Frontiers in fungal biology最新文献

The organization of functionally related gene families oftentimes exhibits a non-random genomic distribution as gene clusters that are prevalent throughout divergent eukaryotic organisms. The molecular and cellular functions of the gene families where clustering has been identified vary, and include those involved in basic metabolism, secondary metabolite biosynthesis, and large gene families (e.g. ribosomal proteins). Many of these gene families exhibit transcriptional coregulation, however the roles that clustering plays and the mechanism(s) underlying co-expression are currently understudied. A comprehensive characterization of these relationships would allow for a greater understanding of the implications of genetic editing and engineering to minimize undesired consequences. Here we report the impact of gene clustering and genomic positioning on the expression of large, coregulated gene families in a haploid strain of the budding yeast, Saccharomyces cerevisiae. Computational analysis identifies a significant and complex role for chromatin remodeling as a mechanism underlying cluster transcription. Functional dissection of the 'vitamin metabolic process', 'ribosome biogenesis', and 'ribosomal protein' gene families, characterized the roles for SNF2, JHD2, HIR2, EAF3, and yKU70 dependent chromatin remodeling during steady state transcription as well as the transcriptional response to glucose replenishment. Finally, mining and analysis of transcription profiles reveals significant transcriptional differences between the clustered and unclustered subsets within coregulated families under specific stressors.

Thelephora palmata is a well-known species morphologically characterized by coralloid and leathery basidiomata with numerous fuscous purple to blackish-brown branches. It was once considered to exhibit a wide ecological range and distribution area. However, comprehensive phylogenetic analysis based on four loci (ITS, nrLSU, rpb2, and nrSSU) revealed that T. palmata sensu lato represents a species complex consisting of at least 12 cryptic taxa, with a biogeographic distribution pattern bounded by geographic regions: Asia, Eurasia, Europe, and North America. In this study, we proposed eight new taxa based on available specimens. Of these, seven new species and one forma from China were described here based on phylogenetic analyses, morphological examinations, and environmental niche comparisons, viz., T. apiculata, T. cornu-damae, T. densa, T. esculenta, T. fuscidula, T. sinopalmata, T. truncicola, and T. truncicola f. pallescens.

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures whose formation is regulated by a developmental program that dynamically responds to environmental changes, such as light intensity. However, the genetic architecture and regulation of this developmental program are poorly known. Here, we characterize a novel Pumilio family gene, ort2, which influences fruiting body development, particularly the formation of dark stipes, a light-dependent alternative developmental trajectory. Phylogenetic analysis of this RNA-binding protein family in fungi revealed a distinct subfamily structure, with high conservation of each subfamily within Agaricomycetes. Reverse genetics experiments in the model species Coprinopsis cinerea revealed that ort2 disruptants produced fruiting bodies, but were deficient in dark stipe formation, whereas the overexpression mutants produced significantly more dark stipes. The gene was named after Orthrus, the two-headed dog of classical mythology, based on rare but reproducible branching fruiting body phenotypes observed upon overexpression. Our findings reveal fruiting-related functions for ort2, a novel conserved RNA-binding protein, and may serve as a novel entry point for understanding the molecular basis of dark stipe development.

Apple is most important fruit crop in Himachal Pradesh, contributing substantially to the state's economy. However, soilborne diseases have emerged as a major concern affecting nursery-raised apples. Trichoderma species produce chitinase, an enzyme that degrades chitin, a major component of the fungal cell wall. This study aimed to optimize the growth parameters for chitinase production, extraction, purification, and characterization and to assess the antifungal potential against soilborne pathogens of apple. A total of 14 isolates of Trichoderma spp. produced chitinases in a colloidal chitin agar (CCA) medium to varying extents. The optimal incubation period, pH, substrate concentration, and incubation temperature were 7 days, 5, 1%, and 30°C, respectively, while the thermal and pH stability ranged from 30°C to 50°C and from 4 to 6, respectively. Chitinases were purified from Trichoderma atroviride UHFTA005 and UHFTA006 and from Trichoderma virens UHFTV017 with a molecular mass of 40 kDa. The chitinase from T. atroviride UHFTA005 at 0.60 μl inhibited the in vitro growth of Dematophora necatrix (92.22%) and Sclerotium rolfsii (91.11%). In a further in vivo evaluation of the chitinases, T. atroviride UHFTA005 was found to be more effective against white root rot and seedling blight of apple, with disease control of 86.67% and 73.33%, respectively, and with 86.67% white root rot disease control in nursery field conditions suggesting its strong potential as a biocontrol agent in nursery field conditions.

