Dataset Information

Genome-wide RNA-sequencing of E. coli strain 55989 from in vitro and in vivo samples

ABSTRACT: RNA-seq comparative analysis of an enteroaggregative Escherichia coli human isolate grown in vitro and in vivo (colon samples from monocolonized mice) revealed candidates genes that are either overexpressed or underexpressed. Comparisons included exponential growth vs stationary growth; exponential vs colon and stationary vs colon.

ORGANISM(S): Escherichia coli 55989

PROVIDER: GSE165634 | GEO | 2021/01/28

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Background: Global patterns of gene expression of Escherichia coli K-12 during growth transitions have been deeply investigated, however, comparable studies of E. coli O157:H7 have not been explored, particularly with respect to factors regulating virulence genes and genomic islands specific to this pathogen. To examine the impact of growth phase on the dynamics of the transcriptome, O157:H7 Sakai strain was cultured in MOPS minimal media (0.1% glucose), RNA harvested at 10 time points from early exponential to full stationary phase, and relative gene expression was measured by co-hybridization on high-density DNA microarrays. Results: Analysis of variance (R/MAANOVA, Fs test) identified 442 (36%) of 1239 O157-specific ORFs and 2110 (59%) of 3647 backbone ORFs that changed in expression significantly over time. QT cluster analysis placed 2468 of the 2552 significant ORFs into 12 groups; each group representing a distinct expression pattern. ORFs from the largest cluster (n=1078) decreased in expression from late exponential to early stationary phase: most of these ORFs are involved in functions associated with steady state growth. Also represented in this cluster are ORFs of the TAI island, encoding tellurite resistance and urease activity, which decreased ~4-fold and most ORFs of the LEE island, which decreased ~2-fold by early stationary phase. ORFs encoding proteins secreted via the LEE encoded type III secretion system, such as tccP and espJ, also decreased in expression from exponential to stationary phase. Three of the clusters (n=154) comprised genes that are transiently upregulated at the transition into stationary phase and included genes involved in nutrient scavenging. Upregulated genes with an increase in mRNA levels from late exponential to early stationary phase belonged to one cluster (n=923) which includes genes involved in stress responses (e.g. gadAB, osmBC, and dps). These transcript levels remained relatively high for >3h in stationary phase. The Shiga toxin genes (stx1AB and stx2B) were significantly induced after transition into stationary phase. Conclusions: Expression of 307 O157-specific ORFs was modulated in a growth dependent manner. These results provide a baseline transcriptional profile that can be compared to patterns of gene expression of this important foodborne pathogen under adverse environmental conditions. Keywords: time course

Dataset Information

Genome-wide RNA-sequencing of E. coli strain 55989 from in vitro and in vivo samples

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets