that this gene is essential for conidial development after conidiophore formation and for near-UV radiation-enhanced photolyase gene expression.

Fungal photoreceptors: sensory molecules for fungal development and behaviour

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

Posttranslational control of the Neurospora circadian clock

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

Seeing the rainbow: light sensing in fungi

Light is essential for photosynthetic organisms, but also serves as an important environmental cue for non-photosynthetic species; thus, light sensing is evolutionarily conserved throughout the kingdoms, from archaea and fungi to humans. Light sensors are chromoproteins, the low-molecular weight compound of which absorbs specific wavelengths and induces a reaction from the protein. In fungi, three light-sensing systems have been described at the molecular level. Blue-light sensing is achieved by a flavin-based photoreceptor, which itself acts as a transcription factor, and red-light sensing is achieved by a phytochrome, a molecule until recently thought to be confined to plants. A retinal-based opsin-system was discovered recently, although a biological function remains to be determined. The challenge for future research will be the identification of further components of signalling cascades, the identification of light-regulated genes and the unravelling of possible functional interplays between the different light control systems.