LC-MS/MS-based targeted carotenoid and anthocyanidin metabolic profile of Auricularia cornea under blue and red LED light exposure

Light exposure significantly impacted the coloration and metabolism of Auricularia cornea, although the underlying mechanisms remain unclear. This study aimed to test the apparent color and pigment metabolic profiles of A. cornea in response to red (λp = 630 nm) and blue (λp = 463 nm) visible light exposure. Colorimeter analysis showed that fruiting bodies appeared bright-white under red-light and deeper-red under blue-light, both with a yellow tinge. On the 40th day of light-exposure, bodies were collected for metabolite detection. A total of 481 metabolites were targeted analysis, resulting in 18 carotenoids and 11 anthocyanins. Under red and blue light exposure, the total carotenoids levels were 1.1652 μg/g and 1.1576 μg/g, the total anthocyanins levels were 0.0799 μg/g and 0.1286 μg/g, respectively. Four differential metabolites and three putative gene linked to the visual coloration of A. cornea were identified. This pioneering study provides new insights into the role of light in regulating A. cornea pigmentation and metabolic profile.

Regulation of Conidiation and Aflatoxin B1 Biosynthesis by a Blue Light Sensor LreA in Aspergillus flavus

Conidia are important for the dispersal of Aspergillus flavus, which usually generates aflatoxin B1 (AFB1) and poses a threat to the safety of agricultural food. The development of conidia is usually susceptible to changes in environmental conditions, such as nutritional status and light. However, how the light signal is involved in the conidiation in A. flavus is still unknown. In this study, LreA was identified to respond to blue light and mediate the promotion of conidiation in A. flavus, which is related to the central development pathway. At the same time, blue light inhibited the biosynthesis of AFB1, which was mediated by LreA and attributed to the transcriptional regulation of aflR and aflS expression. Our findings disclosed the function and mechanism of the blue light sensor LreA in regulating conidiation and AFB1 biosynthesis, which is beneficial for the prevention and control of A. flavus and mycotoxins.

Shedding the Light on Powdery Mildew: The Use of Optical Irradiation in Management of the Disease

Ultraviolet (UV) irradiation below 300 nm may control powdery mildew in numerous crops. Depending on disease pressure, wavelength, and crop growth stage, one to three applications of 100-200 J/m2 per week at night are as effective or better than the best fungicides. Higher doses may harm the plants and reduce yields. Although red light alone or in combination with UV has a suppressive effect on powdery mildew, concomitant or subsequent exposure to blue light or UV-A strongly reduces the efficacy of UV treatments. To be effective, direct exposure of the pathogen/infection sites to UV/red light is important, but there are clear indications for the involvement of induced resistance in the host. Other pathogens and pests are susceptible to UV, but the effective dose may be phytotoxic. Although there are certain limitations, this technology is gradually becoming more used in both protected and open-field commercial production systems.

The Cryptochrome CryA Regulates Lipid Droplet Accumulation, Conidiation, and Trap Formation via Responses to Light in Arthrobotrys oligospora

Light is a key environmental factor affecting conidiation in filamentous fungi. The cryptochrome/photolyase CryA, a blue-light receptor, is involved in fungal development. In the present study, a homologous CryA (AoCryA) was identified from the widely occurring nematode-trapping (NT) fungus Arthrobotrys oligospora, and its roles in the mycelial growth and development of A. oligospora were characterized using gene knockout, phenotypic comparison, staining technique, and metabolome analysis. The inactivation of AocryA caused a substantial decrease in spore yields in dark conditions but did not affect spore yields in the wild-type (WT) and ∆AocryA mutant strains in light conditions. Corresponding to the decrease in spore production, the transcription of sporulation-related genes was also significantly downregulated in dark conditions. Contrarily, the ∆AocryA mutants showed a substantial increase in trap formation in dark conditions, while the trap production and nematode-trapping abilities of the WT and mutant strains significantly decreased in light conditions. In addition, lipid droplet accumulation increased in the ∆AocryA mutant in dark conditions, and the mutants showed an increased tolerance to sorbitol, while light contributed to the synthesis of carotenoids. Finally, AoCryA was found to affect secondary metabolic processes. These results reveal, for the first time, the function of a homologous cryptochrome in NT fungi.

De novo genome assembly and functional insights of the first commercial pink Auricularia cornea

A pioneering pink cultivar of Auricularia cornea, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink A. cornea Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink A. cornea genome and provides a comprehensive insight into its complex functions.

The GATA transcription factor BcWCL2 regulates citric acid secretion to maintain redox homeostasis and full virulence in Botrytis cinerea

Botrytis cinerea is a typical necrotrophic plant pathogenic fungus which can deliberately acidify host tissues and trigger oxidative bursts therein to facilitate its virulence. The white collar complex (WCC), consisting of BcWCL1 and BcWCL2, is recognized as the primary light receptor in B. cinerea. Nevertheless, the specific mechanisms through which the WCC components, particularly BcWCL2 as a GATA transcription factor, control virulence are not yet fully understood. This study demonstrates that deletion of BcWCL2 results in the loss of light-sensitive phenotypic characteristics. Additionally, the Δbcwcl2 strain exhibits reduced secretion of citrate, delayed infection cushion development, weaker hyphal penetration, and decreased virulence. The application of exogenous citric acid was found to restore infection cushion formation, hyphal penetration, and virulence of the Δbcwcl2 strain. Transcriptome analysis at 48 h post-inoculation revealed that two citrate synthases, putative citrate transporters, hydrolytic enzymes, and reactive oxygen species scavenging-related genes were down-regulated in Δbcwcl2, whereas exogenous citric acid application restored the expression of the above genes involved in the early infection process of Δbcwcl2. Moreover, the expression of Bcvel1, a known regulator of citrate secretion, tissue acidification, and secondary metabolism, was down-regulated in Δbcwcl2 but not in Δbcwcl1. ChIP-qPCR and electrophoretic mobility shift assays revealed that BcWCL2 can bind to the promoter sequences of Bcvel1. Overexpressing Bcvel1 in Δbcwcl2 was found to rescue the mutant defects. Collectively, our findings indicate that BcWCL2 regulates the expression of the global regulator Bcvel1 to influence citrate secretion, tissue acidification, redox homeostasis, and virulence of B. cinerea.IMPORTANCEThis study illustrated the significance of the fungal blue light receptor component BcWCL2 protein in regulating citrate secretion in Botrytis cinerea. Unlike BcWCL1, BcWCL2 may contribute to redox homeostasis maintenance during infection cushion formation, ultimately proving to be essential for full virulence. It is also demonstrated that BcWCL2 can regulate the expression of Bcvel1 to influence host tissue acidification, citrate secretion, infection cushion development, and virulence. While the role of organic acids secreted by plant pathogenic fungi in fungus-host interactions has been recognized, this paper revealed the importance, regulatory mechanisms, and key transcription factors that control organic acid secretion. These understanding of the pathogenetic mechanism of plant pathogens can provide valuable insights for developing effective prevention and treatment strategies against fungal diseases.

