Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of differentially expressed genes between clinical and bovine-biased Escherichia coli O157:H7 genotypes

ABSTRACT: Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. Important virulence factors of O157, including locus of enterocyte effacement, enterohemolysin, and pO157 plasmid encoded genes, showed increased expression in clinical genotype. Genes essential for acid resistance such as gadA, gadB, and gadC and other stress fitness-associated genes were up-regulated in the bovine-biased genotype 5. Overall, these results suggest that clinical genotype 1 strains more commonly cause human illness because of an enhanced ability to express O157 virulence factors known to be important for disease pathogenesis. By contrast, strains of the bovine-biased genotype 5 appear to be more resistant to adverse environmental conditions, which enable them to survive well in bovines without causing disease. The results are based on O157:H7 clinical and bovine-biased genotype cultures grown in DMEM medium to exponential phase. Four strains were selected from each genotype and strains were considered as biological replicates. A double loop microarray design was used for comparing the samples. Differences in transcript levels were determined using a mixed model ANOVA in R/MAANOVA which tested for significant differences due to strain (clinical or bovine-biased) using the following linear model: array+dye+sample (biological replicate)+strain+error. We incorporated the dye-swaps among the biological replicates.

ORGANISM(S): Escherichia coli

SUBMITTER: Thomas Besser

PROVIDER: E-GEOD-15783 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes.

Vanaja Sivapriya Kailasan SK Springman Amber C AC Besser Thomas E TE Whittam Thomas S TS Manning Shannon D SD

Applied and environmental microbiology 20091030 1

Escherichia coli O157:H7 strains can be classified into different genotypes based on the presence of specific Shiga toxin-encoding bacteriophage insertion sites. Certain O157:H7 genotypes predominate among human clinical cases (clinical genotypes), while others are more frequently found in bovines (bovine-biased genotypes). To determine whether inherent differences in gene expression explain the variation in infectivity of these genotypes, we compared the expression patterns of clinical genotype ...[more]

PMID: 19880650

Similar Datasets

Project description:DNA microarray analysis was used to compare the differential gene-expression profiles between Leptospira interrogans serovar Lai type strain 56601 and its corresponding attenuated strain IPAV. A 22 kb genomic island covering a cluster of 34 genes (LA0186 to LA0219) was actively expressed in both strains but concomitantly up-expressed in strain 56601 in contrast to that of IPAV. RT-PCR assays proved that the gene cluster comprised five transcripts. Gene annotation of this cluster revealed characteristics of a putative prophage-like remnant with at least 8 out of 34 CDSs encoding prophage-like proteins, of which, LA0195 is probably a putative prophage CI-like regulator. The transcription initiation activities of putative promoter-regulatory sequences of transcripts I, II and III, all proximal to LA0195, were further analyzed in the Escherichia coli promoter probe vector pKK232-8 by assaying the reporter CAT enzyme activities. The strong promoter activities of both transcripts I and II indicated by the E. coli CAT assay were well correlated with the in vitro sequence-specific binding of the recombinant LA0195 protein to the corresponding promoter probes detected by the electrophoresis mobility shift assay. On the other hand, the promoter activity of transcript III was very low in E. coli and failed to show active binding to LA0195 in vitro. These results suggested that LA0195 is likely involved in the transcription of transcripts I and II. However, the identical complete DNA sequences of this prophage remnant from these two strains strongly suggests that possible regulatory factors or signal transduction systems resided outside of this region within the genome maybe responsible for the differential expression profiling in these two strains. Keywords: Differential expression of L.interrogans 56601 and IPAV in 37Â°C The microarray chip was prepared as previously described (42). In brief, the 3528 protein coding sequences (CDSs) successfully amplified by PCR were printed in triplicate on the slides as probes. Three expression profiling experiments were performed via reverse transcription using Superscript (Invitrogen) and with one experiment having the cDNA of IPAV labeled by Cy3 and of 56601 labeled by Cy5, while the other two having the cDNA of 56601 labeled by Cy3 and of IPAV labeled by Cy5. The unincorporated dye was removed using a QIAquick Nucleotide Removal Kit (Qiagen) as specified by the manufacturer's protocol. Samples were hybridized at 42Â°C for 16h, and then washed as described in the manual. Hybridization experiments were performed in triplicate using cDNA derived from three different cultures of virulent strain 56601 and avirulent strain IPAV grown at 37Â°C. The hybridized slides were scanned and analyzed by Tiffsplit (Agilent) to calculate the signal intensities and to determine the presence or absence of each CDS. The data were then normalized, and their backgrounds were defined using GeneSpring 4.0 (Silicon Genetics). The GeneSpring software was used to further analyze the transcription patterns. To identify genes with significantly altered expression levels, cutoff values for expression level ratios 1.5 were used to filter genes with changes (n-fold) greater than Â±1.5 in three independent biological samples (27, 48, 50). Studentâs t test analysis of variance was used to compare the mean expression levels of the test and reference samples. Genes with significant differential expression levels (P < 0.05) were selected.

Project description:PrfA activity was studied in L. monocytogenes strain EGD and in an isogenic prfA deletion mutant (EGDΔprfA) carrying multiple copies of the wild-type prfA or the mutant prfA* gene (strains EGDΔprfApPrfA and EGDΔprfApPrfA*) after growth in brain heart infusion (BHI), Luria-Bertani broth (LB) or a defined minimal medium (MM) supplemented either with one of the three PTS-carbohydrates, glucose, mannose and cellobiose, or the non-PTS carbon source glycerol. Low PrfA activity was observed in the wild-type EGD strain in BHI and LB with either of these carbon sources, while PrfA activity was high in minimal medium in presence of glycerol but significantly reduced in presence of cellobiose. The strains expressing the prfA and prfA* gene under the prfA promoters, P1 and P2, produced equally large amounts of PrfA protein and high PrfA activity was observed in strain EGDΔprfApPrfA* under all growth conditions. In contrast, high PrfA activity in strain EGDΔprfApPrfA was only observed when this strain was cultured in BHI but not in LB or MM (in presence of either carbon source). A ptsH mutant (lacking a functional HPr) was able to grow in BHI suggesting that growth of L. monocytogenes in this culture medium is supported by carbon sources whose uptake and metabolism are independent of the PTS pathway. However, this mutant was unable to grow in LB and MM regardless which of the four carbon sources was added, suggesting that uptake of the used carbohydrates and the catabolism of glycerol depend fully on the functional common PTS pathway. Furthermore, the growth rates of L. monocytogenes are strongly reduced in presence of large amounts of PrfA protein when growing MM but less in LB and only slightly in BHI. The expression profiles of the genes encoding PTS permeases were determined in the three strains under various growth conditions. The data suggest that PrfA activity correlates with the expression level and the phosphorylation state of specific PTS permeases. This SuperSeries is composed of the following subset Series: GSE12143: Listeria monocytogenes EGD after growth BHI vs. LB vs. MM GSE12145: Listeria monocytogenes EGDΔprfApPrfA and EGDΔprfApPrfA* compared to the wild type strain EGD GSE12146: Listeria monocytogenes EGD and EGD-e

Dataset Information

Identification of differentially expressed genes between clinical and bovine-biased Escherichia coli O157:H7 genotypes

Publications

Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets