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ABSTRACT: Isolation and characterization of lytic bacteriophages infecting Pectobacterium atrosepticum

PROVIDER: PRJNA986656 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25015015_1.fastq.gz	Fastqsanger.gz
	SRR25015015_2.fastq.gz	Fastqsanger.gz
	SRR25015016_1.fastq.gz	Fastqsanger.gz
	SRR25015016_2.fastq.gz	Fastqsanger.gz
	SRR25015017_1.fastq.gz	Fastqsanger.gz

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Project description:Broad host lytic bacteriophages infecting Pectobacterium spp in the Philippines

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Transcriptome microarray of wildtype, relA, expI and rpoS Pectobacterium atrosepticum strains in PMB media

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Transcriptome microarray of wildtype, relA, expI and rpoS Pectobacterium atrosepticum strains in PMB media

Project description:Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media. The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369 A 24 chip study using total RNA recovered from three separate wild-type cultures of Pectobacterium atrosepticum SCRI1043 and three separate cultures from three single mutant strains of SCRI1043 possessing deletions within relA (ECA3569), expI (ECA0105) or rpoS (ECA3530) when grown in Pel Minimal Broth (PMB) media to log-phase (6h) or early stationary phase (14h) growth. Each chip measures the expression level of 4,472 genes from Pectobacterium atrosepticum SCRI1043 with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

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Transcription profiling of Pectobacterium atrosepticum wild and ExpI mutants to determine the quorum sensing regulon

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2008-07-01 | E-TABM-384 | biostudies-arrayexpress

Project description:Isolation, Characterization and Evaluation of Lytic Bacteriophages from Wastewater against Salmonella spp

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Biological characterization of virulent therapeutic bacteriophage PAK_P3 infecting Pseudomonas aeruginosa.

2016-07-20 | GSE76513 | GEO

Biological characterization of virulent therapeutic bacteriophage PAK_P4 infecting Pseudomonas aeruginosa

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Biological characterization of virulent therapeutic bacteriophage PAK_P3 infecting Pseudomonas aeruginosa.

Project description:We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa. RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P3. Three biological replicates for each time point.

2016-07-20 | E-GEOD-76513 | biostudies-arrayexpress

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

Project description:Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress response. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 63 sRNAs were differentially expressed with 57 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST (e-value < 0.001) showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. A large number of these sRNAs is starvation-induced, suggesting their role in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.

2016-01-26 | GSE68547 | GEO

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