Search Results (67)

In the filamentous fungus Neurospora crassa, a gene not having a pairing partner during meiosis is seen as a potential intruder and is targeted by a mechanism called meiotic silencing by unpaired DNA (MSUD). MSUD employs core RNA interference (RNAi) components such as the SMS-2 Argonaute, which uses small interfering RNAs (siRNAs) as guides to seek out mRNAs from unpaired genes for silencing. In Drosophila melanogaster, the heat shock protein 70 (Hsp70) chaperone system facilitates the conformational activation of an Argonaute and allows it to load siRNAs. Here, our results demonstrate that an Hsp70 protein in Neurospora interacts with SMS-2 and mediates the silencing of unpaired genes. Full article

The presence of an extra DNA segment in a genome could indicate a transposon or another repetitive element on the move. In Neurospora crassa, a surveillance mechanism called meiotic silencing by unpaired DNA (MSUD) is maintained to monitor these selfish elements. MSUD utilizes common RNA interference (RNAi) factors, including the SMS-2 Argonaute, to target mRNAs from genes lacking a pairing partner during meiosis. In eukaryotes, an mRNA transcript is typically bound at the 5′ cap by the cap-binding complex (CBC), which assists in its nuclear export. Previously, we discovered that CBC and its interactor NCBP3 mediate MSUD, possibly by guiding the perinuclear SMS-2 to effectively recognize exported mRNAs. Here, we report that ARS2, a CBC cofactor, is involved in MSUD. ARS2 interacts with both CBC and NCBP3, and it may help bring them together. In addition to its role in silencing, ARS2 also contributes to vegetative growth and sexual sporulation. Full article

Staurosporine (STS) was discovered in 1977 by Omura and colleagues during a chemical screening for microbial alkaloids. It was the first indolocarbazole compound isolated from a soil-dwelling bacterium, Streptomyces staurosporeus. STS was also found to have antifungal activity, but its potent protein kinase (PK) inhibitory properties, perhaps the most extensively characterized biochemical feature of STS, were only revealed nearly a decade after its discovery. Thereafter, STS has been studied mainly for its anticancer potential with foreseen applications ranging from biomedical (e.g., antiparasitic) to agricultural (e.g., insecticidal). Interestingly, the recent discovery that STS induces apoptosis in the filamentous fungus Neurospora crassa renewed interest in this molecule as a scaffold for antifungal drug development. Studies in fungi and mammalian cell lines suggest that, in addition to PK inhibition, other modes of action are possible for STS. These may involve the targeting of membrane lipid domains and/or alterations of membrane biophysical properties. Here, the studies on the action of STS and its natural and synthetic derivatives against diverse fungal species, since its discovery to the present day, are critically reviewed and discussed with the aim of highlighting their advantages, limitations to be overcome, conceivable mechanisms of action, and potential as antifungal chemotherapeutic agents. Full article

Dehydroshikimate (DHS) dehydratase (DSD) catalyzes the conversion of DHS into 3,4-dihydroxybenzoic acid (3,4-DHBA), a compound with promising applications across various industries. The DSD from Podospora anserina (DSD_Pa) was characterized and its catalytic properties were compared with those of previously investigated enzymes, AsbF (Bacillus thuringiensis), Qa-4 (Neurospora crassa), and QsuB (Corynebacterium glutamicum), both in vitro and in vivo using tube fermentation. Escherichia coli and C. glutamicum were used as platforms to construct model 3,4-DHBA producers. To increase DHS availability in both hosts, shikimate dehydrogenase AroE was inactivated, and the plasmid pVS7-aroG4, encoding 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (E. coli), was introduced. In E. coli, heterologous 3,4-DHBA synthesis was achieved through chromosomal integration of dsd genes. The fungal genes were codon-optimized for this bacterium. The same genes were cloned into the pVK9 vector and introduced into C. glutamicum, where 3,4-DHBA degradation was disrupted (ΔpcaHG). AsbF (k_cat ~ 1 s⁻¹) showed poor 3,4-DHBA accumulation in both hosts (1–1.5 g/L). The enzymes with better catalytic characteristics, QsuB (k_cat ~ 60 s⁻¹), DSD_Pa (k_cat ~ 125 s⁻¹), and Qa-4 (k_cat ~ 220 s⁻¹), provided 5 g/L 3,4-DHBA in E. coli and 3 g/L 3,4-DHBA in C. glutamicum, except for Qa-4. The low production (~1.5 g/L) observed for Qa-4 in C. glutamicum might be attributed to a non-optimal nucleotide sequence rich in codons rare for C. glutamicum. Full article

