Light controls growth and development via a conserved pathway in the fungal kingdom

Biogenesis, germination, and pathogenesis of Cryptococcus spores

SUMMARYSpores are primary infectious propagules for the majority of human fungal pathogens; however, relatively little is known about their fundamental biology. One strategy to address this deficiency has been to develop the basidiospores of Cryptococcus into a model for pathogenic spore biology. Here, we provide an update on the state of the field with a comprehensive review of the data generated from the study of Cryptococcus basidiospores from their formation (sporulation) and differentiation (germination) to their roles in pathogenesis. Importantly, we provide support for the presence of basidiospores in nature, define the key characteristics that distinguish basidiospores from yeast cells, and clarify their likely roles as infectious particles. This review is intended to demonstrate the importance of basidiospores in the field of Cryptococcus research and provide a solid foundation from which researchers who wish to study sexual spores in any fungal system can launch their studies.

Comparative Proteomic Analysis Reveals Candidate Pathways Related to the Effect of Different Light Qualities on the Development of Mycelium and Fruiting Body of Pleurotus ostreatus

Light affects the morphology and physiology of Pleurotus ostreatus. However, the underlying molecular mechanism of this effect remains unclear. In this study, a label-free comparative proteomic analysis was conducted to investigate the global protein expression profile of the mycelia and fruiting bodies of P. ostreatus PH11 growing under four different light quality treatments. Among all the 2234 P. ostreatus proteins, 1349 were quantifiable under all tested conditions. A total of 1100 differentially expressed proteins were identified by comparing the light group data with those of the darkness group. GO and KEGG enrichment analyses indicated that the oxidative phosphorylation, proteasome, and mRNA surveillance pathways were the most related pathways under the light condition. qRT-PCR verified that the expression of the white collar 1 protein was significantly enhanced under white light. Additionally, glutamine synthetase and aldehyde dehydrogenase played important roles during light exposure. This study provides valuable insight into the P. ostreatus light response mechanism, which will lay the foundation for improved cultivation.

Disruption of the FMN-A524 interaction cascade and Glu513-induced collapse of the hydrophobic barrier promotes light-induced Jα-helix unfolding in AsLOV2

The C-terminal Jα-helix of the Avena sativa's Light Oxygen and Voltage (AsLOV2) protein, unfolds on exposure to blue light. This characteristic seeks relevance in applications related to engineering novel biological photoswitches. Using molecular dynamics simulations and the Markov state modeling (MSM) approach we provide the mechanism that explains the stepwise unfolding of the Jα-helix. The unfolding was resolved into seven steps represented by the structurally distinguishable states distributed over the initiation and the post initiation phases. Whereas, the initiation phase occurs due to the collapse of the interaction cascade FMN-Q513-N492-L480-W491-Q479-V520-A524, the onset of the post initiation phase is marked by breaking of the hydrophobic interactions between the Jα-helix and the Iβ-strand. This study indicates that the displacement of N492 out of the FMN binding pocket, not necessarily requiring Q513, is essential for the initiation of the Jα-helix unfolding. Rather, the structural reorientation of Q513 activates the protein to cross the hydrophobic barrier and enter the post initiation phase. Similarly, the structural deviations in N482, rather than its integral role in unfolding, could enhance the unfolding rates. Furthermore, the MSM studies on the wild-type and the Q513 mutant, provide the spatiotemporal roadmap that lay out the possible pathways of structural transition between the dark and the light states of the protein. Overall, the study provides insights useful to enhance the performance of AsLOV2-based photoswitches.

Cryptococcus neoformans adapts to the host environment through TOR-mediated remodeling of phospholipid asymmetry

Cryptococcus spp. are environmental fungi that first must adapt to the host environment before they can cause life-threatening meningitis in immunocompromised patients. Host CO2 concentrations are 100-fold higher than the external environment and strains unable to grow at host CO2 concentrations are not pathogenic. Using a genetic screening and transcriptional profiling approach, we report that the TOR pathway is critical for C. neoformans adaptation to host CO2 partly through Ypk1-dependent remodeling of phosphatidylserine asymmetry at the plasma membrane. We also describe a C. neoformans ABC/PDR transporter (PDR9) that is highly expressed in CO2-sensitive environmental strains, suppresses CO2-induced phosphatidylserine/phospholipid remodeling, and increases susceptibility to host concentrations of CO2. Interestingly, regulation of plasma membrane lipid asymmetry by the TOR-Ypk1 axis is distinct in C. neoformans compared to S. cerevisiae. Finally, host CO2 concentrations suppress the C. neoformans pathways that respond to host temperature (Mpk1) and pH (Rim101), indicating that host adaptation requires a stringent balance among distinct stress responses.

Genome-wide identification of the opsin protein in Leptosphaeria maculans and comparison with other fungi (pathogens of Brassica napus)

The largest family of transmembrane receptors are G-protein-coupled receptors (GPCRs). These receptors respond to perceived environmental signals and infect their host plants. Family A of the GPCR includes opsin. However, there is little known about the roles of GPCRs in phytopathogenic fungi. We studied opsin in Leptosphaeria maculans, an important pathogen of oilseed rape (Brassica napus) that causes blackleg disease, and compared it with six other fungal pathogens of oilseed rape. A phylogenetic tree analysis of 31 isoforms of the opsin protein showed six major groups and six subgroups. All three opsin isoforms of L. maculans are grouped in the same clade in the phylogenetic tree. Physicochemical analysis revealed that all studied opsin proteins are stable and hydrophobic. Subcellular localization revealed that most isoforms were localized in the endoplasmic reticulum membrane except for several isoforms in Verticillium species, which were localized in the mitochondrial membrane. Most isoforms comprise two conserved domains. One conserved motif was observed across all isoforms, consisting of the BACTERIAL_OPSIN_1 domain, which has been hypothesized to have an identical sensory function. Most studied isoforms showed seven transmembrane helices, except for one isoform of V. longisporum and four isoforms of Fusarium oxysporum. Tertiary structure prediction displayed a conformational change in four isoforms of F. oxysporum that presumed differences in binding to other proteins and sensing signals, thereby resulting in various pathogenicity strategies. Protein-protein interactions and binding site analyses demonstrated a variety of numbers of ligands and pockets across all isoforms, ranging between 0 and 13 ligands and 4 and 10 pockets. According to the phylogenetic analysis in this study and considerable physiochemically and structurally differences of opsin proteins among all studied fungi hypothesized that this protein acts in the pathogenicity, growth, sporulation, and mating of these fungi differently.

Transcriptomic profiling revealed important roles of amino acid metabolism in fruiting body formation at different ripening times in Hypsizygus marmoreus

Introduction

Hypsizygus marmoreus is an industrial mushroom that is widely cultivated in East Asia. Its long postripening stage before fruiting severely limits its industrialized production.

Methods

Five different mycelial ripening times (30, 50, 70, 90, and 100 d) were chosen and primordia (30P, 50P, 70P, 90P, and 110P) were collected for comparative transcriptomic analyses. The corresponding substrates (30F, 50F, 70F, 90F, and 110F) were used for nutrient content and enzyme activity determination.

Results

In pairwise comparisons between 110P and other primordia, a total of 1,194, 977, 773, and 697 differentially expressed genes (DEGs) were identified in 30P_110P, 50P_110P, 70P_110P, and 90P_110P, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) functional enrichment analyses revealed that the DEGs were mainly associated with amino acid metabolism, and lipid and carbohydrate metabolism pathways. Tyrosine, tryptophan, phenylalanine and histidine metabolism were enriched in all groups. Among the main carbon nutrients, the contents of cellulose and hemicellulose were high, and the lignin content decreased with the extension of the ripening time. Laccase had the highest activity, and acid protease activity decreased with the extension of the ripening time.

Discussion

The highly enrichment for amino acid metabolic pathways in primordia reveals that these pathways are essential for fruiting body formation in H. marmoreus, and these results will provide a basis for the optimization of its cultivation.

Regulatory basis for reproductive flexibility in a meningitis-causing fungal pathogen

Pathogenic fungi of the genus Cryptococcus can undergo two sexual cycles, involving either bisexual diploidization (after fusion of haploid cells of different mating type) or unisexual diploidization (by autodiploidization of a single cell). Here, we construct a gene-deletion library for 111 transcription factor genes in Cryptococcus deneoformans, and explore the roles of these regulatory networks in the two reproductive modes. We show that transcription factors crucial for bisexual syngamy induce the expression of known mating determinants as well as other conserved genes of unknown function. Deletion of one of these genes, which we term FMP1, leads to defects in bisexual reproduction in C. deneoformans, its sister species Cryptococcus neoformans, and the ascomycete Neurospora crassa. Furthermore, we show that a recently evolved regulatory cascade mediates pre-meiotic unisexual autodiploidization, supporting that this reproductive process is a recent evolutionary innovation. Our findings indicate that genetic circuits with different evolutionary ages govern hallmark events distinguishing unisexual and bisexual reproduction in Cryptococcus.

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.

De Novo Assembly Transcriptome Analysis Reveals the Preliminary Molecular Mechanism of Primordium Formation in Pleurotus tuoliensis

Primordium formation is extremely important for yield of Pleurotus tuoliensis. However, the molecular mechanism underlying primordium formation is largely unknown. This study investigated the transcriptional properties during primordium formation of P. tuoliensis by comparing transcriptome. Clean reads were assembled into 57,075 transcripts and 6874 unigenes. A total of 1397 differentially expressed genes were identified (26 DEGs altered in all stages). GO and KEGG enrichment analysis showed that these DEGs were involved in “oxidoreductase activity”, “glycolysis/gluconeogenesis”, “MAPK signaling pathways”, and “ribosomes”. Our results support further understanding of the transcriptional changes and molecular processes underlying primordium formation and differentiation of P. tuoliensis.

De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia

The genes associated with fruiting body formation of Sparasis latifolia are valuable for improving mushroom breeding. To investigate this process, 4.8 × 10⁸ RNA-Seq reads were acquired from three stages: hyphal knot (SM), primordium (SP), and primordium differentiation (SPD). The de novo assembly generated a total of 48,549 unigenes, of which 71.53% (34,728) unigenes could be annotated by at least one of the KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and KOG (Eukaryotic Orthologous Group) databases. KEGG and KOG analyses respectively mapped 32,765 unigenes to 202 pathways and 19,408 unigenes to 25 categories. KEGG pathway enrichment analysis of DEGs (differentially expressed genes) indicated primordium initiation was significantly related to 66 pathways, such as “Ribosome”, “metabolism of xenobiotics by cytochrome P450”, and “glutathione metabolism” (among others). The MAPK and mTOR signal transduction pathways underwent significant adjustments during the SM to SP transition. Further, our research revealed the PI3K-Akt signaling pathway related to cell proliferation could play crucial functions during the development of SP and SPD. These findings provide crucial candidate genes and pathways related to primordium differentiation and development in S. latifolia, and advances our knowledge about mushroom morphogenesis.

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.

Sexual Crossing, Chromosome-Level Genome Sequences, and Comparative Genomic Analyses for the Medicinal Mushroom Taiwanofungus Camphoratus (Syn. Antrodia Cinnamomea, Antrodia Camphorata)

Taiwanofungus camphoratus mushrooms are a complementary and alternative medicine for hangovers, cancer, hypertension, obesity, diabetes, and inflammation. Though Taiwanofungus camphoratus has attracted considerable biotechnological and pharmacological attention, neither classical genetic nor genomic approaches have been properly established for it. We isolated four sexually competent monokaryons from two T. camphoratus dikaryons used for the commercial cultivation of orange-red (HC1) and milky-white (SN1) mushrooms, respectively. We also sequenced, annotated, and comparatively analyzed high-quality and chromosome-level genome sequences of these four monokaryons. These genomic resources represent a valuable basis for understanding the biology, evolution, and secondary metabolite biosynthesis of this economically important mushrooms. We demonstrate that T. camphoratus has a tetrapolar mating system and that HC1 and SN1 represent two intraspecies isolates displaying karyotypic variation. Compared with several edible mushroom model organisms, T. camphoratus underwent a significant contraction in the gene family and individual gene numbers, most notably for plant, fungal, and bacterial cell-wall-degrading enzymes, explaining why T. camphoratus mushrooms are rare in natural environments, are difficult and time-consuming to artificially cultivate, and are susceptible to fungal and bacterial infections. Our results lay the foundation for an in-depth T. camphoratus study, including precise genetic manipulation, improvements to mushroom fruiting, and synthetic biology applications for producing natural medicinal products. IMPORTANCETaiwanofungus camphoratus (Tc) is a basidiomycete fungus that causes brown heart rot of the aromatic tree Cinnamomum kanehirae. The Tc fruiting bodies have been used to treat hangovers, abdominal pain, diarrhea, hypertension, and other diseases first by aboriginal Taiwanese and later by people in many countries. To establish classical genetic and genomic approaches for this economically important medicinal mushroom, we first isolated and characterized four sexually competent monokaryons from two dikaryons wildly used for commercial production of Tc mushrooms. We applied PacBio single molecule, real-time sequencing technology to determine the near-completed genome sequences of four monokaryons. These telomere-to-telomere and gapless haploid genome sequences reveal all genomic variants needed to be studied and discovered, including centromeres, telomeres, retrotransposons, mating type loci, biosynthetic, and metabolic gene clusters. Substantial interspecies diversities are also discovered between Tc and several other mushroom model organisms, including Agrocybe aegerita, Coprinopsis cinerea, and Schizophyllum commune, and Ganoderma lucidum.

Roles of AaVeA on Mycotoxin Production via Light in Alternaria alternata

Alternaria alternata is a principal plant pathogen responsible for the biosynthesis of mycotoxins, including tenuazonic acid (TeA), alternariol (AOH), and alternariol monomethyl ether (AME). The velvet gene VeA is involved in fungal growth, development, and secondary metabolism, including mycotoxin biosynthesis via light regulation. In this study, the detailed regulatory roles of AaVeA in A. alternata with various light sources were investigated from the comparative analyses between the wild type and the gene knockout strains. In fungal growth and conidiation, mycelial extension was independent of light regulation in A. alternata. Red light favored conidiation, but blue light repressed it. The absence of AaVeA caused the marked reduction of hyphae extension and conidiophore formation even though red light could not induce more spores in ΔAaVeA mutant. The differentially expressed genes (DEGs) enriched in hyphal growth and conidiation were drastically transcribed from the comparatively transcriptomic profile between the wild type and ΔAaVeA mutant strains with or without light. In mycotoxin production, TeA biosynthesis seems no obvious effect by light regulation, but AOH and AME formation was significantly stimulated by blue light. Nevertheless, the disruption of AaVeA resulted in a marked decrease in mycotoxin production and the action of the stimulation was lost via blue light for the abundant accumulation of AOH and AME in the ΔAaVeA strain. From DEG expression and further verification by RT-qPCR, the loss of AaVeA caused the discontinuous supply of the substrates for mycotoxin biosynthesis and the drastic decline of biosynthetic gene expression. In addition, pathogenicity depends on AaVeA regulation in tomato infected by A. alternata in vivo. These findings provide a distinct understanding of the roles of AaVeA in fungal growth, development, mycotoxin biosynthesis, and pathogenicity in response to various light sources.

Low- or high-white light irradiance induces similar conidial stress tolerance in Metarhizium robertsii

White light during mycelial growth influences high conidial stress tolerance of the insect-pathogenic fungus Metarhizium robertsii, but little is known if low- or high-white light irradiances induce different stress tolerances. The fungus was grown either in the dark using two culture media: on minimal medium (Czapek medium without sucrose = MM) or on potato dextrose agar (PDA) or PDA medium under five different continuous white light irradiances. The stress tolerances of conidia produced on all treatments were evaluated by conidial germination on PDA supplemented with KCl for osmotic stress or on PDA supplemented with menadione for oxidative stress. Conidia produced on MM in the dark were more tolerant to osmotic and oxidative stress than conidia produced on PDA in the dark or under the light. For osmotic stress, growth under the lower to higher irradiances produced conidia with similar tolerances but more tolerant than conidia produced in the dark. For oxidative stress, conidia produced under the white light irradiances were generally more tolerant to menadione than conidia produced in the dark. Moreover, conidia produced in the dark germinated at the same speed when incubated in the dark or under lower irradiance treatment. However, at higher irradiance, conidial germination was delayed compared to germination in the dark, which germinated faster. Therefore, growth under light from low to high irradiances induces similar conidial higher stress tolerances; however, higher white light irradiances cause a delay in germination speed.

Conidiation under illumination enhances conidial tolerance of insect-pathogenic fungi to environmental stresses

Light is an important signal for fungi in the environment and induces many genes with roles in stress and virulence responses. Conidia of the entomopathogenic fungi Aschersonia aleyrodis, Beauveria bassiana, Cordyceps fumosorosea, Lecanicillium aphanocladii, Metarhizium anisopliae, Metarhizium brunneum, Metarhizium robertsii, Simplicillium lanosoniveum, Tolypocladium cylindrosporum, and Tolypocladium inflatum were produced on potato dextrose agar (PDA) medium under continuous white light, on PDA medium in the dark, or under nutritional stress (= Czapek medium without sucrose = MM) in the dark. The conidial tolerance of these species produced under these different conditions were evaluated in relation to heat stress, oxidative stress (menadione), osmotic stress (KCl), UV radiation, and genotoxic stress caused by 4-nitroquinoline 1-oxide (4-NQO). Several fungal species demonstrated greater stress tolerance when conidia were produced under white light than in the dark; for instance white light induced higher tolerance of A. aleyrodis to KCl and 4-NQO; B. bassiana to KCl and 4-NQO; C. fumosorosea to UV radiation; M. anisopliae to heat and menadione; M. brunneum to menadione, KCl, UV radiation, and 4-NQO; M. robertsii to heat, menadione, KCl, and UV radiation; and T. cylindrosporum to menadione and KCl. However, conidia of L. aphanocladii, S. lanosoniveum, and T. inflatum produced under white light exhibited similar tolerance as conidia produced in the dark. When conidia were produced on MM, a much stronger stress tolerance was found for B. bassiana to menadione, KCl, UV radiation, and 4-NQO; C. fumosorosea to KCl and 4-NQO; Metarhizium species to heat, menadione, KCl, and UV radiation; T. cylindrosporum to menadione and UV radiation; and T. inflatum to heat and UV radiation. Again, conidia of L. aphanocladii and S. lanosoniveum produced on MM had similar tolerance to conidia produced on PDA medium in the dark. Therefore, white light is an important factor that induces higher stress tolerance in some insect-pathogenic fungi, but growth in nutritional stress always provides in conidia with stronger stress tolerance than conidia produced under white light.

Cloning and analysis of the photoreceptor genes Oxwc-1 and Oxwc-2 from ethnopharmacological fungus Ophiocordyceps xuefengensis

Ophiocordyceps xuefengensis is an ethnopharmacological fungus with broad pharmacological properties. Light is a critical environmental factor for the stromata formation and development of many fungi. In this study, photomorphogenesis and blue light receptor genes were studied using a strain of O. xuefengensis. Light represses vegetative growth, but conidia linked to stromata can be observed under both light and dark conditions. Light and dark conditions had little effect on the accumulation of polysaccharides and adenosine. The genes Oxwc-1 and Oxwc-2 encoding photoreceptors of O. xuefengensis were cloned and predicted to possess polypeptides of 937 and 525 amino acids, respectively. A phylogenetic analysis based on fungal WC-1/2 supported OxWC-1 and OxWC-2 were photoreceptor. The expression of both the Oxwc-1 and Oxwc-2 genes reached a maximum after receiving light stimulation for 15 min, which might relate to the inhibition of stromata growth.

Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis

Ustilago maydis encodes ten predicted light-sensing proteins. The biological functions of only a few of them are elucidated. Among the characterized ones are two DNA-photolyases and two rhodopsins that act as DNA-repair enzymes or green light-driven proton pumps, respectively. Here we report on the role of two other photoreceptors in U. maydis, namely White collar 1 (Wco1) and Phytochrome 1 (Phy1). We show that they bind flavins or biliverdin as chromophores, respectively. Both photoreceptors undergo a photocycle in vitro. Wco1 is the dominant blue light receptor in the saprophytic phase, controlling all of the 324 differentially expressed genes in blue light. U. maydis also responds to red and far-red light. However, the number of red or far-red light-controlled genes is less compared to blue light-regulated ones. Moreover, most of the red and far-red light-controlled genes not only depend on Phy1 but also on Wco1, indicating partial coregulation of gene expression by both photoreceptors. GFP-fused Wco1 is preferentially located in the nucleus, Phy1 in the cytosol, thus providing no hint that these photoreceptors directly interact or operate within the same complex. This is the first report on a functional characterization and coaction of White collar 1 and phytochrome orthologs in basidiomycetes.

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans

Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungal Cryptococcus species, Cryptococcus neoformans and Cryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary between C. neoformans and C. deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype in Cryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomycete Cryptococcus species.

Several mechanisms enforce species boundaries by either preventing the formation of hybrid zygotes, known as pre-zygotic barriers, or preventing the viability and fecundity of hybrids, known as post-zygotic barriers. Despite these barriers, interspecific hybrids form at an appreciable frequency, such as hybrid isolates of the human fungal pathogenic species, Cryptococcus neoformans and Cryptococcus deneoformans, which are regularly isolated from both clinical and environmental sources. C. neoformans x C. deneoformans hybrids are typically highly aneuploid, sterile, and display phenotypes intermediate to those of either parent, although self-fertile isolates and transgressive phenotypes have been observed. One important mechanism known to enforce species boundaries or lead to incipient speciation is the DNA mismatch repair system, which blocks recombination between divergent DNA sequences during meiosis. The aim of this study was to determine if genetically deleting the DNA mismatch repair component Msh2 would relax the species boundary between C. neoformans and C. deneoformans. Progeny derived from C. neoformans x C. deneoformans crosses in which both parental strains lacked Msh2 had higher viability, and unlike previous studies in Saccharomyces, these Cryptococcus hybrid progeny had higher levels of aneuploidy and no observable increase in meiotic recombination at the whole-genome level.

Two white collar proteins protect fungal cells from solar UV damage by their interactions with two photolyases in Metarhizium robertsii

The photolyases PHR1 and PHR2 enable photorepair of fungal DNA lesions in the forms of UV-induced cyclobutane pyrimidine dimer (CPD) and (6-4)-pyrimidine-pyrimidone (6-4PP) photoproducts, but their regulation remains mechanistically elusive. Here, we report that the white collar proteins WC1 and WC2 mutually interacting to form a light-responsive transcription factor regulate photolyase expression required for fungal UV resistance in the insect-pathogenic fungus Metharhizum robertsii. Conidial UVB resistance decreased by 54% in Δwc1 and 67% in Δwc2. Five-hour exposure of UVB-inactivated conidia to visible light resulted in photoreactivation rates of 30% and 9% for the Δwc1 and Δwc2 mutants, contrasting to 79%-82% for wild-type and complemented strains. Importantly, abolished transcription of phr1 in Δwc-2 and of phr2 in Δwc1 resulted in incapable photorepair of CDP and 6-4PP DNA lesions in UVB-impaired Δwc2 and Δwc1 cells respectively. Yeast two-hybrid assays revealed interactions of either WC protein with both PHR1 and PHR2. Therefore, the essential roles for WC1 and WC2 in both photorepair of UVB-induced DNA lesions and photoreactivation of UVB-inactivated conidia rely upon their interactions with, and hence transcriptional activation of, PHR1 and PHR2. These findings uncover a novel WC-cored pathway that mediates filamentous fungal response and adaptation to solar UV irradiation.

Distribution, evolution and expression of GATA-TFs provide new insights into their functions in light response and fruiting body development of Tolypocladium guangdongense

Background

Fungal GATA-type transcription factors (GATA-TFs) are a class of transcriptional regulators involved in various biological processes. However, their functions are rarely analyzed systematically, especially in edible or medicinal fungi, such as Tolypocladium guangdongense, which has various medicinal and food safety properties with a broad range of potential applications in healthcare products and the pharmaceutical industry.

Methods

GATA-TFs in T. guangdongense (TgGATAs) were identified using InterProScan. The type, distribution, and gene structure of TgGATAs were analyzed by genome-wide analyses. A phylogenetic tree was constructed to analyze their evolutionary relationships using the neighbor-joining (NJ) method. To explore the functions of GATA-TFs, conserved domains were analyzed using MEME, and cis-elements were predicted using the PlantCARE database. In addition, the expression patterns of TgGATAs under different light conditions and developmental stages were studied using qPCR.

Results

Seven TgGATAs were identified. They were randomly distributed on four chromosomes and contained one to four exons. Phylogenetic analysis indicated that GATA-TFs in each subgroup are highly conserved, especially for GATA1 to GATA5. Intron distribution analyses suggested that GATA1 and GATA3 possessed the most conserved gene structures. Light treatments induced the expression levels of TgGATA1 and TgGATA5-7, but the expression levels varied depending on the duration of illumination. The predicted protein structures indicate that TgGATA1 and TgGATA2 possess typical light-responsive domains and may function as photoreceptors to regulate downstream biological processes. TgGATA3 and TgGATA5 may be involved in nitrogen metabolism and siderophore biosynthesis, respectively. TgGATA6 and TgGATA7 possess unique Zn finger loop sequences, suggesting that they may have special functions. Furthermore, gene expression analysis indicated that TgGATA1 (WC1) was notably involved in mycelial color transformation, while other genes were involved in fruiting body development to some extent. These results provide valuable information to further explore the mechanisms through which TgGATAs are regulated during fruiting body development.

Critical Factors Involved in Primordia Building in Agaricus bisporus: A Review

The button mushroom Agaricus bisporus is an economically important crop worldwide. Many aspects of its cultivation are well known, except for the precise biological triggers for its fructification. By and large, for most basidiomycete species, nutrient availability, light and a drop in temperature are critical factors for fructification. A. bisporus deviates from this pattern in the sense that it does not require light for fructification. Furthermore its fructification seems to be inhibited by a self-generated factor which needs to be removed by microorganisms in order to initiate fruiting. This review explores what is known about the morphogenesis of fruiting initiation in A. bisporus, the microflora, the self-inhibitors for fruiting initiation and transcription factors involved. This information is subsequently contrasted with an overall model of the regulatory system involved in the initiation of the formation of primordia in basidiomycetes. The comparison reveals a number of the blank spots in our understanding of the fruiting process in A. bisporus.

Sexual Differentiation Is Coordinately Regulated by Cryptococcus neoformans CRK1 and GAT1

The heterothallic basidiomycetous fungus Cryptococcus neoformans has two mating types, MATa and MATα. Morphological progression of bisexual reproduction in C. neoformans is as follows: yeast to hyphal transition, filament extension, basidium formation, meiosis, and sporulation. C. neoformans Cdk-related kinase 1 (CRK1) is a negative regulator of bisexual mating. In this study, we characterized the morphological features of mating structures in the crk1 mutant and determined the genetic interaction of CRK1 in the regulatory networks of sexual differentiation. In the bilateral crk1 mutant cross, despite shorter length of filaments than in the wild-type cross, dikaryotic filaments and other structures still remained intact during bisexual mating, but the timing of basidium formation was approximately 18 h earlier than in the cross between wild type strains. Furthermore, gene expression analyses revealed that CRK1 modulated the expression of genes involved in the progression of hyphal elongation, basidium formation, karyogamy and meiosis. Phenotypic results showed that, although deletion of C. neoformans CRK1 gene increased the efficiency of bisexual mating, filamentation in the crk1 mutant was blocked by MAT2 or ZNF2 mutation. A bioinformatics survey predicted the C. neoformans GATA transcriptional factor Gat1 as a potential substrate of Crk1 kinase. Our genetic and phenotypic findings revealed that C. neoformansGAT1 and CRK1 formed a regulatory circuit to negatively regulate MAT2 to control filamentation progression and transition during bisexual mating.

RNA-seq Profiling Showed Divergent Carbohydrate-Active Enzymes (CAZymes) Expression Patterns in Lentinula edodes at Brown Film Formation Stage Under Blue Light Induction

Lentinula edodes (shiitake mushroom) is one of the most important edible mushrooms worldwide. The L. edodes cultivation cycle includes a unique developing stage called brown film formation that directly affects the development of primordium and the quality of fruiting body. Brown film formation is induced by light, especially blue light. To promote our understanding of the role of blue light in brown film formation mechanisms of L. edodes, we used RNA-seq and compared the transcriptomes of L. edodes grown under blue light and in dark, and validated the expression profiles using qRT-PCR. Blue light stimulated the formation of brown film and increased the content of polysaccharides in L. edodes. Blue light also promoted L. edodes to absorb more polysaccharides by enhancing the activities of enzymes. Among the 730 differentially expressed genes (DEGs), 433 genes were up-regulated and 297 were down-regulated. Most of the DEGs were in the oxidoreductase activity group. Pentose and glucuronic acid conversion and starch and sucrose metabolism were the most important pathways in the formation of brown film. A total of 79 genes of DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes). Fifty-one of the CAZymes genes were up-regulated, suggesting that CAZymes play important roles in brown film formation to provide sufficient nutrition for L. edodes. The results will facilitate future functional investigations of the genes involved in the developmental control of L. edodes.

History of the International Symposium on Fungal Stress - ISFUS, a dream come true!

The International Symposium on Fungal Stress (ISFUS) was born in a dream that Drauzio Eduardo Naretto Rangel had in 2013. This article reviews the first three ISFUSs and prospects for the future meetings. Although ISFUS was born as a small family organized meeting, since the first meeting, ISFUS has achieved great success, receiving very important research grants from FAPESP, FAPEG, and CAPES to bring international scientists to Brazil. Moreover, three special issues in leading journals have been published with articles relating to the talks presented at each ISFUS. For the first meeting, most speakers published in a special issue in Current Genetics. From the second and third meeting, articles from the speakers were published in special issues of the top mycology journal, Fungal Biology, published by Elsevier on behalf of the British Mycological Society. Here we show that following the dreams with a full heart and adding lots of love, passion, and hard work can achieve success.

Zinc Finger Proteins in the Human Fungal Pathogen Cryptococcus neoformans

Zinc is one of the essential trace elements in eukaryotes and it is a critical structural component of a large number of proteins. Zinc finger proteins (ZNFs) are zinc-finger domain-containing proteins stabilized by bound zinc ions and they form the most abundant proteins, serving extraordinarily diverse biological functions. In recent years, many ZNFs have been identified and characterized in the human fungal pathogen Cryptococcus neoformans, a fungal pathogen causing fatal meningitis mainly in immunocompromised individuals. It has been shown that ZNFs play important roles in the morphological development, differentiation, and virulence of C. neoformans. In this review, we, first, briefly introduce the ZNFs and their classification. Then, we explain the identification and classification of the ZNFs in C. neoformans. Next, we focus on the biological role of the ZNFs functionally characterized so far in the sexual reproduction, virulence factor production, ion homeostasis, pathogenesis, and stress resistance in C. neoformans. We also discuss the perspectives on future function studies of ZNFs in C. neoformans.

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

Light is an essential environmental factor for Sparassis latifolia primordia formation, but the molecular mechanism is still unclear. In this study, differential expression profiling of light-induced primordia formation (LIPF) was established by integrating the assay for transposase accessible chromatin by sequencing (ATAC-seq) and RNA-seq technology. The integrated results from the ATAC-seq and RNA-seq showed 13 down-regulated genes and 17 up-regulated genes in both the L vs. D and P vs. D groups, for both methods. According to the gene ontology (GO) annotation of these differentially expressed genes (DEGs), the top three biological process categories were cysteine biosynthetic process via cystathionine, vitamin B6 catabolic, and glycine metabolic; the top three molecular function categories were 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, glycine binding, and pyridoxal phosphate binding; cellular component categories were significantly enriched in the glycine cleavage complex. The KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that these genes were associated with vitamin B6 metabolism; selenocompound metabolism; cysteine and methionine metabolism; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism pathways. The expression of most of the DEGs was validated by qRT-PCR. To the best of our knowledge, this study is the first integrative analysis of ATAC-seq and RNA-seq for macro-fungi. These results provided a new perspective on the understanding of key pathways and hub genes in LIPF in S. latifolia. It will be helpful in understanding the primary environmental response, and provides new information to the existing models of primordia formation in edible and medicinal fungi.

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.

The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis of Cryptococcus Human Pathogenic Fungi

Cryptococcus species utilize a variety of sexual reproduction mechanisms, which generate genetic diversity, purge deleterious mutations, and contribute to their ability to occupy myriad environmental niches and exhibit a range of pathogenic potential. The bisexual and unisexual cycles of pathogenic Cryptococcus species are stimulated by properties associated with their environmental niches and proceed through well-characterized signaling pathways and corresponding morphological changes. Genes governing mating are encoded by the mating-type (MAT) loci and influence pathogenesis, population dynamics, and lineage divergence in Cryptococcus. MAT has undergone significant evolutionary changes within the Cryptococcus genus, including transition from the ancestral tetrapolar state in nonpathogenic species to a bipolar mating system in pathogenic species, as well as several internal reconfigurations. Owing to the variety of established sexual reproduction mechanisms and the robust characterization of the evolution of mating and MAT in this genus, Cryptococcus species provide key insights into the evolution of sexual reproduction.

Cryptococcus neoformans Recovered From Olive Trees (Olea europaea) in Turkey Reveal Allopatry With African and South American Lineages

Cryptococcus species are life-threatening human fungal pathogens that cause cryptococcal meningoencephalitis in both immunocompromised and healthy hosts. The natural environmental niches of Cryptococcus include pigeon (Columba livia) guano, soil, and a variety of tree species such as Eucalyptus camaldulensis, Ceratonia siliqua, Platanus orientalis, and Pinus spp. Genetic and genomic studies of extensive sample collections have provided insights into the population distribution and composition of different Cryptococcus species in geographic regions around the world. However, few such studies examined Cryptococcus in Turkey. We sampled 388 Olea europaea (olive) and 132 E. camaldulensis trees from seven locations in coastal and inland areas of the Aegean region of Anatolian Turkey in September 2016 to investigate the distribution and genetic diversity present in the natural Cryptococcus population. We isolated 84 Cryptococcus neoformans strains (83 MATα and 1 MAT a) and 3 Cryptococcus deneoformans strains (all MATα) from 87 (22.4% of surveyed) O. europaea trees; a total of 32 C. neoformans strains were isolated from 32 (24.2%) of the E. camaldulensis trees, all of which were MATα. A statistically significant difference was observed in the frequency of C. neoformans isolation between coastal and inland areas (P < 0.05). Interestingly, the MAT a C. neoformans isolate was fertile in laboratory crosses with VNI and VNB MATα tester strains and produced robust hyphae, basidia, and basidiospores, thus suggesting potential sexual reproduction in the natural population. Sequencing analyses of the URA5 gene identified at least five different genotypes among the isolates. Population genetics and genomic analyses revealed that most of the isolates in Turkey belong to the VNBII lineage of C. neoformans, which is predominantly found in southern Africa; these isolates are part of a distinct minor clade within VNBII that includes several isolates from Zambia and Brazil. Our study provides insights into the geographic distribution of different C. neoformans lineages in the Mediterranean region and highlights the need for wider geographic sampling to gain a better understanding of the natural habitats, migration, epidemiology, and evolution of this important human fungal pathogen.

Metabolic Basis of Pathogenesis and Host Adaptation in Rice Blast

The blast disease, caused by the ascomycete Magnaporthe oryzae, poses a great threat to rice production worldwide. Increasing use of fungicides and/or blast-resistant varieties of rice (Oryza sativa) has proved to be ineffective in long-term control of blast disease under field conditions. To develop effective and durable resistance to blast, it is important to understand the cellular mechanisms underlying pathogenic development in M. oryzae. In this review, we summarize the latest research in phototropism, autophagy, nutrient and redox signaling, and intrinsic phytohormone mimics in M. oryzae for cellular and metabolic adaptation(s) during its interactions with the host plants.

Life Cycle of Cryptococcus neoformans

Cryptococcus neoformans is a ubiquitous environmental fungus and an opportunistic pathogen that causes fatal cryptococcal meningitis. Advances in genomics, genetics, and cellular and molecular biology of C. neoformans have dramatically improved our understanding of this important pathogen, rendering it a model organism to study eukaryotic biology and microbial pathogenesis. In light of recent progress, we describe in this review the life cycle of C. neoformans with a special emphasis on the regulation of the yeast-to-hypha transition and different modes of sexual reproduction, in addition to the impacts of the life cycle on cryptococcal populations and pathogenesis.

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.

WC-1 and the Proximal GATA Sequence Mediate a Cis-/Trans-Acting Repressive Regulation of Light-Dependent Gene Transcription in the Dark

Simple Summary

We observed that both the proximal GATA sequence in light-responsive elements (LREs) of the albino-3 promoter and the Zinc Finger Domain of WC-1 are involved in the dark-related repressive control mechanism of light-regulated genes.

Abstract

Light influences a wide range of physiological processes from prokaryotes to mammals. Neurospora crassa represents an important model system used for studying this signal pathway. At molecular levels, the WHITE COLLAR Complex (WCC), a heterodimer formed by WC-1 (the blue light photo-sensor) and WC-2 (the transcriptional activator), is the critical positive regulator of light-dependent gene expression. GATN (N indicates any other nucleotide) repeats are consensus sequences within the promoters of light-dependent genes recognized by the WCC. The distal GATN is also known as C-box since it is involved in the circadian clock. However, we know very little about the role of the proximal GATN, and the molecular mechanism that controls the transcription of light-induced genes during the dark/light transition it is still unclear. Here we showed a first indication that mutagenesis of the proximal GATA sequence within the target promoter of the albino-3 gene or deletion of the WC-1 zinc finger domain led to a rise in expression of light-dependent genes already in the dark, effectively decoupling light stimuli and transcriptional activation. This is the first observation of cis-/trans-acting repressive machinery, which is not consistent with the light-dependent regulatory mechanism observed in the eukaryotic world so far.

Opsin 1 and Opsin 2 of the Corn Smut Fungus Ustilago maydis Are Green Light-Driven Proton Pumps

In fungi, green light is absorbed by rhodopsins, opsin proteins carrying a retinal molecule as chromophore. The basidiomycete Ustilago maydis, a fungal pathogen that infects corn plants, encodes three putative photoactive opsins, called ops1 (UMAG_02629), ops2 (UMAG_00371), and ops3 (UMAG_04125). UmOps1 and UmOps2 are expressed during the whole life cycle, in axenic cultures as well as in planta, whereas UmOps3 was recently shown to be absent in axenic cultures but highly expressed during plant infection. Here we show that expression of UmOps1 and UmOps2 is induced by blue light under control of white collar 1 (Wco1). UmOps1 is mainly localized in the plasma membrane, both when expressed in HEK cells and U. maydis sporidia. In contrast, UmOps2 was mostly found intracellularly in the membranes of vacuoles. Patch-clamp studies demonstrated that both rhodopsins are green light-driven outward rectifying proton pumps. UmOps1 revealed an extraordinary pH dependency with increased activity in more acidic environment. Also, UmOps1 showed a pronounced, concentration-dependent enhancement of pump current caused by weak organic acids (WOAs), especially by acetic acid and indole-3-acetic acid (IAA). In contrast, UmOps2 showed the typical behavior of light-driven, outwardly directed proton pumps, whereas UmOps3 did not exhibit any electrogenity. With this work, insights were gained into the localization and molecular function of two U. maydis rhodopsins, paving the way for further studies on the biological role of these rhodopsins in the life cycle of U. maydis.

Red- and Blue-Light Sensing in the Plant Pathogen Alternaria alternata Depends on Phytochrome and the White-Collar Protein LreA

Light controls many processes in filamentous fungi. The study of light regulation in a number of model organisms revealed an unexpected complexity. Although the molecular components for light sensing appear to be widely conserved in fungal genomes, the regulatory circuits and the sensitivity of certain species toward specific wavelengths seem different. In N. crassa, most light responses are triggered by blue light, whereas in A. nidulans, red light plays a dominant role. In Alternaria alternata, both blue and red light appear to be important. In A. alternata, photoreceptors control morphogenetic pathways, the homeostasis of reactive oxygen species, and the production of secondary metabolites. On the other hand, high-osmolarity sensing required FphA and LreA, indicating a sophisticated cross talk between light and stress signaling.

The filamentous fungus Alternaria alternata is a common postharvest contaminant of food and feed, and some strains are plant pathogens. Many processes in A. alternata are triggered by light. Interestingly, blue light inhibits sporulation, and red light reverses the effect, suggesting interactions between light-sensing systems. The genome encodes a phytochrome (FphA), a white collar 1 (WC-1) orthologue (LreA), an opsin (NopA), and a cryptochrome (CryA) as putative photoreceptors. Here, we investigated the role of FphA and LreA and the interplay with the high-osmolarity glycerol (HOG) mitogen-activated protein (MAP) kinase pathway. We created loss-of function mutations for fphA, lreA, and hogA using CRISPR-Cas9 technology. Sporulation was reduced in all three mutant strains already in the dark, suggesting functions of the photoreceptors FphA and LreA independent of light perception. Germination of conidia was delayed in red, blue, green, and far-red light. We found that light induction of ccgA (clock-controlled gene in Neurospora crassa and light-induced gene in Aspergillus nidulans) and the catalase gene catA depended on FphA, LreA, and HogA. Light induction of ferA (a putative ferrochelatase gene) and bliC (bli-3, light regulated, unknown function) required LreA and HogA but not FphA. Blue- and green-light stimulation of alternariol formation depended on LreA. A lack of FphA or LreA led to enhanced resistance toward oxidative stress due to the upregulation of catalases and superoxide dismutases. Light activation of FphA resulted in increased phosphorylation and nuclear accumulation of HogA. Our results show that germination, sporulation, and secondary metabolism are light regulated in A. alternata with distinct and overlapping roles of blue- and red-light photosensors.

Genome-Wide Analysis of the Zn(II)₂Cys₆ Zinc Cluster-Encoding Gene Family in Tolypocladium guangdongense and Its Light-Induced Expression

The Zn(II)₂Cys₆ zinc cluster gene family is a subclass of zinc-finger proteins, which are transcriptional regulators involved in a wide variety of biological processes in fungi. We performed genome-wide identification and characterization of Zn(II)₂Cys₆ zinc-cluster gene (C6 zinc gene) family in Tolypocladiumguangdongense, Cordycepsmilitaris and Ophiocordycepssinensis. Based on the structures of the C6 zinc domains, these proteins were observed to be evolutionarily conserved in ascomycete fungi. We focused on T.guangdongense, a medicinal fungus, and identified 139 C6 zinc genes which could be divided into three groups. Among them, 49.6% belonged to the fungal specific transcriptional factors, and 16% had a DUF3468 domain. Homologous and phylogenetic analysis indicated that 29 C6 zinc genes were possibly involved in the metabolic process, while five C6 zinc genes were supposed to be involved in asexual or sexual development. Gene expression analysis revealed that 54 C6 zinc genes were differentially expressed under light, including two genes that possibly influenced the development, and seven genes that possibly influenced the metabolic processes. This indicated that light may affect the development and metabolic processes, at least partially, through the regulation of C6 zinc genes in T.guangdongense. Our results provide comprehensive data for further analyzing the functions of the C6 zinc genes.

Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Background

Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features.

Results

In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies.

Conclusions

This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5509-4) contains supplementary material, which is available to authorized users.

PAS Domain Protein Pas3 Interacts with the Chromatin Modifier Bre1 in Regulating Cryptococcal Morphogenesis

For the ubiquitous environmental pathogen Cryptococcus neoformans, the morphological transition from yeast to filament confers resistance to natural predators like soil amoeba and is an integral differentiation event to produce infectious spores. Interestingly, filamentation is immuno-stimulatory and attenuates cryptococcal virulence in a mammalian host. Consistently, the morphogenesis transcription factor Znf2 profoundly shapes cryptococcal interaction with various hosts. Identifying the signaling pathways activating filamentation is thus, conductive to a better understanding of cryptococcal biology. In this study, we identified a PAS domain protein Pas3 that functions upstream of Znf2 in regulating cryptococcal filamentation. Interestingly, Pas3 interacts with the chromatin modifier Bre1 in the nucleus to regulate the transcript level of Znf2 and its prominent downstream targets. This is the first example of a PAS domain signaling regulator interacting with a chromatin modifier to control filamentation through their impact on cryptococcal transcriptome.

Switching between different morphotypes is an adaptive cellular response in many microbes. In Cryptococcus neoformans, the yeast-to-hypha transition confers resistance to microbial predation in the soil and is an integral part of its life cycle. Morphogenesis is also known to be associated with virulence, with the filamentous form being immune-stimulatory and protective in mammalian models of cryptococcosis. Previous studies identified the transcription factor Znf2 as a master regulator of cryptococcal filamentation. However, the upstream regulators of Znf2 remain largely unknown. PAS domain proteins have long been recognized as transducers of diverse environmental signals. Here, we identified a PAS domain protein Pas3 as an upstream regulator of Znf2. Surprisingly, this small Pas3 protein lacks a nuclear localization signal but is enriched in the nucleus where it regulates the transcript level of ZNF2 and its prominent downstream targets. We discovered that the PAS domain is essential for Pas3’s nuclear enrichment and function. Intriguingly, Pas3 interacts with Bre1, which is required for Cryptococcus histone H2B monoubiquitination (H2Bub1) and H3 lysine 4 dimethylation (H3K4me2), two histone modifications known to be associated with active gene transcription. Indeed, Bre1 functions together with Pas3 in regulating cryptococcal filamentation based on loss-of-function, epistasis, and transcriptome analysis. These findings provide the first evidence of a signaling regulator acting with a chromatin modifier to control cryptococcal filamentation.

Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar

Rhizopus delemar is an invasive fungal pathogen responsible for the frequently fatal disease mucormycosis. Germination, a crucial mechanism by which infectious spores of Rhizopus delemar cause disease, is a key developmental process that transforms the dormant spore state into a vegetative one. The molecular mechanisms that underpin this transformation may be key to controlling mucormycosis; however, the regulation of germination remains poorly understood. This study describes the phenotypic and transcriptional changes that take place over the course of germination. This process is characterized by four distinct stages: dormancy, isotropic swelling, germ tube emergence, and hyphal growth. Dormant spores are shown to be transcriptionally unique, expressing a subset of transcripts absent in later developmental stages. A large shift in the expression profile is prompted by the initiation of germination, with genes involved in respiration, chitin, cytoskeleton, and actin regulation appearing to be important for this transition. A period of transcriptional consistency can be seen throughout isotropic swelling, before the transcriptional landscape shifts again at the onset of hyphal growth. This study provides a greater understanding of the regulation of germination and highlights processes involved in transforming Rhizopus delemar from a single-cellular to multicellular organism.IMPORTANCE Germination is key to the growth of many organisms, including fungal spores. Mucormycete spores exist abundantly within the environment and germinate to form hyphae. These spores are capable of infecting immunocompromised individuals, causing the disease mucormycosis. Germination from spore to hyphae within patients leads to angioinvasion, tissue necrosis, and often fatal infections. This study advances our understanding of how spore germination occurs in the mucormycetes, identifying processes we may be able to inhibit to help prevent or treat mucormycosis.

The contribution of the White Collar complex to Cryptococcus neoformans virulence is independent of its light-sensing capabilities

The White Collar complex is responsible for sensing light and transmitting that signal in many fungal species. In Cryptococcus neoformans and C. deneoformans the complex is involved in protection against damage from ultraviolet (UV) light, repression of mating in response to light, and is also required for virulence. The mechanism by which the Bwc1 photoreceptor contributes to virulence is unknown. In this study, a bwc1 deletion mutant of C. neoformans was transformed with three versions of the BWC1 gene, the wild type, BWC1^C605A or BWC1^C605S, in which the latter two have the conserved cysteine residue replaced with either alanine or serine within the light-oxygen-voltage (LOV) domain that interacts with the flavin chromophore. The bwc1+ BWC1 strain complemented the UV sensitivity and the repression of mating in the light. The bwc1+ BWC1^C605A and bwc1+ BWC1^C605S strains were not fully complemented for either of the phenotypes, indicating that these BWC1 alleles impair the light responses for strains with them. Transcript analysis showed that neither of the mutated strains (bwc1+ BWC1^C605A and bwc1+ BWC1^C605S) showed the light-inducible expression pattern of the HEM15 and UVE1 genes as occurs in the wild type strain. These results indicate that the conserved flavin-binding site in the LOV domain of Bwc1 is required for sensing and responding to light in C. neoformans. In contrast to defects in light responses, the wild type, bwc1+ BWC1, bwc1+ BWC1^C605A and bwc1+ BWC1^C605S strains were equally virulent, whereas the bwc1 knock out mutant was less virulent. Furthermore, pre-exposure of the strains to light prior to inoculation had no influence on the outcome of infection. These findings define a division in function of the White Collar complex in fungi, in that in C. neoformans the role of Bwc1 in virulence is independent of light sensing.

Expression of putative circadian clock components in the arbuscular mycorrhizal fungus Rhizoglomus irregulare

Arbuscular mycorrhizal fungi (AMF) are obligatory plant symbionts that live underground, so few studies have examined their response to light. Responses to blue light by other fungi can be mediated by White Collar-1 (WC-1) and WC-2 proteins. These wc genes, together with the frequency gene (frq), also form part of the endogenous circadian clock. The clock mechanism has never been studied in AMF, although circadian growth of their hyphae in the field has been reported. Using both genomic and transcriptomic data, we have found homologs of wc-1, wc-2, and frq and related circadian clock genes in the arbuscular mycorrhizal fungus Rhizoglomus irregulare (synonym Rhizophagus irregularis). Gene expression of wc-1, wc-2, and frq was analyzed using RT-qPCR on RNA extracted from germinating spores and from fungal material cultivated in vitro with transformed carrot roots. We found that all three core clock genes were expressed in both pre- and post-mycorrhizal stages of R. irregulare growth. Similar to the model fungus Neurospora crassa, the core circadian oscillator gene frq was induced by brief light stimulation. The presence of circadian clock and output genes in R. irregulare opens the door to the study of circadian clocks in the fungal partner of plant-AMF symbiosis. Our finding also provides new insight into the evolution of the circadian frq gene in fungi.

Fungal Gene Mutation Analysis Elucidating Photoselective Enhancement of UV-C Disinfection Efficiency Toward Spoilage Agents on Fruit Surface

Short-wave ultraviolet (UV-C) treatment represents a potent, clean and safe substitute to chemical sanitizers for fresh fruit preservation. However, the dosage requirement for microbial disinfection may have negative effects on fruit quality. In this study, UV-C was found to be more efficient in killing spores of Botrytis cinerea in dark and red light conditions when compared to white and blue light. Loss of the blue light receptor gene Bcwcl1, a homolog of wc-1 in Neurospora crassa, led to hypersensitivity to UV-C in all light conditions tested. The expression of Bcuve1 and Bcphr1, which encode UV-damage endonuclease and photolyase, respectively, were strongly induced by white and blue light in a Bcwcl1-dependent manner. Gene mutation analyses of Bcuve1 and Bcphr1 indicated that they synergistically contribute to survival after UV-C treatment. In vivo assays showed that UV-C (1.0 kJ/m²) abolished decay in drop-inoculated fruit only if the UV-C treatment was followed by a dark period or red light, while in contrast, typical decay appeared on UV-C irradiated fruits exposed to white or blue light. In summary, blue light enhances UV-C resistance in B. cinerea by inducing expression of the UV damage repair-related enzymes, while the efficiency of UV-C application for fruit surface disinfection can be enhanced in dark or red light conditions; these principles seem to be well conserved among postharvest fungal pathogens.

A Comparative Proteome Approach Reveals Metabolic Changes Associated with Flammulina velutipes Mycelia in Response to Cold and Light Stress

In some industrial processes, cold and light stresses are recognized as two important environmental triggers for the transformation of mycelia into fruit-bodies via intermediate primordia in Flammulina velutipes cultivation. To gain insights into the mechanism of regulation of F. velutipes mycelia in response to cold and light stress, proteins expressed abundantly and characteristically at particular stress states were investigated by using the isobaric tags for the relative and absolute quantitation labeling technique. Among the 1046 nonredundant proteins identified with a high degree of confidence, 264 proteins, which were detected as differentially expressed proteins, were associated with 176 specific KEGG pathways. In-depth data analysis revealed that the regulatory network underlying the cold and light response mechanisms of F. velutipes mycelia was complex and multifaceted, as it included varied functions such as rapid energy supply, the biosynthesis of lysine, phenylalanine, tyrosine, and γ-aminobutyric acid, the calcium signal transduction process, dynein-dependent actin and microtubule cytoskeleton formation, autolysis, oxidative stress adaptation, pigment secretion, tissue and organ morphogenesis, and other interesting stress-related processes. Insights into the proteins might shed light on an intuitive understanding of the cold and light stress response mechanism underlying the fruiting processes of F. velutipes. Furthermore, the data might also provide further insights into the stress response mechanism of macro-fungi and valuable information for scientific improvement of some mushroom cultivation techniques in practice.

Light-regulated promoters for tunable, temporal, and affordable control of fungal gene expression

Regulatable promoters are important genetic tools, particularly for assigning function to essential and redundant genes. They can also be used to control the expression of enzymes that influence metabolic flux or protein secretion, thereby optimizing product yield in bioindustry. This review will focus on regulatable systems for use in filamentous fungi, an important group of organisms whose members include key research models, devastating pathogens of plants and animals, and exploitable cell factories. Though we will begin by cataloging those promoters that are controlled by nutritional or chemical means, our primary focus will rest on those who can be controlled by a literal flip-of-the-switch: promoters of light-regulated genes. The vvd promoter of Neurospora will first serve as a paradigm for how light-driven systems can provide tight, robust, tunable, and temporal control of either autologous or heterologous fungal proteins. We will then discuss a theoretical approach to, and practical considerations for, the development of such promoters in other species. To this end, we have compiled genes from six previously published light-regulated transcriptomic studies to guide the search for suitable photoregulatable promoters in your fungus of interest.