Project description:Polyporus umbellatus sclerotia are medicinal tissue, but little is known about acetylome of sclerotia generated from hyphae. Acetylated peptides in P. umbellatus were enriched by anti-acetyl-lysine antibody beaded agarose and DDA data were acquired by AB Triple TOF 5600+. Raw data were analyzed by ProteinPilot software to obtained acetylated peptides and proteins, and carried out bioinformatics analysis.
Project description:Polyporus umbellatus sclerotia are medicinal tissue, but little is known about acetylome of sclerotia generated from hyphae. Based on acetylome analysis results and expression levels of targeted protein that associated with sclerotia generation were verified by PRM using Orbitrap Fusion (Thermo-Fisher Scientific, San Jose, CA) mass spectrometer equipped with a nanospray Flex Ion Source and the UltiMate3000 RSLC nano (Dionex, Sunnyvale, CA).
Project description:The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded programme. Fruiting bodies reached highest complexity levels in the Agaricomycetes, yet, the underlying genetics is currently poorly known. In this work, we functionally characterised an unannotated gene we term snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologues of snb1 are present in almost all Agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. Snb1 mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed a multitude of differentially regulated genes and gene families that may be related to tissue differentiation and the formation of structures. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying tissue differentiation in the Agaricomycetes.
Project description:This transcriptome analysis accompanies the genome sequencing of Pyronema confluens for purposes of annotation and gene expression quantification. P. confluens is a basal filamentous ascomycete that forms primitive fruiting bodies (apothecia) to generate its sexual spores. We have performed RNA-seq for two growth conditions allowing only vegetative growth and one condition allowing sexual development to identify genes that are differentially regulated during fruiting body formation.
Project description:In response to starvation, Myxococcus xanthus initiates a developmental program that results in the formation of spore-filled multicellular fruiting bodies. Here we have used cDNA microarray analysis to determine changes in the global gene expression at different time points of the developmental process. The expression of nearly 900 genes was found to be altered at least two-fold during development as compared to vegetative cells. Genes encoding proteins with typical vegetative functions such as protein synthesis and energy metabolism were transcriptionally down-regulated in the early stages of development. Among the 430 genes transcriptionally up-regulated during development genes with regulatory functions were overrepresented; underlining that fruiting body formation relies on a complex signalling network. Notably, almost 40% of all genes with increased expression at different stages of development encoded hypothetical proteins indicating a large unexplored potential of proteins important for fruiting body formation. Keywords: Time course of development with 9 time points 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5