Endocytosis in filamentous fungi is spatially restricted to a subapical zone known as the endocytic collar, which plays essential roles in membrane recycling and the maintenance of polarized growth. In this study, we investigated the ontogeny of the endocytic collar in Neurospora crassa by tracking fimbrin-labeled endocytic patches using confocal microscopy during conidial germination, hyphal branching, and regeneration following mechanical injury. We consistently observed an initial accumulation of endocytic patches at the hyphal tip, forming an apical cap, which later reorganized into a subapical collar. This transition was correlated with a significant increase in elongation rate and the appearance of a Spitzenkörper, indicating a link between exocytosis and collar positioning. Although this correlation is robust, our data do not establish causality; rather, collar formation appears to occur after surpassing a critical elongation. Our findings suggest that exocytosis displaces endocytosis from the apex, resulting in the formation of the collar, which is not required for the establishment of polarized growth but is essential for its maintenance. These results support the development of a unified model of collar formation in filamentous fungi and provide new insight into the spatial coordination between endocytic and exocytic processes during hyphal development. Full article

Fungi, from saprophytes to pathogens, face predictable daily fluctuations in light, temperature, humidity, and nutrient availability. To cope, they have evolved an internal circadian clock that confers a major adaptive advantage. This review critically synthesizes current knowledge on the molecular architecture and physiological relevance of fungal circadian systems, moving beyond the canonical Neurospora crassa model to explore the broader phylogenetic diversity of timekeeping mechanisms. We examine the core transcription-translation feedback loop (TTFL) centered on the FREQUENCY/WHITE COLLAR (FRQ/WCC) system and contrast it with divergent and non-canonical oscillators, including the metabolic rhythms of yeasts and the universally conserved peroxiredoxin (PRX) oxidation cycles. A central theme is the clock’s role in gating cellular defenses against oxidative, osmotic, and nutritional stress, enabling fungi to anticipate and withstand environmental insults through proactive regulation. We provide a detailed analysis of chrono-pathogenesis, where the circadian control of virulence factors aligns fungal attacks with windows of host vulnerability, with a focus on experimental evidence from pathogens like Botrytis cinerea, Fusarium oxysporum, and Magnaporthe oryzae. The review explores the downstream pathways—including transcriptional cascades, post-translational modifications, and epigenetic regulation—that translate temporal signals into physiological outputs such as developmental rhythms in conidiation and hyphal branching. Finally, we highlight critical knowledge gaps, particularly in understudied phyla like Basidiomycota, and discuss future research directions. This includes the exploration of novel clock architectures and the emerging, though speculative, hypothesis of “chrono-therapeutics”—interventions designed to disrupt fungal clocks—as a forward-looking concept for managing fungal infections. Full article

Thermostable cellulases and xylanases have broad acceptance in food, feed, paper and pulp, and bioconversion of lignocellulosics. Thermophilic fungi serve as an excellent source of thermostable enzymes. This study characterized four endo-β-1,4-glucanases (two glycoside hydrolase (GH) family 5 and two GH7 members) and four endo-β-1,4-xylanases (two GH10 and two GH11 members) from thermophilic fungus Thielavia terrestris, along with one GH10 endo-β-1,4-xylanase each from thermophilic fungus Chaetomium thermophilum and mesophilic fungus Chaetomium globosum. Comparative analysis was conducted against three previously reported GH10 endoxylanases: two thermostable enzymes from the thermophilic fungus Humicola insolens and thermophilic bacterium Halalkalibacterium halodurans, and one mesophilic enzyme from model fungus Neurospora crassa. The GH10 xylanase TtXyn10C (Thite_2118148; UniProt G2R8T7) from T. terrestris demonstrated high thermostability and activity, with an optimal temperature of 80–85 °C. It retained over 60% of its activity after 2 h at 70 °C, maintained approximately 30% activity after 15 min at 80 °C, and showed nearly complete stability following 1 min of exposure to 95 °C. TtXyn10C exhibited specific activity toward beechwood xylan (1130 ± 15 U/mg) that exceeded xylanases from H. insolens and H. halodurans while being comparable to N. crassa xylanase activity. Furthermore, TtXyn10C maintained stability across a pH range of 3–9 and resisted trypsin digestion, indicating its broad applicability. The study expands understanding of enzymes from thermophilic fungi. The discovery of the TtXyn10C offers a new model for investigating the high activity-stability trade-off and structure-activity relationships critical for industrial enzymes. Full article

