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Comparison of global gene expression between Pseudomonas aeruginosa strains 383 and 2192

ABSTRACT: At mid-log phase (OD600 of 0.5), unique gene expression patterns were observed between these two strains with 3.4% of the transcripts (188/5570) expressed differentially. Of the 188 significantly varied (>1.8 fold) genes, 115 were up-regulated in 383 while 73 were up-regulated in 2192. Keywords: Different strains of bacterium

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE9621 | GEO | 2007/11/20

SECONDARY ACCESSION(S): PRJNA103471

REPOSITORIES: GEO

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Transcription profiling of Pseudomonas aeruginosa strains 383 and 2192

Project description:At mid-log phase (OD600 of 0.5), unique gene expression patterns were observed between these two strains with 3.4% of the transcripts (188/5570) expressed differentially. Of the 188 significantly varied (>1.8 fold) genes, 115 were up-regulated in 383 while 73 were up-regulated in 2192. Experiment Overall Design: The goal of this experiment was to identify the differentially expressed genes from two genetically similar but phenotypically distinct P. aeruginosa strains 383 and 2192. Two strains were isolated two days apart from the sputum of the same cystic fibrosis patient. Following proper culture RNA was extracted from the two strains. Affymetrix GeneChip Pseudomonas aeruginosa was used to examine the gene expression paterns of the two strains.

2008-06-16 | E-GEOD-9621 | biostudies-arrayexpress

Pseudomonas aeruginosa

Project description:Comparison of global gene expression between Pseudomonas aeruginosa strains 383 and 2192

| PRJNA103471 | ENA

Comparative transcriptomic analysis of Pseudomonas aeruginosa isolates from ICU patients with acute and chronic pneumonia

Project description:In this study, a comparative analysis was performed on two clinical Pa strains from pneumonia patients, 1) an acute strain (CMC-115) and 2) a chronic multidrug- and carbapenem-resistant strain (CMC-097), with distinct phenotypic and genetic characteristics. A transcriptome analysis using both the Pseudomonas DNA GeneChip microarray and Illumina RNA-Seq technologies was carried out for both strains at early-stationary growth phase in laboratory culture. The comparative transcriptomic analysis identified 134 genes differentially expressed ≥4.0-fold by both technologies between the two strains, which included virulence genes such as flagellar, pyoverdine, and phenazine genes, that were higher in the acute strain, CMC-115, and type 3 secretory system (T3SS) and pyochelin biosynthesis genes, that were higher in the chronic strain, CMC-097. In particular, the DNA microarrays suggested and the RNA-Seq analysis confirms the type 3 secretory system genes were completely missing from the acute strain, CMC-115. The combined analysis using the RNA-Seq and DNA microarray methods also identified important genes that were either missing or highly divergent from the Reference PAO1 genome used for the DNA microarray design. For example, the RNA-Seq data identified an operon containing several multidrug resistance genes: aacA27, beta-lactamase (blaOXA-2), qacΔE, sul1, and GNAT-N, in the chronic strain, CMC-097.

2021-07-23 | GSE180499 | GEO

Transcriptomic profiles of S. Typhimurium SL1344 parent strain and ΔrpoS and ΔrelAΔspoT and ΔrelAΔspoTΔrpoS mutant strains grown to various optical densities during late-log and stationary phase in LB aerobic batch culture

Project description:S. Typhimurium SL1344 parental strain and isogenic ΔrpoS, ΔrelAΔspoT and ΔrelAΔspoTΔrpoS strains were grown to OD600=1.0, OD600=2.3, OD600=3.0 and OD600=4.2 in Luria-Bertani medium.

2015-05-31 | GSE63714 | GEO

Transcriptomic profiles of S. Typhimurium SL1344 parent strain and ΔdksA and ΔrelAΔspoTΔdksA mutant strains grown to various optical densities during late-log and stationary phase in LB aerobic batch culture

Project description:S. Typhimurium SL1344 parental strain and isogenic ΔrpoS, ΔdksA and ΔrelAΔspoT, ΔrelAΔspoTΔrpoS and ΔrelAΔspoTΔdksA strains were grown to OD600=1.0, OD600=2.3, OD600=3.0 and OD600=4.2 in Luria-Bertani medium.

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Transcription data for Pseudomonas aeruginosa isolates TBCF10839 and TBCF121838 grown to early and late exponential growth phase

Project description:We used Affymetrix microarrays to monitor the gene expression of genomically related but phenotypically divergent strains TBCF10839 and TBCF121838 Cultures were grown in LB medium 37Â°C. In mid-exp. phase (OD600 1.5) cell aliquots were harvested for subsequent RNA extraction. Culturing was continued until late exponential phase (OD600 3.0) when another aliquot was harvested for RNA extraction.

2012-06-29 | E-GEOD-36647 | biostudies-arrayexpress

Label-free Quantitative Acetylomics Revealed Toxoplasma gondii Genotype-Specific Acetylome Signatures

Project description:Distinct genotypic and pathogenicity differences exist between strains of the opportunistic protozoan Toxoplasma gondii. The label-free quantitative acetylomics approach was applied to investigate the differences in the level of acetylation between RH strain, PRU strain and PYS strain of T. gondii. The results showed that lysine acetylation in RH strain was the largest (458 acetylated proteins) among the three strains. The PYS strain had the second-largest acetylome (188 acetylated proteins), whereas lysine acetylation in PRU strain (115 acetylated proteins) was the smallest. Motif analysis revealed four, three and four motifs enriched from lysine acetylation sequences in RH strain, PRU strain and PYS strain respectively, suggesting specificity of acetyltransferases in these strains. Our analysis also identified 15 DAPs (differentially expressed acetylated proteins), 3 DAPs and 26 DAPs in RH strain vs PRU strain, PRU strain vs PYS strain and PYS strain vs RH strain, respectively. Compared with PYS strain and PRU strain, histone acetyltransferase and glycyl-tRNA synthase had higher expression levels in RH strain, reflecting genotype-specific differences in stress tolerance. These findings provide novel insight into the acetylomic profiles of major genotypes of T. gondii and provide an important resource for further analysis of the roles of the acetylated parasite proteins in the regulation of cellular functions.

2020-05-27 | PXD015031 | Pride

Transcription profiling of Pseudomonas aeruginosa roxSR and anr mutant strains under aerobic conditions

Project description:To assess the role of two redox-sensitive transcriptional regulators, RoxSR and ANR, in Pseudomonas aeruginosa under aerobic conditions, microarray analysis was performed. Transcriptome profiles of roxSR mutant and anr mutant aerobically grown in LB medium were determined by Affymetrix GeneChip at both the exponential phase and early stationary phase and compared to that of the wild type strain. Experiment Overall Design: Pseudomonas aeruginosa wild type (PAO1ut), roxSR mutant (ROX1), and anr mutant (PAO6261) strains were cultivated aerobically in LB in Erlenmeyer flasks, and total RNAs were extracted at both the exponential phase (OD600 = 0.3) and early stationary phase (OD600 = 1.4). The experiment was performed in duplicate independent cultures.

2009-08-09 | E-GEOD-17296 | biostudies-arrayexpress

Transcription profiling of Pseudomonas aeruginosa parental strain PAO1 and PAOQ_psrA::Tn5 knock out mutant

Project description:5 Biological repeats of bacterial strain PAO1(parent, control) were compared to 5 biological repeats of PAO1_psrA::Tn5 knockout mutant, both strains were grown in BM2-glucose media containing 2mM MgSO4. Cells were grown to mid-log phase, OD600 0.50 Cells were immediately harvested and RNA was extracted

2008-07-04 | E-FPMI-14 | biostudies-arrayexpress

Transcriptome analyses of continuous cultures of Pseudomonas aeruginosa growing slowly under oxygen and nitrate limitation

Project description:Chemostats have been used for decades in studying cell growth under controlled environments. Whole transcriptome sequencing by RNA-seq is a relatively new method for gene expression analysis. We utilized both tools for expression analysis of Pseudomonas aeruginosa growing slowly in synthetic cystic fibrosis medium under growth-limiting nitrate and oxygen levels. We established steady-state cultures under two divergent growth rates and found that during slower growth at a doubling time of 9.8 h, 76 known quorum genes were up-expressed while just 11 were down-expressed. Quorum-controlled genes were also more expressed in response to oxygen limitation. 21% of up-expressed genes under slow, oxygen-limited growth are quorum controlled while just 6% are up-expressed under slow, nitrate-limited growth. We found that the autoinducer for regulator RhlR, C4-HSL, is ~3.4 times higher when cells are growing slowly under oxygen limitation while the concentration of the autoinducer for LasR remained unchanged. Experiments with deletion mutants show the importance of rhlR for expression of quorum-controlled genes under slow, oxygen-limited conditions. This is an intriguing observation since P. aeruginosa is likely growing in similar environments in the cystic fibrosis lung, and lasR mutations are known to arise during chronic infection.

2016-12-01 | GSE71880 | GEO

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