Ontology highlight
ABSTRACT:
PROVIDER: PRJEB25405 | ENA |
REPOSITORIES: ENA
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Project description:This study describes the gel-free phosphoproteomic analysis the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea grown in vitro under non-limiting conditions.
2014-06-09 | PXD000817 | Pride
Project description:Extracellular vesicles (EVs) are increasingly recognized as an important mechanism for cell-cell interactions. Their role in fungi is still poorly understood and they have been isolated from only a handful of species. Here, we isolated and characterized EVs from Aureobasidium pullulans, a biotechnologically important black yeast-like fungus that is increasingly used for biocontrol of phytopathogenic fungi and bacteria. After optimization of the isolation protocol, characterization of EVs from A. pullulans by transmission electron microscopy (TEM) revealed a typical cup-shaped morphology and different subpopulations of EVs. These results were confirmed by nanoparticle tracking analysis (NTA), which revealed that A. pullulans produced 6.1 × 10^8 nanoparticles per milliliter of culture medium. Proteomic analysis of EVs detected 642 proteins. A small fraction of them had signal peptides for secretion and transmembrane domains. Proteins characteristic of different synthesis pathways were found, suggesting that EVs are synthesized by multiple pathways in A. pullulans. Enrichment analysis using Gene Ontology showed that most of the proteins found in the EVs were associated with primary metabolism. When sequencing the small RNA fraction of A. pullulans EVs, we found two hypothetical novel mil-RNAs. Finally, we tested the biocontrol potential of EVs from A. pullulans. The EVs did not inhibit the germination of spores of three important phytopathogenic fungi – Botrytis cinerea, Colletotrichum acutatum, and Penicillium expansum. However, exposure of grown cultures of C. acutatum and P. expansum to A. pullulans EVs resulted in visible changes in morphology of colonies. These preliminary results suggest that EVs may be part of the antagonistic activity of A. pullulans, which is so far only partially understood. Thus, the first isolation and characterization of EVs from A. pullulans provides a starting point for further studies of EVs in the biotechnologically important traits of the biocontrol black fungus A. pullulans in particular and in the biological role of fungal EVs in general.
2022-11-09 | PXD037103 | Pride
Project description:In this work, we have used deep sequencing to study the viral small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species and have different type of genome (dsRNA, (+)ssRNA, and (-)ssRNA). In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking concomitances with vsiRNAs produced by plant viruses suggesting similar pathways of viral targeting in plants and fungi
2016-09-15 | GSE83282 | GEO
Project description:In plant-associated fungi, the role of the epigenome is increasingly recognized as an important regulator of genome structure and of the expression of genes involved in the interaction(s) with the host plant. Two closely-related phytopathogenic species, Leptosphaeria maculans ‘brassicae’ (Lmb) and L. maculans ‘lepidii’ (Lml) exhibit a large conservation of genome synteny but contrasted genome structure. Lmb has undergone massive invasion of its genome by transposable elements summing up one third of its genome and clustered in large TE-rich regions on chromosomal arms, while Lml genome has a low amount of repeats (3% of the genome). Previous information also showed that the TE-rich regions of Lmb host a few species-specific effector genes, expressed during plant infection, with main incidence on the adaptive potential of the fungus. The distinct genome organisation between Lmb and Lml thus provides us with a model of choice for the comparison of the epigenomic organization in two closely related phytopathogenic fungi, in order to investigate pathogenicity/effector gene landscape with respect to the chromatin landscape. To address this, we performed chromatin immunoprecipitation, targeting either histone modifications typical for heterochromatin or euchromatin, during axenic culture, combined with transcriptomic analysis to analyse the influence of the chromatin organisation on gene expression. Our data comfort in both species the postulate that facultative heterochromatin landscapes, associated with H3K27me3 domains, are enriched in genes with no annotation, including numerous candidate effector and species-specific genes. Notably orthologous genes located in the same H3K27me3 domains are enriched in genes encoding putative proteinaceous and metabolic effectors. These genes are mostly silenced in vegetative growth conditions and are likely to be involved in interaction with the host. Compared to other fungal species, including Lml, Lmb has the particularity to have large H3K9me3-domains within chromosomal arms, strongly associated to TEs, and hosting numerous species-specific effector-encoding genes. These two distinct heterochromatin landscapes hosting genes involved in interaction with the host now questions their involvement in regulation of pathogenicity, the dynamics of the domains during plant infection, and the selective advantage for the fungus to host effector genes in H3K9me3 or H3K27me3 domains.
2021-06-02 | GSE150125 | GEO
Project description:Deadwood plays a crucial role in forest ecosystems, but we have limited information about the specific fungal taxa and extracellular lignocellulolytic enzymes that are actively involved in the decomposition process in situ. To investigate this, we studied the fungal metaproteome of twelve deadwood tree species in a replicated, eight-year experiment. Key fungi observed included genera of white-rot fungi (Basidiomycota, e.g. Armillaria, Hypholoma, Mycena, Ischnoderma, Resinicium), brown-rot fungi (Basidiomycota, e.g. Fomitopsis, Antrodia), diverse Ascomycota including xylariacous soft-rot fungi (e.g. Xylaria, Annulohypoxylon, Nemania) and various wood-associated endophytes and saprotrophs (Ascocoryne, Trichoderma, Talaromyces). These fungi used a whole range of extracellular lignocellulolytic enzymes, such as peroxidases, peroxide-producing enzymes, laccases, cellulases, glucosidases, hemicellulases (xylanases) and lytic polysaccharide monooxygenases (LPMOs). Both the fungi and enzymes were tree-specific, with specialists and generalists being distinguished by network analysis. The extracellular enzymatic system was highly redundant, with many enzyme classes of different origins present simultaneously in all decaying logs. Strong correlations were found between peroxide-producing enzymes (oxidases) and peroxidases as well as LPMOs, and between ligninolytic, cellulolytic and hemicellulolytic enzymes. The overall protein abundance of lignocellulolytic enzymes was reduced by up to -30% in gymnosperm logs compared to angiosperm logs, and gymnosperms lacked ascomycetous enzymes, which may have contributed to the lower decomposition of gymnosperm wood. In summary, we have obtained a comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in several temperate forest tree species, which can help to improve our understanding of the complex ecological processes in forest ecosystems.
2024-04-22 | PXD041962 | Pride
Project description:Rhizosphere is a complex system of interactions between plant roots, bacteria, fungi and animals, where the release of plant root exudates stimulates bacterial density and diversity. However, the majority of the bacteria in soil results to be unculturable but active. The aim of the present work was to characterize the microbial community associated to the root of V. vinifera cv. Pinot Noir not only under a taxonomic perspective, but also under a functional point of view, using a metaproteome approach. Our results underlined the difference between the metagenomic and metaproteomic approach and the large potentiality of proteomics in describing the environmental bacterial community and its activity. In fact, by this approach, that allows to investigate the mechanisms occurring in the rhizosphere, we showed that bacteria belonging to Streptomyces, Bacillus and Pseudomonas genera are the most active in protein expression. In the rhizosphere, the identified genera were involved mainly in phosphorus and nitrogen soil metabolism.
2022-02-28 | PXD007670 | Pride