Enhancing Eritadenine Production in Submerged Cultures of Shiitake (Lentinula edodes Berk. Pegler) Using Blue LED Light and Activated Charcoal. Revealing Eritadenine's Novel In Vitro Bioherbicidal Activity Against Chrysanthemum morifolium

Eritadenine from shiitake mushroom is a secondary metabolite with hypocholesterolemic, hypotensive and antiparasitic properties, thus promising for pharmaceutical and agricultural applications. Eritadenine is obtained from submerged mycelial cultures of shiitake, but the actual yields remain unsatisfactory to explore potential applications or industrial-scale production. In this study, green and blue LED lights were tested to increase yields of eritadenine in submerged cultures of shiitake. Notably, blue LEDs increased yields by 13-14 times, reaching 165.7 mg/L, compared to darkness (11.2 mg/L) and green light (12.1 mg/L) (p < 0.05, Tukey test). Nitrogen sources yeast extract (YE) and peptone (at 2 g/L) increased eritadenine production. YE promoted 22.6 mg/L, while peptone 18.3 mg/L. The recovery of eritadenine was evaluated using amberlite and activated charcoal (AC) adsorption isotherms. AC demonstrated the highest adsorption rate, with 75 mg of eritadenine per gram of AC, according to the Freundlich isotherm. The desorption rate reached 93.95% at pH 10. The extract obtained from submerged cultures had eritadenine content of 63.31%, corresponding to 87.86% of recovery, according to HPLC analysis. Furthermore, the novel bioherbicidal potential of eritadenine was tested on in vitro Chrysanthemum morifolium plants. The cultures extract containing eritadenine had a detrimental impact on plant development, generating mortality of 100% at 3%, 0.5%, and 0.25%. Moreover, pure eritadenine exhibited a phytotoxic effect similar than glyphosate on leaves, stems and roots. These findings highlight the significant bioherbicidal properties of eritadenine. Further studies are needed to understand the biosynthetic pathway of eritadenine and its bioherbicidal properties on weeds and illicit crops.

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.

The LOV-domain blue-light receptor LreA of the fungus Alternaria alternata binds predominantly FAD as chromophore and acts as a light and temperature sensor

Light and temperature sensing are important features of many organisms. Light may provide energy but may also be used by non-photosynthetic organisms for orientation in the environment. Recent evidence suggests that plant and fungal phytochrome and plant phototropin serve dual functions as light and temperature sensors. Here we characterized the fungal LOV-domain blue-light receptor LreA of Alternaria alternata and show that it predominantly contains FAD as chromophore. Blue-light illumination induced ROS production followed by protein agglomeration in vitro. In vivo ROS may control LreA activity. LreA acts as a blue-light photoreceptor but also triggers temperature-shift-induced gene expression. Both responses required the conserved amino acid cysteine 421. We therefore propose that temperature mimics the photoresponse, which could be the ancient function of the chromoprotein. Temperature-dependent gene expression control with LreA was distinct from the response with phytochrome suggesting fine-tuned, photoreceptor-specific gene regulation.

Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Light as a source of information regulates morphological and physiological processes of fungi, including development, primary and secondary metabolism, or the circadian rhythm. Light signaling in fungi depends on photoreceptors and downstream components that amplify the signal to govern the expression of an array of genes. Here, we investigated the effects of red and far-red light in the mycoparasite Trichoderma guizhouense on its mycoparasitic potential. We show that the invasion strategy of T. guizhouense depends on the attacked species and that red and far-red light increased aerial hyphal growth and led to faster overgrowth or invasion of the colonies. Molecular experiments and transcriptome analyses revealed that red and far-red light are sensed by phytochrome FPH1 and further transmitted by the downstream MAPK HOG pathway and the bZIP transcription factor ATF1. Overexpression of the red- and far-red light-induced fluffy gene fluG in the dark resulted in abundant aerial hyphae formation and thereby improvement of its antagonistic ability against phytopathogenic fungi. Hence, light-induced fluG expression is important for the mycoparasitic interaction. The increased aggressiveness of fluG-overexpressing strains was phenocopied by four random mutants obtained after UV mutagenesis. Therefore, aerial hyphae formation appears to be a trait for the antagonistic potential of T. guizhouense.

Photoregulation of the biosynthetic activity of the edible medicinal mushroom Lentinula edodes in vitro

The findings of the study demonstrate the impact of low-intensity laser and quasi-monochromatic light on the biosynthetic activity of the edible medicinal fungus L. edodes during submerged cultivation. An artificial lighting installation based on matrices of light-emitting diodes (LED) emitting light at 470 nm (blue), 530 nm (green), 650 nm (red), and argon gas laser (488 nm) was used. Irradiation with blue and red LED and laser led to a shortening of the lag phase by 2 days and an increase in the mycelial mass. Irradiation with laser light resulted in the highest mycelial mass yield (14.1 g/L) on the 8th day of cultivation. Irradiation in all used wavelength ranges caused an increase in the synthesis of both extracellular and intracellular polysaccharides. Laser light at 488 nm and LED at 470 nm proved to be the most effective. Irradiation with red, green, and blue laser light caused an increase in the total amount of fatty acids in the mycelial mass compared to the control. A significant distinction in qualitative composition was observed: short-chain acids C6‒C12 compounds were produced under red light irradiation, whereas long-chain C20‒C24 were formed under green light irradiation. The most significant changes in the aromatic profile of the mycelial mass and culture liquid were recorded upon irradiation with green light. The content of aromatic components increased 24.6 times in the mycelial mass and 38.5 times in the culture liquid. The results suggest the possibility of using low-intensity quasi-monochromatic light for targeted regulation of L. edodes biosynthetic activity.

Integrated transcriptome and metabolome analysis provides insights into blue light response of Flammulina filiformis

Blue light promotes primordium differentiation and fruiting body formation of mushroom. However, the blue light response mechanism of mushroom remains unclear. In this study, mycelium of Flammulina filiformis was exposed to blue light, red light and dark conditions, and then the comparative metabolome and transcriptome analysis was applied to explore metabolic regulation mechanism of F. filiformis under blue light and red light conditions. The yield of the fruiting body of F. filiformis under blue light condition was much higher than that under dark and red light conditions. Metabolome analysis showed that blue light treatment reduced the concentrations of many low molecular weight carbohydrates in the pilei, but it promoted the accumulation of some low molecular weight carbohydrates in the stipes. Blue light also decreased the accumulation of organic acids in the stipes. Blue light treatment reduced the levels of tyrosine and tryptophan in the stipes, but it largely promoted the accumulation of lysine in this organ. In the stipes of F. filiformis, blue light shifted metabolite flow to synthesis of lysine and carbohydrates through inhibiting the accumulation of aromatic amino acids and organic acids, thereby enhancing its nutritional and medicinal values. The transcriptome analysis displayed that blue light enhanced accumulation of lysine in fruiting body of F. filiformis through downregulation of lysine methyltransferase gene and L-lysine 6-monooxygenase gene. Additionally, in the stipes, blue light upregulated many hydrolase genes to improve the ability of the stipe to biodegrade the medium and elevated the growth rate of the fruiting body.