The increasing multi-drug resistance observed in the turfgrass pathogen Clarireedia spp. has emerged as a critical issue. Understanding the mechanisms underlying fungicide resistance is crucial to address this challenge. This study focuses on comparing a highly propiconazole-resistant isolate of Clarireedia jacksonii, HRI11, with a sensitive isolate, HRS10. Genomes were sequenced using the Oxford Nanopore MinION sequencing platform, and hybrid assembly was performed using this data and existing Pacific Biosciences long reads and Illumina short reads. HRI11 genome assembly represents the most contiguous and complete genome assembly reported for Clarireedia to date, spanning 43.6 MB with 12,831 predicted protein-coding genes across 51 scaffolds. In contrast, the HRS10 had an assembly size of 39.6 MB and encoded 12,161 putative proteins distributed over 100 scaffolds. While the two isolates share substantial sequence similarity and overall protein content, the fungicide resistance observed in HRI11 appears to arise primarily from genetic variants, particularly in genes encoding transcription factors, transporters, and fungicide target genes. These genetic variants establish a foundational resistance level against fungicides. Furthermore, induced resistance in HRI11 involves increased expression of proteins that facilitate fungicide efflux, thereby optimizing energy allocation during fungicide exposures. Together, these mechanisms-inherent genetic variation and adaptive transcriptional responses-contribute to the heightened resilience of HRI11 under fungicide treatment.

Background/objectives: Tremella fuciformis is an edible fungus prized for its culinary value. The polysaccharide content of T. fuciformis grown on a Cyclobalanopsis substrate (TY3) was significantly higher than those grown on a mixed substrate (TF1) made of wheat bran and cottonseed hull.

Methods: Metabolomics and proteomics were used to assess the effects of lignocellulose (consisting of cellulose, hemicellulose, and lignin) in different growth substrates on the polysaccharide content of T. fuciformis and its formation mechanism.

Results: TY3 had a higher lignocellulose content than TF1. The metabolites of carbohydrates and carbohydrate conjugates in TY3-grown specimens were significantly upregulated. Among the 21 identified metabolic pathways with enriched proteins, carbohydrate metabolism was the most enriched. The Carbohydrate-Active Enzyme (CAZyme) database was used to annotate 161 carbohydrate enzymes, and 67 of them were differentially expressed proteins. Carbohydrate synthetases were upregulated much more using TY3.

Conclusions: Tremella fuciformis grown on TY3 was verified to possess a lower ability for lignocellulose degradation (as evidenced by decreased synthesis of cellulase, xylanase, and lignin peroxidase) but a stronger ability for carbohydrate synthesis (as evidenced by increased synthesis of cellulose and hemicellulose). Our study enhances the control of polysaccharide content in T. fuciformis, thereby facilitating its processing for food applications.

Introduction: Candida (Candidozyma) auris and Pseudomonas aeruginosa are frequently found in hospital environments and on medical equipment, where they commonly colonize and infect hospitalized patients, contributing to healthcare-associated infections (HAIs). Although they share similar ecological niches and may interact, the mechanisms underlying their interspecies communication remain largely unknown.

Methods: This study investigated the in vitro interaction between planktonic cells of C. auris and P. aeruginosa through co-culture experiments in various growth media, with or without iron supplementation. Fluorescence microscopy was employed to assess yeast viability, and the effect of lyophilized, cell-free P. aeruginosa supernatants on C. auris was also evaluated.

Results: P. aeruginosa significantly inhibited the growth of C. auris, regardless of the initial microbial concentrations. Growth suppression began after 8 hours of co-culture and persisted for up to 72 hours. Fluorescence microscopy suggested that this antagonistic effect was predominantly fungistatic, as most C. auris cells remained viable in the presence of the bacterium. The inhibitory effect was consistent across different culture media, and iron supplementation partially restored C. auris growth. Similarly, concentrated cell-free supernatants from P. aeruginosa inhibited C. auris, further supporting the role of secreted molecules. In this case as well, iron addition partially reversed the inhibitory effect.

Discussion and conclusion: These findings suggest that P. aeruginosa produces and secretes molecules with fungistatic activity against C. auris, and that this effect is at least partially modulated by iron availability. This discovery provides a foundation for future research into the identity and mechanisms of action of these secreted compounds, as well as the broader clinical implications of microbial interactions during co-colonization or co-infection.

Introduction: Inhaled conidia of the opportunistic fungi Aspergillus fumigatus settle in the airway mucosa and in alveolar spaces. Different immune cells typically provide crucial defense against fungal germination. However, in immunocompromised patients, the lack of sufficient pro-inflammatory immune response often leads to invasive aspergillosis, with current treatments being limited by insufficient understanding of the precise conidial distribution patterns in the airways.

Methods: Therefore, we employed advanced imaging techniques, including immunohistochemistry, optical clearing, and confocal laser scanning microscopy, to map A. fumigatus conidial distribution in both immunocompetent and neutropenic mouse airways. We developed a 3D airway model distinguishing the main bronchus, intermediate bronchi, and terminal bronchioles, enabling quantitative analysis of conidial location. In addition, we analyzed the interactions of CD11c⁺ cells with conidia in the conducting airway mucosa.

Results: Our findings revealed that while the majority of conidia reached the alveolar space in both groups, neutropenic mice showed significantly higher conidial concentrations in bronchial branches, particularly in the main bronchus, compared with immunocompetent mice. Simultaneously, in the conducting airway mucosa of neutropenic mice, CD11c⁺ cells ingested an elevated number of conidia compared with immunocompetent mice.

Discussion: Thus, detailed mapping of the conidial distribution patterns provides crucial insights into the spatial aspects of antifungal treatment in neutropenic patients. The enhanced contribution of CD11c⁺ cells to conidial internalization in the conducting airway mucosa of neutropenic mice demonstrated in the present study emphasizes the potential of these cells in the development of more effective, cell-targeted antifungal treatments.