The spatial navigation of filamentous fungi was compared for three species, namely Pycnoporus cinnabarinus, Neurospora crassa wild type and ro-1 mutant, and Armillaria mellea, in microfluidic structures. The analysis of the navigation of these filamentous fungi in open and especially confining environments suggests that they perform space exploration using a hierarchical, three-layered system of information processing. The output of the space navigation of a single hypha is the result of coordination and competition between three programs with their corresponding subroutines: (i) the sensing of narrow passages (remote- or contact-based); (ii) directional memory; and (iii) branching (collision-induced or stochastic). One information-processing level up, the spatial distribution of multiple, closely collocated hyphae is the result of a combination of (i) negative autotropism and (ii) cytoplasm reallocation between closely related branches (with anastomosis as an alternative subroutine to increase robustness). Finally, the mycelium is the result of the sum of quasi-autonomous sub-populations of hyphae performing distribution in space in parallel based on the different spatial conditions and constraints found locally. The efficiency of space exploration by filamentous fungi appears to be the result of the synergy of various biological algorithms integrated into a hierarchical architecture of information processing, balancing complexity with specialization. Full article

Background/Objectives: Codon usage bias affects gene expression and translation efficiency across species. The effective number of codons (ENC) and GC content influence codon preference, often displaying unimodal or bimodal distributions. This study investigates the correlation between ENC and GC rankings across species and how their relationship affects codon usage distributions. Methods: I analyzed nuclear-encoded genes from 17 species representing six kingdoms: one bacteria (Escherichia coli), three fungi (Saccharomyces cerevisiae, Neurospora crassa, and Schizosaccharomyces pombe), one archaea (Methanococcus aeolicus), three protists (Rickettsia hoogstraalii, Dictyostelium discoideum, and Plasmodium falciparum),), three plants (Musa acuminata, Oryza sativa, and Arabidopsis thaliana), and six animals (Anopheles gambiae, Apis mellifera, Polistes canadensis, Mus musculus, Homo sapiens, and Takifugu rubripes). Genes in all 17 species were ranked by GC content and ENC, and correlations were assessed. I examined how adding or subtracting these rankings influenced their overall distribution in a new method that I call Two-Rank Order Normalization or TRON. The equation, TRON = SUM(ABS((GC rank₁:GC rank_N) − (ENC rank₁:ENC rank_N))/(N²/3), where (GC rank₁:GC rank_N) is a rank-order series of GC rank, (ENC rank₁:ENC rank_N) is a rank-order series ENC rank, sorted by the rank-order series GC rank. The denominator of TRON, N²/3, is the normalization factor because it is the expected value of the sum of the absolute value of GC rank–ENC rank for all genes if GC rank and ENC rank are not correlated. Results: ENC and GC rankings are positively correlated (i.e., ENC increases as GC increases) in AT-rich species such as honeybees (R² = 0.60, slope = 0.78) and wasps (R² = 0.52, slope = 0.72) and negatively correlated (i.e., ENC decreases as GC increases) in GC-rich species such as humans (R² = 0.38, slope = −0.61) and rice (R² = 0.59, slope = −0.77). Second, the GC rank–ENC rank distributions change from unimodal to bimodal as GC content increases in the 17 species. Third, the GC rank+ENC rank distributions change from bimodal to unimodal as GC content increases in the 17 species. Fourth, the slopes of the correlations (GC versus ENC) in all 17 species are negatively correlated with TRON (R² = 0.98) (see Graphic Abstract). Conclusions: The correlation between ENC rank and GC rank differs among species, shaping codon usage distributions in opposite ways depending on whether a species’ nuclear-encoded genes are AT-rich or GC-rich. Understanding these patterns might provide insights into translation efficiency, epigenetics mediated by CpG DNA methylation, epitranscriptomics of RNA modifications, RNA secondary structures, evolutionary pressures, and potential applications in genetic engineering and biotechnology. Full article