Role of histone H3K4 methyltransferase in regulating Monascus pigments production by red light-coupled magnetic field

Light, magnetic field, and methylation affected the growth and secondary metabolism of fungi. The regulation effect of the three factors on the growth and Monascus pigments (MPs) synthesis of Monascus purpureus was investigated in this study. 5-azacytidine (5-AzaC), DNA methylation inhibitor, was used to treat M. purpureus (wild-type, WT). Twenty micromolar 5-AzaC significantly promoted the growth, development, and MPs yield. Moreover, 250 lux red light and red light coupled magnetic field (RLCMF) significantly promoted the biomass. For WT, red light, and RLCMF significantly promoted MPs yield. But compared with red light treatment, only 0.2 mT RLCMF promoted the alcohol-soluble MPs yield. For histone H3K4 methyltransferase complex subunit Ash2 gene knockout strain (ΔAsh2), only 0.2 mT RLCMF significantly promoted water-soluble MPs yield. Yet red light, 1.0 and 0.2 mT RLCMF significantly promoted alcohol-soluble MPs yield. This indicated that methylation affected the MPs biosynthesis. Red light and weaker MF had a synergistic effect on the growth and MPs synthesis of ΔAsh2. This result was further confirmed by the expression of related genes. Therefore, histone H3K4 methyltransferase was involved in the regulation of the growth, development, and MPs synthesis of M. purpureus by the RLCMF.

The bZIP transcription factor ATF1 regulates blue light and oxidative stress responses in Trichoderma guizhouense

In several filamentous fungi, incident light and environmental stress signaling share the mitogen-activated protein kinase (MAPK) HOG (SAK) pathway. It has been revealed that short-term illumination with blue light triggers the activation of the HOG pathway in Trichoderma spp. In this study, we demonstrate the crucial role of the basic leucine zipper transcription factor ATF1 in blue light responses and signaling downstream of the MAPK HOG1 in Trichoderma guizhouense. The lack of ATF1 severely impaired photoconidiation and delayed vegetative growth and conidial germination. Upon blue light or H2O2 stimuli, HOG1 interacted with ATF1 in the nucleus. Genome-wide transcriptome analyses revealed that 61.8% (509 out of 824) and 85.2% (702 out of 824) of blue light-regulated genes depended on ATF1 and HOG1, respectively, of which 58.4% (481 out of 824) were regulated by both of them. Our results also show that blue light promoted conidial germination and HOG1 and ATF1 played opposite roles in controlling conidial germination in the dark. Additionally, the lack of ATF1 led to reduced oxidative stress resistance, probably because of the downregulation of catalase-encoding genes. Overall, our results demonstrate that ATF1 is the downstream component of HOG1 and is responsible for blue light responses, conidial germination, vegetative growth, and oxidative stress resistance in T. guizhouense.

Integration of Metabolomes and Transcriptomes Provides Insights into Morphogenesis and Maturation in Morchella sextelata

True morels (Morchella, Pezizales) are a popular edible and medicinal fungus with great nutritional and economic value. The dynamics and regulatory mechanisms during the morphogenesis and maturation of morels are poorly understood. In this study, the metabolomes and transcriptomes of the mycelium (MY), primordium differentiation (PR), young fruiting body (YFB), and mature fruiting body (MFB) were comprehensively analyzed to reveal the mechanism of the morphogenesis and maturation of Morchella sextelata. A total of 748 differentially expressed metabolites (DEMs) and 5342 differentially expressed genes (DEGs) were detected, mainly enriched in the carbohydrate, amino acid, and lipid metabolism pathways, with the transition from the mycelium to the primordium being the most drastic stage at both the metabolic and transcriptional levels. The integrated metabolomics and transcriptomics highlighted significant correlations between the DEMs and DEGs, and specific amino acid and nucleotide metabolic pathways were significantly co-enriched, which may play key roles in morphological development and ascocarp maturation. A conceptual model of transcriptional and metabolic regulation was proposed during morphogenesis and maturation in M. sextelata for the first time, in which environmental factors activate the regulation of transcription factors, which then promote metabolic and transcriptional regulation from vegetative to reproductive growth. These results provide insights into the metabolic dynamics and transcriptional regulation during the morphogenesis and maturation of morels and valuable resources for future breeding enhancement and sustainable artificial cultivation.

Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution

Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.

Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications

Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.

Light regulation of secondary metabolism in fungi

Fungi have evolved unique metabolic regulation mechanisms for adapting to the changing environments. One of the key features of fungal adaptation is the production of secondary metabolites (SMs), which are essential for survival and beneficial to the organism. Many of these SMs are produced in response to the environmental cues, such as light. In all fungal species studied, the Velvet complex transcription factor VeA is a central player of the light regulatory network. In addition to growth and development, the intensity and wavelength of light affects the formation of a broad range of secondary metabolites. Recent studies, mainly on species of the genus Aspergillus, revealed that the dimer of VeA-VelB and LaeA does not only regulate gene expression in response to light, but can also be involved in regulating production of SMs. Furthermore, the complexes have a wide regulatory effect on different types of secondary metabolites. In this review, we discussed the role of light in the regulation of fungal secondary metabolism. In addition, we reviewed the photoreceptors, transcription factors, and signaling pathways that are involved in light-dependent regulation of secondary metabolism. The effects of transcription factors on the production of secondary metabolites, as well as the potential applications of light regulation for the production of pharmaceuticals and other products were discussed. Finally, we provided an overview of the current research in this field and suggested potential areas for future research.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

White Collar 1 Modulates Oxidative Sensitivity and Virulence by Regulating the HOG1 Pathway in Fusarium asiaticum

