Proteomics research and related functional classification of liquid sclerotial exudates of Sclerotinia ginseng

Genome-wide survey of the bipartite structure and pathogenesis-related genes of Neostagonosporella sichuanensis, a causal agent of Fishscale bamboo rhombic-spot disease

Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16-0001 and strain SICAUCC 23-0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within AT-rich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis, including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo.

Morphology of Four Strains of Phellinoid Agaricomycetes and Microstructural and Physiological Properties of Their Exudates

To study and compare the morphology of the phellinoid Agaricomycetes strains and find other strategies to improve Phellinus spp. growth and metabolism. In this study, the morphological characteristics of four Phellinus igniarius strains (phellinoid Agaricomycetes) were observed under a light microscope. The exudates from these fungi were observed using light microscopy, scanning electron microscopy (SEM), and energy-dispersive spectrometry (EDS). The exudates were initially transparent with a water-like appearance, and became darker with time at neutral pH. Microscopy of air-dried exudates revealed regular shapes and crystals. Cl- (chloride) and K+ were the two key elements analyzed using EDS. Polyphenol oxidase (POD), catalase (CAT), and laccase activities were detected in mycelia from each of the four Phellinus strains. The K+ content of the three strains was higher than that of the wild strain. Cl- content correlated negatively with that of K+. Laccase activities associated with each mycelia and its corresponding media differed under cold and contaminated conditions.

Analysis of Aspergillus versicolor exudate composition

Aspergillus versicolor, a widely distributed fungus, is associated with pollution and carcinogenic hazards. This study aimed to examine the functions of the A. versicolor exudate and laid a scientific foundation for improving our understanding, utilization, and control of A. versicolor. The A. versicolor exudate proteome, ion content, and amino acid components were determined using label-free quantitation, atomic absorption spectrophotometry, and high-performance liquid chromatography, respectively. In total, 502 proteins were identified in the A. versicolor exudate. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and cluster of orthologous group analyses were used to annotate the functional classification and pathways of the aligned proteins. Proteins identified in the exudate were mainly enriched in carbohydrate metabolic process, translation, oxidoreductase activity, oxidoreductase activity, hydrolase activity, cell wall-related processes, catalytic activity, and unknown functions. The exudate comprised Na, K, Ca, Fe, and Mg cations. Among the 17 types of amino acids detected in the exudate, 7 were essential and 10 were nonessential. The exudate may be involved in the vital processes of A. versicolor. Additionally, the exudate may play an important role in the growth, development, reproduction, homeostasis, nutrient supply for regrowth, and virulence of A. versicolor.

Fungal Guttation, a Source of Bioactive Compounds, and Its Ecological Role-A Review

Guttation is a common phenomenon in the fungal kingdom. Its occurrence and intensity depend largely on culture conditions, such as growth medium composition or incubation temperature. As filamentous fungi are a rich source of compounds, possessing various biological activities, guttation exudates could also contain bioactive substances. Among such molecules, researchers have already found numerous mycotoxins, antimicrobials, insecticides, bioherbicides, antiviral, and anticancer agents in exudate droplets. They belong to either secondary metabolites (SMs) or proteins and are secreted with different intensities. The background of guttation, in terms of its biological role, in vivo, and promoting factors, has been explored only partially. In this review, we describe the metabolites present in fungal exudates, their diversity, and bioactivities. Pointing to the significance of fungal ecology and natural products discovery, selected aspects of guttation in the fungi are discussed.

Proteomic Analysis of Mycelial Exudates of Ustilaginoidea virens

Rice false smut (RFS) disease, which is caused by Ustilaginoidea virens, has been widespread all over the world in recent years, causing irreversible losses. Under artificial culture conditions, exudates will appear on colonies of U. virens during the growth of the hyphae. Exudation of droplets is a common feature in many fungi, but the functions of exudates are undetermined. As the executors of life functions, proteins can intuitively reflect the functions of exudates. Shotgun proteomics were used in this study. A total of 650 proteins were identified in the exudate of U. virens, and the raw data were made available via ProteomeXchange with the identifier PXD019861. There were 57 subcategories and 167 pathways annotated with Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, respectively. Through protein–protein interaction (PPI) network analysis, it was found that 20 proteins participated in the biosynthesis of secondary metabolites. Two separate PPI analyses were performed for carbon metabolism and microbial metabolism in diverse environments. After comparing and annotating the functions of proteins of the exudate, it was speculated that the exudate was involved in the construction and remodeling of the fungal cell wall. Pathogenicity, sporulation, and antioxidant effects might all be affected by the exudate.