Waste nanomaterials pose environmental and human health concerns and they need to be urgently and efficiently managed. In this study, a fungal biotemplate was used to accumulate and recover nano-Fe₂O₃ materials from an aqueous solution. Then, recovered nano-Fe₂O₃ materials were activated to form a high-performance magnetic porous carbon composite (FePC) for energy storage and organic pollutant removal. The results indicate that high concentrations (500 mg/L) of 50 nm Fe₂O₃ particles can be completely recovered using a cross-linked Neurospora crassa fungus (NC), primarily because of its encapsulation function. In addition, the surface area, degree of graphitization, and heteroatom content of the FePC materials can be boosted by the catalytic effects of the incorporated Fe atoms. The developed FePC materials exhibit potential as high electrical double-layer capacitors as well as strong retention capabilities, excellent stability, and efficient adsorption of triclosan (TCS, ~526 mg/g). Additionally, these FePC materials exhibit superior capacities for energy storage and pollutant reduction compared to commercial and reported carbon materials. These results reveal a sustainable route for the recovery and reutilization of nanomaterials. Full article

The efficient hydrolysis of lignocellulosic biomass relies on the action of enzymes, which are crucial for the development of economically feasible cellulose bioconversion processes. However, low hydrolysis efficiency and the inhibition of cellulase production by carbon catabolite repression (CCR) have been significant obstacles in this process. The aim of this study was to identify the patterns of cellulose degradation and related genes through the genome analysis of a newly isolated lignocellulose-degrading fungus Flavodon sp. x-10. The whole-genome sequencing showed that the genome size of Flavodon sp. x-10 was 37.1 Mb, with a GC content of 49.48%. A total of 11,277 genes were predicted, with a total length of 18,218,150 bp and an average length of 1615 bp. Additionally, 157 tRNA genes responsible for transporting different amino acids were predicted, and the repeats and tandem repeats accounted for only 0.76% of the overall sequences. A total of 5039 genes were annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, representing 44.68% of all genes, and 368 metabolic pathways were involved. Of the 595 genes annotated in the carbohydrate-active enzyme (CAZy) database, 183 are associated with plant cell wall-degrading enzymes (PCWDEs), surpassing those of Aspergillus niger (167), Trichoderma reesei (64), and Neurospora crassa (86). Compared to these three fungi, Flavodon sp. x-10 has a higher number of enzyme genes related to lignin degradation in its genome. Transporters were further identified by matching the whole-genome sequence to the Transporter Classification Database (TCDB), which includes 20 sugar transporters (STs) closely linked to sugar utilization. Through the comprehensive exploration of the whole-genome sequence, this study uncovered more vital lignocellulase genes and their degradation mechanisms, providing feasible strategies for improving the strains to reduce the cost of biofuel production. Full article

Cordyceps militaris, a fungus widely used in traditional Chinese medicine and pharmacology, is recognized for its abundant bioactive compounds, including cordycepin and carotenoids. The growth, development, and metabolite production in various fungi are influenced by the complex interactions between regulatory cascades and light-signaling pathways. However, the mechanisms of gene regulation in response to light exposure in C. militaris remain largely unexplored. This study aimed to identify light-responsive genes and potential transcription factors (TFs) in C. militaris through an integrative transcriptome analysis. To achieve this, we reconstructed an expanded gene regulatory network (eGRN) comprising 507 TFs and 8662 regulated genes using both interolog-based and homolog-based methods to build the protein–protein interaction network. Aspergillus nidulans and Neurospora crassa were chosen as templates due to their relevance as fungal models and the extensive study of their light-responsive mechanisms. By utilizing the eGRN as a framework for comparing transcriptomic responses between light-exposure and dark conditions, we identified five key TFs—homeobox TF (CCM_07504), FlbC (CCM_04849), FlbB (CCM_01128), C6 zinc finger TF (CCM_05172), and mcrA (CCM_06477)—along with ten regulated genes within the light-responsive subnetwork. These TFs and regulated genes are likely crucial for the growth, development, and secondary metabolite production in C. militaris. Moreover, molecular docking analysis revealed that two novel TFs, CCM_05727 and CCM_06992, exhibit strong binding affinities and favorable docking scores with the primary light-responsive protein CmWC-1, suggesting their potential roles in light signaling pathways. This information provides an important functional interactive network for future studies on global transcriptional regulation in C. militaris and related fungi. Full article

