Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pseudomonas classification

ABSTRACT: Classification of the plant-associated phenotype of Pseudomonas strains using genome properties

PROVIDER: PRJEB45033 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR6293213.fastq.gz	Fastqsanger.gz
	ERR6293214.fastq.gz	Fastqsanger.gz
	ERR6293215.fastq.gz	Fastqsanger.gz
	ERR6325940.fastq.gz	Fastqsanger.gz
	ERR6325980.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 7

Similar Datasets

Label-free melanoma phenotype classification using AI-based morphological profiling

Project description:Label-free melanoma phenotype classification using AI-based morphological profiling

| PRJNA1140860 | ENA

Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila

Project description:Quorum sensing is a communication strategy that bacteria use to collectively alter gene expression in response to cell density. Pathogens use quorum sensing systems to control activities vital to infection, such as the production of virulence factors and biofilm formation. The Pseudomonas virulence factor (pvf) gene cluster encodes a quorum sensing system (Pvf) that is present in over 500 strains of proteobacteria, including strains that infect a variety of plant and human hosts. We have shown that the Pvf quorum sensing system regulates the production of secreted proteins and small molecules in the insect pathogen Pseudomonas entomophila L48. Here, we identified genes that are likely regulated by Pvf using the model strain P. entomophila L48 which does not contain other known quorum sensing systems. Pvf regulated genes were identified through comparing the transcriptomes of wildtype P. entomophila and a pvf deletion mutant (ΔpvfA-D). We found that deletion of pvfA-D affected the expression of approximately 300 genes involved in virulence, the type VI secretion system, siderophore transport, and branched chain amino acid biosynthesis. Additionally, we identified seven putative biosynthetic gene clusters whose expression are reduced in ΔpvfA-D. Our results indicate that Pvf controls multiple virulence mechanisms in P. entomophila L48. Characterizing genes regulated by Pvf will aid understanding of host-pathogen interactions and development of anti-virulence strategies against P. entomophila and other pvf-containing strains.

2023-03-19 | GSE216056 | GEO

Dual-transcriptomic analysis of Nicotiana benthamiana and two compatible Pseudomonas strains

Project description:We sought to compare and contrast plant host and bacterial transcriptional changes during compatible infections that cause disease (albeit within different symptoms). We investigated the infection by the two Pseudomonas syringae sensu lato strains P. syringae pv. syringae B728a (Psy) and P. amygdali pv. tabaci 11528 (Pta) of Nicotiana benthamiana at an early time point post inoculation to understand how a plant host responds to two related bacteria with different infection strategies. Plant and bacterial transcriptomes were analyzed prior to and five hours post inoculation.

2023-09-01 | GSE201377 | GEO

Diversity of HrpL-regulons across Pseudomonas syringae isolates

Project description:We implemented transcriptional analysis methods using cDNA and high-throughput sequencing data to identify HrpL-regulated genes for six strains of Pseudomonas syringae

2014-01-01 | GSE46930 | GEO

mgo promotes the expression of a gene cluster that contributes to the survival of Pseudomonas syringae in tomato leaflets

Project description:Pseudomonas syringae is an important plant pathogen that infects a wide variety of crops. The mgo (mangotoxin-generating operon) gene cluster produces an extracellular signaling molecule, leudiazen, and is highly conserved in Pseudomonas syringae strains. Here, we genetically removed mgo in Pseudomonas syringae pv. syringae (Pss) UMAF0158 to interrogate its impacts on bacterial infection. Loss of mgo not only alleviated the chlorosis symptom caused by Pss UMAF0158 infection, but also reduced bacterial population in tomato leaflets. Structure-activity relationship revealed that the diazeniumdiolate group and the isobutyl side chain of leudiazen are critical for its signaling activity. Through global transcriptome analysis, we found that mgo regulates the expression of a new gene cluster in addition to mangotoxin biosynthetic operon, namely RS17235-RS17245. This new gene cluster contributes to in planta survival of Pss UMAF0158 and is widely distributed in Pseudomonas syringae strains. Our results demonstrate that chemical signaling systems in plant pathogens play prominent roles in virulence and population increase and set stages for understanding downstream components of mgo-regulated signaling pathways.

2024-10-16 | GSE261242 | GEO

Gene expression in AES-2 clonal isolates of Pseudomonas aeruginosa

Project description:Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Most CF patients acquire unique P. aeruginosa strains from the environment; however clonal strains have been identified in CF communities in several countries. Two clonal strains infect 10% to 40% of patients in three CF clinics in mainland eastern Australia. The expression profiles of four planktonically-grown isolates of one Australian clonal strain (AES-2), and four non–clonal CF P. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1. The isolates were subsequently grown as 3-day old biofilms and similarly extracted for RNA and compared as above. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization

2009-02-05 | GSE10304 | GEO

Gene expression in PAO1, clonal AES-1 and non-clonal isolates of Pseudomonas aeruginosa

Project description:Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Most CF patients acquire unique P. aeruginosa strains from the environment; however clonal strains have been identified in CF communities in several countries. Two clonal strains infect 10% to 40% of patients in three CF clinics in mainland eastern Australia. The expression profiles of four planktonically-grown isolates of one Australian clonal strain (AES-1), and four non–clonal CF P. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1. The isolates were subsequently grown as 3-day old biofilms and similarly extracted for RNA and compared as above. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization

2008-12-05 | GSE6122 | GEO

Systemic responses to Pseudomonas syringae infection

Project description:We used three different strains of Pseudomonas syringae pv tomato DC3000 to investigate systemic responses to infection in Arabidopsis and the development of SAR. Wildtype DC3000, the hrpA mutant and DC3000 carrying the avirulence gene avrRpm1 were syringe infiltrated into 4-week-old plants at a concentration of 10e8 cfu/ml. At least 5 leaves per plant were infiltrated and at least 10 plants were pooled for each sample. Systemic, uninfected tissue was then harvested at 8, 12 and 21h after inoculation. Three independent experiments were carried out to give three biological replicates for each timepoint.

2009-12-10 | GSE19264 | GEO

Genomic DNA hybridization of Pseudomonas aeruginosa strains PAO1 and PA14

Project description:Genomic DNA from Pseudomonas aeruginosa strains PAO1 and PA14

2015-11-15 | GSE67038 | GEO

Pseudomonas

Project description:Complete genome sequence of plant-root associated Pseudomonas

| PRJDB10928 | ENA