Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1150653 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To characterize the differentially expressed genes between adding fungal elicitor and without fungal elicitor on Streptomyces natalensis HW-2
2018-03-31 | GSE112559 | GEO
Project description:Worldwide, 20-25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply handling chain due to spoilage by fungal pathogens. Most impactful postharvest pathogens exhibit necrotrophic lifestyles, resulting in rotting of the host tissues and complete loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit, or remain quiescent until host and environmental conditions stimulate a successful infection. Current research on necrotrophic infections of fruit was mainly focused on the host by characterizing genetic and physicochemical factors that inhibit or promote the disease. However, the pathogenicity and virulence strategies employed by necrotrophic pathogens in ripe and unripe fruit are mostly understudied. Here, we provide a first comparative transcriptomics study of fungal postharvest pathogens: Botrytis cinerea, Rhizopus stolonifer and Fusarium acuminatum, all of which display necrotrophic behavior when infecting fruit. We de novo assembled and annotated the transcriptomes of R. stolonifer, and F. acuminatum and performed a differential gene expression analysis comparing the three fungal transcriptomes during fruit infection with that of fungal in-vitro growth. Analysis of the differentially expressed genes for enrichment of functional annotations revealed shared strategies of the three fungi during infection of compatible (ripe fruit) and incompatible (unripe fruit) hosts. We furthermore selected candidate genes that are involved in these strategies to characterize their expression during infection of unripe and ripe-like fruit of the non-ripening (nor) tomato mutant, both of which are physiologically and biochemically similar to unripe wildtype fruit. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and development of early detection tools and effective management strategies.
2018-12-01 | GSE122555 | GEO
Project description:Many of the world’s most devastating crop diseases are caused by fungal pathogens which elaborate specialized infection structures to invade plant tissue. Here we present a quantitative mass spectrometry-based phosphoproteomic analysis of infection-related development by the rice blast fungus Magnaporthe oryzae, which threatens global food security. We mapped 8,005 phosphosites on 2,062 fungal proteins, revealing major re-wiring of phosphorylation-based signaling cascades during fungal infection. Comparingme phosphosite conservation across 41 fungal species reveals phosphorylation signatures specifically associated with biotrophic and hemibiotrophic fungal infection. We then used parallel reaction monitoring to identify phosphoproteins directly regulated by the Pmk1 MAP kinase that controls plant infection by M. oryzae. We define 33 substrates of Pmk1 and show that Pmk1-dependent phosphorylation of a newly identified regulator, Vts1, is required for rice blast disease. Defining the phosphorylation landscape of infection therefore identifies potential therapeutic interventions for control of plant diseases.
2024-04-03 | PXD044865 | panorama
Project description:Amplicon-based fungal metagenomic sequencing for the identification of fungal species in brain tissue from Alzheimer's disease. The study consists in 14 samples, sequenced using Illumina's paired-end technology.
| EGAD00001003196 | EGA
Project description:Identification of fungal species present in the central nervous system tissue from Alzheimer's disease patients by next-generation sequencing.
| EGAS00001002228 | EGA
Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. This ChIP-Seq experiment was carried out to determine the binding sites of SigE under conditions of cell envelope stress induced by 10 ug / ml vancomycin for 30 minutes. A 3xFLAG tagged SigE was introduced in a SigE deletion strain and ChIP-Seq was carried out using M2 (Sigma Aldrich A2220) gel suspension. Non-immunoprecipitated (total) DNA preparations were used for background determination and the wild type M600 was used as the negative control.
2019-04-24 | E-MTAB-7827 | biostudies-arrayexpress
Project description:Many of the world’s most devastating crop diseases are caused by fungal pathogens which elaborate specialized infection structures to invade plant tissue. Here we present a quantitative mass spectrometry-based phosphoproteomic analysis of infection-related development by the rice blast fungus Magnaporthe oryzae, which threatens global food security. We mapped 8,005 phosphosites on 2,062 fungal proteins, revealing major re-wiring of phosphorylation-based signaling cascades during fungal infection. Comparingme phosphosite conservation across 41 fungal species reveals phosphorylation signatures specifically associated with biotrophic and hemibiotrophic fungal infection. We then used parallel reaction monitoring to identify phosphoproteins directly regulated by the Pmk1 MAP kinase that controls plant infection by M. oryzae. We define 33 substrates of Pmk1 and show that Pmk1-dependent phosphorylation of a newly identified regulator, Vts1, is required for rice blast disease. Defining the phosphorylation landscape of infection therefore identifies potential therapeutic interventions for control of plant diseases.
2024-04-03 | PXD044830 | Pride
Project description:Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare fourteen Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis.
2009-01-31 | GSE13621 | GEO
Project description:Biofilms are ubiquitous in natural, medical, and engineering environments. While most antibiotics that primarily aim to inhibit cell growth may result in bacterial drug resistance, biofilm inhibitors do not affect cell growth and there is less chance of developing resistance. This work sought to identify novel, non-toxic and potent biofilm inhibitors from Streptomyces bacteria for reducing the biofilm formation of Pseudomonas aeruginosa PAO1. Out of 4300 Streptomyces strains, one species produced and secreted peptide(s) to inhibit P. aeruginosa biofilm formation by 93% without affecting the growth of planktonic cells. Global transcriptome analyses (DNA microarray) revealed that the supernatant of the Streptomyces 230 strain induced phenazine, pyoverdine, and pyochelin synthesis genes. Electron microscopy showed that the supernatant of Streptomyces 230 strain reduced the production of polymeric matrix in P. aeruginosa biofilm cells, while the Streptomyces species enhanced swarming motility of P. aeruginosa. Therefore, current study suggests that Streptomyces bacteria are an important resource of biofilm inhibitors as well as antibiotics.
2013-03-21 | GSE28194 | GEO