With the widespread adoption of next-generation sequencing technologies, the speed and convenience of genome sequencing have significantly improved, and many biological genomes have been sequenced. However, during the assembly of small genomes, we still face a series of challenges, including repetitive fragments, inverted repeats, low sequencing coverage, and the limitations of sequencing technologies. These challenges lead to unknown gaps in small genomes, hindering complete genome assembly. Although there are many existing assembly software options, they do not fully utilize the potential of artificial intelligence technologies, resulting in limited improvement in gap filling. Here, we propose a novel method, DLGapCloser, based on deep learning, aimed at assisting traditional tools in further filling gaps in small genomes. Firstly, we created four datasets based on the original genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Micromonas pusilla. To further extract effective information from the gene sequences, we also added homologous genomes to enrich the datasets. Secondly, we proposed the DGCNet model, which effectively extracts features and learns context from sequences flanking gaps. Addressing issues with early pruning and high memory usage in the Beam Search algorithm, we developed a new prediction algorithm, Wave-Beam Search. This algorithm alternates between expansion and contraction phases, enhancing efficiency and accuracy. Experimental results showed that the Wave-Beam Search algorithm improved the gap-filling performance of assembly tools by 7.35%, 28.57%, 42.85%, and 8.33% on the original results. Finally, we established new gap-filling standards and created and implemented a novel evaluation method. Validation on the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa, and Micromonas pusilla showed that DLGapCloser increased the number of filled gaps by 8.05%, 15.3%, 1.4%, and 7% compared to traditional assembly tools. Full article

The Neurospora crassa genome has a gene cluster for the synthesis of galactosaminogalactan (GAG). The gene cluster includes the following: (1) UDP-glucose-4-epimerase to convert UDP-glucose and UDP-N-acetylglucosamine to UDP-galactose and UDP-N-acetylgalactosamine (NCU05133), (2) GAG synthase for the synthesis of an acetylated GAG (NCU05132), (3) GAG deacetylase (/NCW-1/NCU05137), (4) GH135-1, a GAG hydrolase with specificity for N-acetylgalactosamine-containing GAG (NCU05135), and (5) GH114-1, a galactosaminidase with specificity for galactosamine-containing GAG (NCU05136). The deacetylase was previously shown to be a major cell wall glycoprotein and given the name of NCW-1 (non-GPI anchored cell wall protein-1). Characterization of the polysaccharides found in the growth medium from the wild type and the GAG synthase mutant demonstrates that there is a major reduction in the levels of polysaccharides containing galactosamine and N-acetylgalactosamine in the mutant growth medium, providing evidence that the synthase is responsible for the production of a GAG. The analysis also indicates that there are other galactose-containing polysaccharides produced by the fungus. Phenotypic characterization of wild-type and mutant isolates showed that deacetylated GAG from the wild type can function as an adhesin to a glass surface and provides the fungal mat with tensile strength, demonstrating that the deacetylated GAG functions as an intercellular adhesive. The acetylated GAG produced by the deacetylase mutant was found to function as an adhesive for chitin, alumina, celite (diatomaceous earth), activated charcoal, and wheat leaf particulates. Full article

The model organism Neurospora crassa has been cultivated in laboratories since the 1920s and its saprotrophic lifestyle has been established for decades. However, beyond their role as saprotrophs, fungi engage in intricate relationships with plants, showcasing diverse connections ranging from mutualistic to pathogenic. Although N. crassa has been extensively investigated under laboratory conditions, its ecological characteristics remain largely unknown. In contrast, Brachypodium distachyon, a sweet grass closely related to significant crops, demonstrates remarkable ecological flexibility and participates in a variety of fungal interactions, encompassing both mutualistic and harmful associations. Through a comprehensive microscopic analysis using electron, fluorescence, and confocal laser scanning microscopy, we discovered a novel endophytic interaction between N. crassa and B. distachyon roots, where fungal hyphae not only thrive in the apoplastic space and vascular bundle but also may colonize plant root cells. This new and so far hidden trait of one of the most important fungal model organisms greatly enhances our view of N. crassa, opening new perspectives concerning the fungus‘ ecological role. In addition, we present a new tool for studying plant–fungus interspecies communication, combining two well-established model systems, which improves our possibilities of experimental design on the molecular level. Full article