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.

2013-08-30 | E-GEOD-50468 | biostudies-arrayexpress

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

Project description:Genome-wide in planta determination of the quorum sensing regulon in Pectobacterium atrosepticum, through gene expression analysis of ExpI mutants using Agilent custom microarrays.

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

Pectobacterium atrosepticum

Project description:Pectobacterium atrosepticum Genome sequencing

| PRJNA258504 | ENA

Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots

Project description:Pectobacterium atrosepticum (Pba) is a gram-negative bacterium which causes blackleg and tuber soft rot on potato. To investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions, we used total RNA-sequencing to measure the gene expression patterns from all three species. Samples from infected and non-infected plant roots were collected after fourteen days of inoculation with Pba SCRI_1039 and subjected to total RNA-sequencing on an Illumina sequencing platform.

2024-01-17 | E-MTAB-13434 | biostudies-arrayexpress

Pectobacterium atrosepticum strain:21a

Project description:Pectobacterium atrosepticum strain:21a Genome sequencing

| PRJNA252906 | ENA

Transcriptome analysis of Pectobacterium atrosepticum

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Pectobacterium upon treatment of polyphenol compound.

2022-10-05 | GSE196675 | GEO

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

Pectobacterium atrosepticum strain:36A

Project description:Pectobacterium atrosepticum strain:36A Genome sequencing and assembly

| PRJNA419060 | ENA