Fusarium asiaticum is an epidemiologically important pathogen of cereal crops in east Asia, accounting for both yield losses and mycotoxin contamination problems in food and feed products. FaWC1, a component of the blue-light receptor White Collar complex (WCC), relies on its transcriptional regulatory zinc finger domain rather than the light-oxygen-voltage domain to regulate pathogenicity of F. asiaticum, although the downstream mechanisms remain obscure. In this study, the pathogenicity factors regulated by FaWC1 were analyzed. It was found that loss of FaWC1 resulted in higher sensitivity to reactive oxygen species (ROS) than in the wild type, while exogenous application of the ROS quencher ascorbic acid restored the pathogenicity of the ΔFawc1 strain to the level of the wild type, indicating that the reduced pathogenicity of the ΔFawc1 strain is due to a defect in ROS tolerance. Moreover, the expression levels of the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway genes and their downstream genes encoding ROS scavenging enzymes were downregulated in the ΔFawc1 mutant. Upon ROS stimulation, the FaHOG1-green fluorescent protein (GFP)-expressing signal driven by the native promoter was inducible in the wild type but negligible in the ΔFawc1 strain. Overexpressing Fahog1 in the ΔFawc1 strain could recover the ROS tolerance and pathogenicity of the ΔFawc1 mutant, but it remained defective in light responsiveness. In summary, this study dissected the roles of the blue-light receptor component FaWC1 in regulating expression levels of the intracellular HOG-MAPK signaling pathway to affect ROS sensitivity and pathogenicity in F. asiaticum. IMPORTANCE The well-conserved fungal blue-light receptor White Collar complex (WCC) is known to regulate virulence of several pathogenic species for either plant or human hosts, but how WCC determines fungal pathogenicity remains largely unknown. The WCC component FaWC1 in the cereal pathogen Fusarium asiaticum was previously found to be required for full virulence. The present study dissected the roles of FaWC1 in regulating the intracellular HOG MAPK signaling pathway to affect ROS sensitivity and pathogenicity in F. asiaticum. This work thus extends knowledge of the association between fungal light receptors and the intracellular stress signaling pathway to regulate oxidative stress tolerance and pathogenicity in an epidemiologically important fungal pathogen of cereal crops.

Effect of Different Light Wavelengths on Zymoseptoria tritici Development and Leaf Colonization in Bread Wheat

The wheat pathogen Zymoseptoria tritici can respond to light by modulating its gene expression. Because several virulence-related genes are differentially expressed in response to light, different wavelengths could have a crucial role in the Z. tritici-wheat interaction. To explore this opportunity, the aim of this study was to analyze the effect of blue (470 nm), red (627 nm), blue-red, and white light on the in vitro and in planta development of Z. tritici. The morphology (mycelium appearance, color) and phenotypic (mycelium growth) characteristics of a Z. tritici strain were evaluated after 14 days under the different light conditions in two independent experiments. In addition, bread wheat plants were artificially inoculated with Z. tritici and grown for 35 days under the same light treatments. The disease incidence, severity, and fungal DNA were analyzed in a single experiment. Statistical differences were determined by using an ANOVA. The obtained results showed that the different light wavelengths induced specific morphological changes in mycelial growth. The blue light significantly reduced colony growth, while the dark and red light favored fungal development (p < 0.05). The light quality also influenced host colonization, whereby the white and red light had stimulating and repressing effects, respectively (p < 0.05). This precursory study demonstrated the influence of light on Z. tritici colonization in bread wheat.

An Anatomy of Fungal Eye: Fungal Photoreceptors and Signalling Mechanisms

Organisms have developed different features to capture or sense sunlight. Vertebrates have evolved specialized organs (eyes) which contain a variety of photosensor cells that help them to see the light to aid orientation. Opsins are major photoreceptors found in the vertebrate eye. Fungi, with more than five million estimated members, represent an important clade of living organisms which have important functions for the sustainability of life on our planet. Light signalling regulates a range of developmental and metabolic processes including asexual sporulation, sexual fruit body formation, pigment and carotenoid production and even production of secondary metabolites. Fungi have adopted three groups of photoreceptors: (I) blue light receptors, White Collars, vivid, cryptochromes, blue F proteins and DNA photolyases, (II) red light sensors, phytochromes and (III) green light sensors and microbial rhodopsins. Most mechanistic data were elucidated on the roles of the White Collar Complex (WCC) and the phytochromes in the fungal kingdom. The WCC acts as both photoreceptor and transcription factor by binding to target genes, whereas the phytochrome initiates a cascade of signalling by using mitogen-activated protein kinases to elicit its cellular responses. Although the mechanism of photoreception has been studied in great detail, fungal photoreception has not been compared with vertebrate vision. Therefore, this review will mainly focus on mechanistic findings derived from two model organisms, namely Aspergillus nidulans and Neurospora crassa and comparison of some mechanisms with vertebrate vision. Our focus will be on the way light signalling is translated into changes in gene expression, which influences morphogenesis and metabolism in fungi.

Genome-Wide Characterization of Light-Regulated Gene Expression in Botrytis cinerea Reveals Underlying Complex Photobiology

Botrytis cinerea is a necrotrophic fungus characterized mainly by its wide host range of infected plants. The deletion of the white-collar-1 gene (bcwcl1), which encodes for a blue-light receptor/transcription factor, causes a decrease in virulence, particularly when assays are conducted in the presence of light or photocycles. However, despite ample characterization, the extent of the light-modulated transcriptional responses regulated by BcWCL1 remains unknown. In this study, pathogen and pathogen:host RNA-seq analyses, conducted during non-infective in vitro plate growth and when infecting Arabidopsis thaliana leaves, respectively, informed on the global gene expression patterns after a 60 min light pulse on the wild-type B05.10 or ∆bcwcl1 B. cinerea strains. The results revealed a complex fungal photobiology, where the mutant did not react to the light pulse during its interaction with the plant. Indeed, when infecting Arabidopsis, no photoreceptor-encoding genes were upregulated upon the light pulse in the ∆bcwcl1 mutant. Differentially expressed genes (DEGs) in B. cinerea under non-infecting conditions were predominantly related to decreased energy production in response to the light pulse. In contrast, DEGs during infection significantly differ in the B05.10 strain and the ∆bcwcl1 mutant. Upon illumination at 24 h post-infection in planta, a decrease in the B. cinerea virulence-associated transcripts was observed. Accordingly, after a light pulse, biological functions associated with plant defense appear enriched among light-repressed genes in fungus-infected plants. Taken together, our results show the main transcriptomic differences between wild-type B. cinerea B05.10 and ∆bcwcl1 after a 60 min light pulse when growing saprophytically on a Petri dish and necrotrophically over A. thaliana.

Co-Regulatory Roles of WC1 and WC2 in Asexual Development and Photoreactivation of Beauveria bassiana

The white collar proteins WC1 and WC2 interact with each other to form a white collar complex acting as a well-known transcription regulator required for the operation of the circadian clock in Neurospora, but their roles in insect-pathogenic fungal lifecycles remain poorly understood. Here, we report that WC1 and WC2 orthologs co-regulate the conidiation capacity and conidial resistance to solar ultraviolet-B (UVB) irradiation in Beauveria bassiana, after their high activities in the photorepair of UVB-induced DNA damages were elucidated previously in the insect mycopathogen, which features non-rhythmic conidiation and high conidiation capacity. The conidial yield, UVB resistance, and photoreactivation rate of UVB-impaired conidia were greatly reduced in the null mutants of wc1 and wc2 compared to their control strains. However, many other lifecycle-related phenotypes, except the antioxidant response, were rarely affected in the two mutants. Transcriptomic analysis revealed largely overlapping roles for WC1 and WC2 in regulating the fungal gene networks. Most of the differentially expressed genes identified from the null mutants of wc1 (1380) and wc2 (1001) were co-downregulated (536) or co-upregulated (256) at similar levels, including several co-downregulated genes required for aerial conidiation and DNA photorepair. These findings expand a molecular basis underlying the fungal adaptation to solar UV irradiation and offer a novel insight into the genome-wide co-regulatory roles of WC1 and WC2 in B. bassiana's asexual development and in vivo photoreactivation against solar UV damage.