Proteomic analysis of exudate of Cercospora armoraciae from Armoracia rusticana

Background

Cercospora armoraciae causes leaf spot disease on Armoracia rusticana. Exudation of droplets, when grown on PDA, distinguishes this fungi from other members of the genus Cercospora. The role this exudate plays in the virulence of this pathogen has not been elucidated. To explore this, we characterized the transcriptome of C. armoraciae and the proteome of exudate associated with this plant pathogen.

Methods

Virulence of three strains of C. armoraciae was evaluated in greenhouse assays. De novo sequencing was applied to assemble transcriptome from these strains. Nano-HPLC-MS/MS analysis was used to identify proteins in the pathogen exudate. Identified proteins were functionally classified and annotated using GO, KEGG, and COG/KOG bioinformatics analysis methods.

Results

When treated with the exudate of C. armoraciae strain SCa-01, leaves of A. rusticana showed yellowing and necrosis of the leaves and similar symptoms to plants inoculated with this fungi. A total of 14,937 unigenes were assembled from C. armoraciae, and 576 proteins comprising 1,538 peptides, 1,524 unique peptide, were identified from the exudate. GO annotation classified 411 proteins (71%) into 27 functional categories, namely, 12, seven and eight biological process, cellular component, and molecular function subcategories, respectively. KEGG analysis assigned 314 proteins to 84 signaling/metabolic pathways, and 450 proteins were annotated against the COG/KOG database.

Discussion

Transcriptome and GO analysis of C. armoraciae found most proteins in the exudate. GO analysis suggested that a considerable proportion of proteins were involved in cellular process and metabolic process, which suggests exudates maintain the metabolic balance of this fungi. Some proteins annotated to the phenylalanine metabolism, which suggests that the exudates may enhance the virulence of this pathogen. Some proteins annotated to the phenylalanine metabolism, which suggests that the exudates may enhance the pathogenicity of the pathogen. Also some proteins were annotated to the peroxisome metabolic pathway and the fatty acid biosynthesis pathways. These pathways may confer antifungal, antioxidant and antimicrobial activity on the exudates.

Formation of sclerotia in Sclerotinia ginseng and composition of the sclerotial exudate

Background

Sclerotinia ginseng is a major devastating soil-borne pathogen of ginseng that can cause irreparable damage and large economic losses. This pathogen produces sclerotia, which are among the most persistent resting structures produced by filamentous fungi. The production of an exudate is a common feature of sclerotial development.

Methods

S. ginseng was cultured on 10 different media and the following parameters were measured: mycelial growth rate (mm/day), initial formation time of exudate droplets, total quantity of exudate, number of sclerotia per dish, and sclerotial fresh/dry weight. The composition of the sclerotial exudate was analyzed using four methods (high performance liquid chromatography, gas chromatography-mass spectrometry, flame atomic absorption spectrometry, and Nessler’s reagent spectrophotometry).

Results

We found that PDA was the optimal medium for exudate production, while SDA medium resulted in the highest mycelial growth rate. The earliest emergence of exudate droplets from sclerotia was on OA-YE and V8 media. The largest amount of sclerotia and the smallest sclerotia were produced on V8 medium. The maximum and minimum dry/fresh weight were obtained on MEA medium and V8 medium, respectively. The exudate contained organic acids (oxalic acid, gallic acid, ferulic acid, vanillic acid, caffeic acid, and tannic acid), carbohydrates (inositol, glucose, and trehalose), various ions (potassium, sodium, and magnesium), and ammonia.

Discussion

The functions of the identified compounds are discussed within the context of pathogenicity, sclerotial development, and antimicrobial activity. Our findings provide information about the production of sclerotia and the composition of sclerotial exudate that may be useful to develop strategies to control this disease.