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Gene expression-based analysis of Streptococcus uberis 0140J and the MtuR (sub0472) mutant

ABSTRACT: Comparison of bacterial strain S. uberis 0140J with an isogenic mutant (same strain) with a lesion 338 basepairs downstream of the ATG start codon of the MtuR or sub0472 gene. Bacteria were grown in stationary culture in THB media at 37°C in the presence of 1mM manganese with triplicate samples of RNA extracted at early exponential (OD550 =0.43) and late exponential (OD550 =0.78) phases of growth. Microarray analysis was performed on custom-made S. uberis 0140J arrays containing 3780 features of 60mer oligonucleotides in triplicate with two probes for each individual gene.

ORGANISM(S): Streptococcus uberis 0140J Streptococcus uberis

PROVIDER: GSE36677 | GEO | 2015/11/01

SECONDARY ACCESSION(S): PRJNA153583

REPOSITORIES: GEO

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Gene expression-based analysis of Streptococcus uberis 0140J and the MtuR (sub0472) mutant

Project description:Comparison of bacterial strain S. uberis 0140J with an isogenic mutant (same strain) with a lesion 338 basepairs downstream of the ATG start codon of the MtuR or sub0472 gene. Bacteria were grown in stationary culture in THB media at 37Â°C in the presence of 1mM manganese with triplicate samples of RNA extracted at early exponential (OD550 =0.43) and late exponential (OD550 =0.78) phases of growth. Microarray analysis was performed on custom-made S. uberis 0140J arrays containing 3780 features of 60mer oligonucleotides in triplicate with two probes for each individual gene. We investigated the role of MtuR in vivo and the effect of its absence on the transcriptional control of gene expression using a custom-designed genome-wide S. uberis 0140J microarray containing 3780 features in triplicate with two probes for each individual gene. Triplicate samples were analysed in a loop design with Cy5 and Cy3 dye-swaps performed, and gene expression was compared at two different phases of bacterial growth (early and late logarithmic).

2015-11-01 | E-GEOD-36677 | biostudies-arrayexpress

Gene expression based analysis of Streptococcus uberis 0140J and vru (sub0144) mutant

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Gene expression based analysis of Streptococcus uberis 0140J and vru (sub0144) mutant

Project description:Comparison of bacterial strains S. uberis 0140J with isogenic mutant (same strain) with lesion 5 basepairs upstream of ATG start codon of the vru or sub0144 gene. Bacteria were grown in stationary culture in THB media at 37C with triplicate samples extracted at early exponential (OD550 =0.42) at late exponential (OD550 =0.75) phases of growth Microarray analysis performed on custom made S. uberis 0140J array containing 3780 features of 60mer oligonucleotides in triplicate with two probes for each individual gene We investigated the role of Vru in vivo and the effect of its absence on transcriptional control of gene expression using a custom designed genome-wide microarray performed on custom made S. uberis 0140J array containing 3780 features in triplicate with two probes for each individual gene. Triplicate samples analysed in loop design with Cy5 and Cy3 dye swap performed and gene expression compared at two difference phases of bacterial growth

2012-06-30 | E-GEOD-33186 | biostudies-arrayexpress

Virulence associated genes in Streptococcus uberis

Project description:Infection caused by bacteria from environmental reservoirs such as E. coli and S. uberis have not decreased in prevalence. Lack of success in controlling bovine mastitis due to S. uberis is associated with the route of infection which is not well understood and there is inadequate information on pathogenesis of S. uberis. Therefore, this study was to investigate the virulence factors of S. uberis using comparative genome analyses using isolates from cows with clinical mastitis and isolates from cows with a low cell count in their milk using a Subtracted Diversity Array (SDA). This study also reports the construction and validation of a microarray capable of fingerprinting the virulent and non-virulent isolates using the SDA technique.

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Gene content differences across strains of Streptococcus uberis identified using oligonucleotide microarray CGH

Project description:Streptococcus uberis is one of the principal causative agents of bovine mastitis. The organism is typically considered an environmental pathogen, however, recent studies also suggest possible host adaptation. In this study, two multilocus sequence typing (MLST) schemes and whole genome DNA microarrays were used to evaluate the degree and nature of genome flexibility between S. uberis strains. The 21 isolates examined in this study arise from a collection of 232 international isolates for which previous epidemiological and preliminary genotyping data existed. The microarray analysis resulted in an estimate of the core genome for S. uberis, consisting of 1530 ORFs, among 1855 tested, representing 82.5% of the S. uberis 0140J genome. The remaining ORFs were variable in gene content across the 21 tested strains. A total of 26 regions of difference (RDs), consisting of three or more contiguous ORFs, were identified among the variable genes. Core genes mainly encoded housekeeping functions, while the variable genes primarily fell within categories such as protection responses, degradation of small molecules, laterally acquired elements, and two component systems. Recombination detection procedures involving the MLST loci suggested S. uberis is a highly recombinant species, precluding accurate phylogenetic reconstructions involving these data. On the other hand, the microarray data did provide limited support for an association of gene content with strains found in multiple cows and/or multiple herds, suggesting the possibility of genes related to bovine transmissibility or host-adaptation. Keywords: comparative genomic hybridization

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Project description:S. uberis proteins from sub-cellular fractions (both cell wall-attached and secreted) were separated with SDS-PAGE, trypsine digested and identified with MS/MS analysis. Extracellular proteins were clustered into functional group based on in silico analysis. Concerning the database search: Mascot 2.2.0 was used with the following parameters: significance threshold p<0.05, Mascot MS/MS ion search : database NCBI, allow up to 1 miss cleavage, fixed modification - carbamidomethyl(C), variable modification- oxidation, peptide tol. +/- 1.5 Da, MS/MS tol. +/- 0.5 Da, monoisotopic.

2013-02-13 | PXD000142 | Pride

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