Identification, Pathogenicity, and Culture Conditions of a New Isolate of Cordyceps javanica (Hypocreales: Cordycipitaceae) From Soil

This study decribes a highly effective insecticidal isolate of Cordyceps javanica (Frieder. & Bally) (Hypocreales: Cordycipitaceae) named IJ-tg19, which was isolated from soil. Spray bioassays were performed with IJ-tg19 on Myzus persicae (Sulzer) (Hemiptera: Aphididae) adults, third-instar nymphs of Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae), and third-instar larvae of Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) to determine the pathogenicity of the isolate. The corrected mortality rates for all three pests were 100% when the conidia concentration was 1 × 106 conidia/ml, the lowest concentration in this study, and the median survival times (MST) were 4, 4, and 3 d. The MST shortens with increasing conidia concentration. The effects of laboratory culture conditions on the sporulation and growth of the isolate were also studied. This isolate had the greatest conidia production and fastest growth rate on malt extract agar medium at 25°C. The amount of conidia produced had positive correlation to light duration, with the highest production at 24 hr light. The growth of mycelium can adapt to a moderately alkaline environment, but the optimum conidial production occurred at the pH of 7. Our finding and research will be useful in biocontrol programs that are considering using the new isolate of C. javanica against greenhouse pests.

MAPkinases regulate secondary metabolism, sexual development and light dependent cellulase regulation in Trichoderma reesei

The filamentous fungus Trichoderma reesei is a prolific producer of plant cell wall degrading enzymes, which are regulated in response to diverse environmental signals for optimal adaptation, but also produces a wide array of secondary metabolites. Available carbon source and light are the strongest cues currently known to impact secreted enzyme levels and an interplay with regulation of secondary metabolism became increasingly obvious in recent years. While cellulase regulation is already known to be modulated by different mitogen activated protein kinase (MAPK) pathways, the relevance of the light signal, which is transmitted by this pathway in other fungi as well, is still unknown in T. reesei as are interconnections to secondary metabolism and chemical communication under mating conditions. Here we show that MAPkinases differentially influence cellulase regulation in light and darkness and that the Hog1 homologue TMK3, but not TMK1 or TMK2 are required for the chemotropic response to glucose in T. reesei. Additionally, MAPkinases regulate production of specific secondary metabolites including trichodimerol and bisorbibutenolid, a bioactive compound with cytostatic effect on cancer cells and deterrent effect on larvae, under conditions facilitating mating, which reflects a defect in chemical communication. Strains lacking either of the MAPkinases become female sterile, indicating the conservation of the role of MAPkinases in sexual fertility also in T. reesei. In summary, our findings substantiate the previously detected interconnection of cellulase regulation with regulation of secondary metabolism as well as the involvement of MAPkinases in light dependent gene regulation of cellulase and secondary metabolite genes in fungi.

Comparative proteomic analysis reveals differential protein expression of Hypsizygus marmoreus in response to different light qualities

Light is important environmental stress that influences the growth, development, and metabolism of Hypsizygus marmoreus (white var.). However, the molecular basis of the light effect on H. marmoreus remains unclear. In this study, a label-free comparative proteomic analysis was applied to investigate the global protein expression profile of H. marmoreus mycelia growing under white, red, green, and blue light qualities and darkness (control). Among 3149 identified proteins in H. marmoreus, 2288 were found to be expressed in all tested conditions. Data of Each light quality was compared with darkness for further analysis, numerous differentially expressed proteins (DEPs) were identified and the white light group showed the most. All the up-regulated and down-regulated DEPs were annotated and analyzed with the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The KEGG enrichment analysis revealed that light stress was associated with primary metabolism, glycolysis/gluconeogenesis, MAPK, proteasome, and carbohydrate-active enzyme pathways. This study advances valuable insights into the molecular mechanisms underlying the role of different light qualities in mushroom growth and development.

Mechanism Underlying Light Intensity-Induced Melanin Synthesis of Auricularia heimuer Revealed by Transcriptome Analysis

Auricularia heimuer is a traditional edible and medicinal mushroom, which is widely used in biochemical research and is regarded as a good dietary supplement. The color of the ear-like fruiting body is an important indicator of its commercial quality. However, the mechanism by which light intensity influences the melanin synthesis of A. heimuer remains unclear. Here, we show that fruiting body color is significantly affected by light intensity. Transcriptional profiles of the fruiting bodies of A. heimuer grown in different light intensities were further analyzed. More differentially expressed genes (DEGs) were identified with a greater light intensity difference. A total of 1388 DEGs were identified from six comparisons, including 503 up-regulated genes and 885 down-regulated genes. The up-regulated genes were mainly associated with light sensing via photoreceptors, signal transduction via the mitogen-activated protein kinase (MAPK) signaling pathway, and melanin synthesis via the tyrosine metabolic pathway. Therefore, the genes involved in these processes may participate in regulating melanin synthesis under high light intensity. This insight into the transcriptional regulation of A. heimuer to light intensity should help to further comprehensively elucidate the underlying mechanism of light-induced melanin synthesis.

Light conditions affect the growth, chemical composition, antioxidant and antimicrobial activities of the white-rot fungus Lentinus crinitus mycelial biomass

The mycelial biomass of basidiomycetes is a promising source of compounds and represents an alternative for industrial and biotechnological applications. Fungi use light as information and hold photoresponse mechanisms, in which sensors respond to light wavelengths and regulate various biological processes. Therefore, this study aimed to investigate the effects of blue, green, and red lights on the growth, chemical composition, and antioxidant and antimicrobial activity of Lentinus crinitus mycelial biomass. The chemical composition of the mycelial biomass was determined by chromatographic methods, antioxidant activity was analyzed by in vitro assays, and antimicrobial activity was investigated by the microdilution assay. The highest mycelial biomass yield was observed under blue-light cultivation. Many primordia arose under blue or green light, whereas the stroma was formed under red light. The presence of light altered the primary fungal metabolism, increasing the carbohydrate, tocopherol, fatty acid, and soluble sugar contents, mostly mannitol, and reducing the protein and organic acid concentrations. Cultivation under red light increased the phenol concentration. In contrast, cultivation under blue and green lights decreased phenol concentration. Benzoic and gallic acids were the main phenolic acids in the hydroalcoholic extracts, and the latter acids increased in all cultures under light, especially red light. Mycelial biomass cultivated under red light showed the highest antioxidant activity in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. The ferric reducing antioxidant power (FRAP) method showed that all light wavelengths increased the antioxidant activity of mycelial biomass, with the highest value under red light. Moreover, the β-carotene/linoleic acid co-oxidation (BCLA) assay demonstrated that the antioxidant activity was affected by light cultivation. Mycelial biomass grown under all conditions exhibited antibacterial and antifungal activities. Thus, mycelial biomass cultivation of L. crinitus under light conditions may be a promising strategy for controlling the mycelial chemical composition and biomass yield.

Placing human gene families into their evolutionary context

Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.

Blue Light-Dependent Pre-mRNA Splicing Controls Pigment Biosynthesis in the Mushroom Terana caerulea

Light induces the production of ink-blue pentacyclic natural products, the corticin pigments, in the cobalt crust mushroom Terana caerulea. Here, we describe the genetic locus for corticin biosynthesis and provide evidence for a light-dependent dual transcriptional/cotranscriptional regulatory mechanism. Light selectively induces the expression of the corA gene encoding the gateway enzyme, the first described mushroom polyporic acid synthetase CorA, while other biosynthetic genes for modifying enzymes necessary to complete corticin assembly are induced only at lower levels. The strongest corA induction was observed following exposure to blue and UV light. A second layer of regulation is provided by the light-dependent splicing of the three introns in the pre-mRNA of corA. Our results provide insight into the fundamental organization of how mushrooms regulate natural product biosynthesis. IMPORTANCE The regulation of natural product biosyntheses in mushrooms in response to environmental cues is poorly understood. We addressed this knowledge gap and chose the cobalt crust mushroom Terana caerulea as our model. Our work discovered a dual-level regulatory mechanism that connects light as an abiotic stimulus with a physiological response, i.e., the production of dark-blue pigments. Exposure to blue light elicits strongly increased transcription of the gene encoding the gateway enzyme, the polyporic acid synthetase CorA, that catalyzes the formation of the pigment core structure. Additionally, light is a prerequisite for the full splicing of corA pre-mRNA and, thus, its proper maturation. Dual transcriptional/cotranscriptional light-dependent control of fungal natural product biosynthesis has previously been unknown. As it allows the tight control of a key metabolic step, it may be a much more prevalent mechanism among these organisms.

In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface

Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.

GATA transcription factor WC2 regulates the biosynthesis of astaxanthin in yeast Xanthophyllomyces dendrorhous

Astaxanthin is a type of carotenoid widely used as powerful antioxidant and colourant in aquaculture and the poultry industry. Production of astaxanthin by yeast Xanthophyllomyces dendrorhous has attracted increasing attention due to high cell density and low requirements of water and land compared to photoautotrophic algae. Currently, the regulatory mechanisms of astaxanthin synthesis in X. dendrorhous remain obscure. In this study, we obtained a yellow X. dendrorhous mutant by Atmospheric and Room Temperature Plasma (ARTP) mutagenesis and sequenced its genome. We then identified a putative GATA transcription factor, white collar 2 (XdWC2), from the comparative genome data and verified that disruption of the XdWC2 gene resulted in a similar carotenoid profile to that of the ARTP mutant. Furthermore, transcriptomic analysis and yeast one-hybrid (Y1H) assay showed that XdWC2 regulated the expression of phytoene desaturase gene CrtI and astaxanthin synthase gene CrtS. The yeast two-hybrid (Y2H) assay demonstrated that XdWC2 interacted with white collar 1 (XdWC1) forming a heterodimer WC complex (WCC) to regulate the expression of CrtI and CrtS. Increase of the transcriptional levels of XdWC2 or CrtS in the wild-type strain did not largely modify the carotenoid profile, indicating translational and/or post-translational regulations involved in the biosynthesis of astaxanthin. Overexpression of CrtI in both the wild-type strain and the XdWC2-disrupted strain apparently improved the production of monocyclic carotenoid 3-hydroxy-3', 4'-didehydro-β, ψ-carotene-4-one (HDCO) rather than β-carotene and astaxanthin. The regulation of carotenoid biosynthesis by XdWC2 presented here provides the foundation for further understanding the global regulation of astaxanthin biosynthesis and guides the construction of astaxanthin over-producing strains.

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.

Tools for adapting to a complex habitat: G-protein coupled receptors in Trichoderma

Sensing the environment and interpretation of the received signals are crucial competences of living organisms in order to properly adapt to their habitat, succeed in competition and to reproduce. G-protein coupled receptors (GPCRs) are members of a large family of sensors for extracellular signals and represent the starting point of complex signaling cascades regulating a plethora of intracellular physiological processes and output pathways in fungi. In Trichoderma spp. current research involves a wide range of topics from enzyme production, light response and secondary metabolism to sexual and asexual development as well as biocontrol, all of which require delicate balancing of resources in response to the environmental challenges or biotechnological needs at hand, which are crucially impacted by the surroundings of the fungi and their intercellular signaling cascades triggering a precisely tailored response. In this review we summarize recent findings on sensing by GPCRs in Trichoderma, including the function of pheromone receptors, glucose sensing by CSG1 and CSG2, regulation of secondary metabolism by GPR8 and impacts on mycoparasitism by GPR1. Additionally, we provide an overview on structural determinants, posttranslational modifications and interactions for regulation, activation and signal termination of GPCRs in order to inspire future in depth analyses of their function and to understand previous regulatory outcomes of natural and biotechnological processes modulated or enabled by GPCRs.

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.

The Zymoseptoria tritici white collar-1 gene, ZtWco-1, is required for development and virulence on wheat

The fungus Zymoseptoria tritici causes Septoria Tritici Blotch (STB), which is one of the most devastating diseases of wheat in Europe. There are currently no fully durable methods of control against Z. tritici, so novel strategies are urgently required. One of the ways in which fungi are able to respond to their surrounding environment is through the use of photoreceptor proteins which detect light signals. Although previous evidence suggests that Z. tritici can detect light, no photoreceptor genes have been characterised in this pathogen. This study characterises ZtWco-1, a predicted photoreceptor gene in Z. tritici. The ZtWco-1 gene is a putative homolog to the blue light photoreceptor from Neurospora crassa, wc-1. Z. tritici mutants with deletions in ZtWco-1 have defects in hyphal branching, melanisation and virulence on wheat. In addition, we identify the putative circadian clock gene ZtFrq in Z. tritici. This study provides evidence for the genetic regulation of light detection in Z. tritici and it open avenues for future research into whether this pathogen has a circadian clock.

A light-sensing system in the common ancestor of the fungi

Diverse light-sensing organs (i.e., eyes) have evolved across animals. Interestingly, several subcellular analogs have been found in eukaryotic microbes.¹ All of these systems have a common “recipe”: a light occluding or refractory surface juxtaposed to a membrane-layer enriched in type I rhodopsins.1, 2, 3, 4 In the fungi, several lineages have been shown to detect light using a diversity of non-homologous photo-responsive proteins.5, 6, 7 However, these systems are not associated with an eyespot-like organelle with one exception found in the zoosporic fungus Blastocladiella emersonii (Be).⁸Be possesses both elements of this recipe: an eyespot composed of lipid-filled structures (often called the side-body complex [SBC]), co-localized with a membrane enriched with a gene-fusion protein composed of a type I (microbial) rhodopsin and guanylyl cyclase enzyme domain (CyclOp-fusion protein).^8,9 Here, we identify homologous pathway components in four Chytridiomycota orders (Chytridiales, Synchytriales, Rhizophydiales, and Monoblepharidiales). To further explore the architecture of the fungal zoospore and its lipid organelles, we reviewed electron microscopy data (e.g., the works of Barr and Hartmann¹⁰ and Reichle and Fuller¹¹) and performed fluorescence-microscopy imaging of four CyclOp-carrying zoosporic fungal species, showing the presence of a variety of candidate eyespot-cytoskeletal ultrastructure systems. We then assessed the presence of canonical photoreceptors across the fungi and inferred that the last common fungal ancestor was able to sense light across a range of wavelengths using a variety of systems, including blue-green-light detection. Our data imply, independently of how the fungal tree of life is rooted, that the apparatus for a CyclOp-organelle light perception system was an ancestral feature of the fungi.

•

A wide diversity of flagellated fungi possess the CyclOp light response circuit

•

The same fungi possess the subcellular equipment to build lipid-based eyespots

•

The last common ancestor of fungi possessed the CyclOp eyespot system

•

The ancestral fungus could see a rainbow of light wavelengths

Interactions between Core Elements of the Botrytis cinerea Circadian Clock Are Modulated by Light and Different Protein Domains

Botrytis cinerea possesses a complex light-sensing system composed of eleven photoreceptors. In B. cinerea, bcwcl1 encodes for the BcWCL1 protein, the orthologue of the blue-light photoreceptor WC-1 from Neurospora crassa. The functional partner of BcWCL1 is the BcWCL2 protein, both interacting in the nucleus and forming the B. cinerea white collar complex (BcWCC). This complex is required for photomorphogenesis and circadian regulation. However, no molecular evidence shows a light-dependent interaction between the BcWCC components or light-sensing capabilities in BcWCL1. In this work, by employing a yeast two-hybrid system that allows for the in vivo analysis of protein-protein interactions, we confirm that BcWCL1 and BcWCL2 interact in the absence of light as well as upon blue-light stimulation, primarily through their PAS (Per-Arnt-Sim) domains. Deletion of the PAS domains present in BcWCL1 (BcWCL1PAS∆) or BcWCL2 (BcWCL2PAS∆) severely impairs the interaction between these proteins. Interestingly, the BcWCL1PAS∆ protein shows a blue-light response and interacts with BcWCL2 or BcWCL2PAS∆ upon light stimulation. Finally, we demonstrate that BcWCL1 and BcWCL1PAS∆ respond to blue light by introducing a point mutation in the photoactive cysteine, confirming that both proteins are capable of light sensing. Altogether, the results revealed the complexity of protein-protein interactions occurring between the core elements of the B. cinerea circadian clock.

The facilitating effect of blue light on the antifungal agent susceptibilities of passaged conidia from the ocular-derived Fusarium solani species complex

The eye is a light-receiving organ and has anatomical advantages to accept phototherapy. Fungi colonizing on the eyes, which cause ocular mycoses, are affected by daily blue light and could easily accept additional light irritation. Ocular mycoses are recalcitrant and blindness-causing eye diseases, and antifungal agent treatments are insufficient. Our team previously found that blue light could inhibit Fusarium solani hyphal growth but promote conidiation. Here, we investigated the antifungal susceptibilities and biological characteristics of the passaged conidia. Twelve Fusarium solani strains (11 ocular-derived strains and 1 standard laboratory strain) were inoculated under blue light (0.5 mW/cm2) and darkness conditions, respectively, to obtain the passaged conidia of blue light group (n = 12) and darkness group (n = 12). Two groups were tested to determine the growth abilities and in vitro antifungal susceptibilities to five antifungal drugs (voriconazole (VRC), amphotericin B (AMB), terbinafine (TRB), caspofungin (CAS), and 5-flucytosine (5FC)), which were examined by microscopy for morphological observation and spectrophotometry for turbidity analysis. The results showed that blue light group passaged conidia were more sensitive to antifungal drugs (AMB, VRC, TRB, and CAS) compared to darkness group. The MIC50 of VRC significantly decreased after blue light treatment (P < 0.05). The fungal inhibition rate significantly increased for VRC, AMB, and TRB in the low concentration range (P < 0.05 or P < 0.01). Blue light did not affect germination or hyphal extension of passaged conidia. These results suggested that blue light could facilitate fungal inhibition effect of AMB, VRC, TRB, and CAS and may improve the therapeutic efficiency in VRC and AMB clinical applications. Blue light phototherapy may provide a new adjuvant approach for the treatment of ocular mycosis.

Involvement of VIVID in white light-responsive pigmentation, sexual development and sterigmatocystin biosynthesis in the filamentous fungus Podospora anserina

Light serves as a source of information and regulates diverse physiological processes in living organisms. Fungi perceive and respond to light through a complex photosensory system. Fungi have evolved the desensitization mechanism to adapt to the changing light signal in a natural environment. White light exerts multiple essential impacts on the model filamentous fungus P. anserina. However, the light sensing and response in this species has not been investigated. In this study, we demonstrated that the loss of function of the light desensitization protein VIVID (VVD) in P. anserina triggered exacerbated light responses, and therefore led to drastic morphological and physiological changes. The white light-sensitive mutant Δvvd showed growth reduction, spermatia overproduction, enhanced hyphae pigmentation and reduced oxidative stress tolerance. We observed the decreased expression level of sterigmatocystin gene cluster by transcriptome analysis, and finally detected the reduced production of sterigmatocystin in Δvvd in response to white light. Our data indicate that VVD acts as a repressor of white collar complex. This study exhibits a vital role of VVD in governing white light-responsive gene expression and secondary metabolite production, and contributes to a better understanding of the photoreceptor VVD in P. anserina. This article is protected by copyright. All rights reserved.

Blue Light Alters the Composition of the Jejunal Microbiota and Promotes the Development of the Small Intestine by Reducing Oxidative Stress

Environmental light has an important impact on the growth, development and oxidative stress of chicks. Thus, we investigated the effects of colored lights on microbes and explored the molecular mechanism by which external color light information alters the gut microbiota and induces the cell response in vivo. We raised 96 chicks under 400-700 nm white (WL), 660 nm red (RL), 560 nm green (GL) or 480 nm blue light (BL) for 42 days. We used 16S rRNA high-throughput pyrosequencing and gas chromatography to explore the effect of different monochromatic lights on the jejunal microbiota. We used qRT-PCR, western blotting, immunohistochemistry and Elisa to determine the effect of different monochromatic lights on small intestine development and oxidative stress levels. With consistency in the upregulation of antioxidant enzyme ability and anti-inflammatory cytokine level, the 16S rRNA and gas chromatography results showed that BL significantly increased the diversity and richness of the jejunal microbiota and improved the relative abundances of Faecalibacterium, Ruminiclostridium_9 and metabolite butyrate content compared with WL, RL and GL (p < 0.05). In addition, we observed that BL increased the goblet cell numbers, PCNA cell numbers, villus-length-to-crypt-depth (V/C) ratios, ZO-1, Occludin, and Claudin-1 protein expression; decreased permeability; and enhanced the digestion and absorption capacity in the jejunum (p < 0.05). In the in vitro experiment, we found that butyrate promoted chick small intestinal epithelial cell (CIEC) proliferation and inhibited apoptosis (p < 0.05). These responses were abrogated by the Gi inhibitor, PI3K inhibitor or AKT inhibitor, but were mimicked by GPR43 agonists or the GSK-3β inhibitor (p < 0.05). Overall, these findings suggested that BL increased the relative abundance of Faecalibacterium, Ruminiclostridium_9 and butyrate production. Butyrate may act as one of the signals to mediate blue-light-induced small intestinal development and mucosal barrier integrity enhancement and promote cell proliferation via the GPR43/Gi/PI3K/AKT/p-GSK-3β/β-catenin pathway.

A Simple and Low-Cost Strategy to Improve Conidial Yield and Stress Resistance of Trichoderma guizhouense through Optimizing Illumination Conditions

Light is perceived by photoreceptors in fungi and further integrated into the stress-activated MAPK HOG pathway, and thereby potentially activates the expression of genes for stress responses. This indicates that the precise control of light conditions can likely improve the conidial yield and stress resistance to guarantee the low cost and long shelf life of Trichoderma-based biocontrol agents and biofertilizers. In this study, effects of wavelengths and intensities of light on conidial yield and stress tolerance to osmotic, oxidative and pH stresses in Trichoderma guizhouense were investigated. We found that 2 μmol photons/(m² × s) of blue light increased the conidial yield more than 1000 folds as compared to dark condition and simultaneously enhanced conidial stress resistance. The enhanced conidial stress resistance is probably due to the upregulated stress-related genes in blue light, which is under the control of the blue light receptor BLR1 and the MAP kinase HOG1.

Photobiology of the keystone genus Metarhizium

Metarhizium fungi are soil-inhabiting ascomycetes which are saprotrophs, symbionts of plants, pathogens of insects, and participate in other trophic/ecological interactions, thereby performing multiple essential ecosystem services. Metarhizium species are used to control insect pests of crop plants and insects that act as vectors of human and animal diseases. To fulfil their functions in the environment and as biocontrol agents, these fungi must endure cellular stresses imposed by the environment, one of the most potent of which is solar ultraviolet (UV) radiation. Here, we examine the cellular stress biology of Metarhizium species in context of their photobiology, showing how photobiology facilitates key aspects of their ecology as keystone microbes and as mycoinsectides. The biophysical basis of UV-induced damage to Metarhizium, and mechanistic basis of molecular and cellular responses to effect damage repair, are discussed and interpreted in relation to the solar radiation received on Earth. We analyse the interplay between UV and visible light and how the latter increases cellular tolerance to the former via expression of a photolyase gene. By integrating current knowledge, we propose the mechanism through which Metarhizium species use the visible fraction of (low-UV) early-morning light to mitigate potentially lethal damage from intense UV radiation later in the day. We also show how this mechanism could increase Metarhizium environmental persistence and improve its bioinsecticide performance. We discuss the finding that visible light modulates stress biology in the context of further work needed on Metarhizium ecology in natural and agricultural ecosystems, and as keystone microbes that provide essential services within Earth's biosphere.

Fungal electronics

Fungal electronics is a family of living electronic devices made of mycelium bound composites or pure mycelium. Fungal electronic devices are capable of changing their impedance and generating spikes of electrical potential in response to external control parameters. Fungal electronics can be embedded into fungal materials and wearables or used as stand alone sensing and computing devices.

Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis

The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body plans are highly conserved. At the same time, insights into the genetic bases of fruiting body development have been achieved using forward and reverse genetic approaches in selected model systems. Phylogenetic and developmental studies of fruiting bodies have each yielded major advances, but they have produced largely disjunct bodies of knowledge. An integrative approach, combining phylogenetic, developmental, and functional biology, is needed to achieve a true fungal evolutionary developmental biology (evo-devo) synthesis for fungal fruiting bodies.

Transcriptome sequencing and global analysis of blue light-responsive genes provide clues for high carotenoid yields in Blakeslea trispora

Blakeslea trispora has great potential uses in industrial production because of the excellent capability of producing a large quantity of carotenoids. However, the mechanisms of light-induced carotenoid biosynthesis even the structural and regulatory genes in pathways remain unclear. In this paper, we reported the first transcriptome study in B. trispora in which we have carried out global survey of expression changes of genes participated in blue light response. We verified that the yield of β-carotene increased 3-fold when transferred from darkness to blue light for 24 h and the enhancement of transcription levels of carRA and carB presented a positive correlation with the increase in carotenoid production. RNA-seq analysis revealed that 1124 genes were upregulated and 740 genes were downregulated respectively after blue light exposure. Annotation through GO, KEGG, Swissprot, and COG databases showed 11119 unigenes compared well with known gene sequences, 5514 unigenes were classified into Gene Ontology, and 4675 unigenes were involved in distinct pathways. Among the blue light-responsive genes, 4 genes (carG1, carG3, carRA and carB) identified to function in carotenoid metabolic pathways were dominantly upregulated. We also discovered that 142 TF genes belonging to 45 different superfamilies showed significant differential expression (p≤ 0.05), 62 of which were obviously repressed by blue light. The detailed profile of transcription data will not only allow us to conduct further functional genomics study in B. trispora, but also enhance our understanding of potential metabolic pathway and regulatory network involved in light-regulated carotenoid synthesis.

Timing and duration of light exposure during conidia development determine tolerance to ultraviolet radiation

Metarhizium is an important genus of soil-inhabiting fungi that are used for the biological control of insects. The efficiency of biocontrol is dependent on the maintenance of inoculum viability under adverse field conditions such as solar ultraviolet (UV) radiation. Therefore, increasing the tolerance of Metarhizium to UV radiation is necessary. It was previously established that, in mycelium, exposure to visible light increases tolerance to UV radiation. Similarly, growth under visible light for 14 days induces the production of tolerant conidia. However, a study evaluating if and how visible light affects conidia and their relationship with UV radiation was never performed. Here, we report that a relatively short and timed exposure to light around the time of conidiation is sufficient to induce the production of conidia with increased photoreactivating capacity and UV tolerance in Metarhizium acridum. Conidia produced by this method retain their characteristic higher tolerance even after many days of being transferred to the dark. Furthermore, we show that mature conidia of M. acridum and Metarhizium brunneum can still answer to light and regulate UV tolerance, suggesting that gene expression is possible even in dormant spores. Being able to respond to light in the dormant stages of development is certainly an advantage conferring improved environmental persistence to Metarhizium.