Pseudomonas aeruginosa PA14
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA867727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20997476.fastq.gz | Fastqsanger.gz | |||
| SRR20997477.fastq.gz | Fastqsanger.gz | |||
| SRR20997478.fastq.gz | Fastqsanger.gz | |||
| SRR20997479.fastq.gz | Fastqsanger.gz | |||
| SRR20997480.fastq.gz | Fastqsanger.gz |
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Project description:Recent studies have shown that the concentrations of proteins expressed from orthologous genes are often conserved across organisms, and to a greater extent than the abundances of the corresponding mRNAs. However, such studies have not distinguished between evolutionary (e.g., sequence divergence) and environmental (e.g., growth condition) effects on the regulation of steady-state protein and mRNA abundances. Here we systematically investigated the transcriptome and proteome of two closely related Pseudomonas aeruginosa strains, PAO1 and PA14, under identical experimental conditions, thus controlling for environmental effects. For 703 genes observed by both shotgun proteomics and microarray experiments, we find that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains, to an extent comparable to protein and mRNA abundances. In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level. Our data demonstrate that post-transcriptional regulation is important for understanding the discordance between mRNA and protein abundance.
2014-05-08 | PXD000684 | Pride
Project description:Recent studies have shown that the concentrations of proteins expressed from orthologous genes are often conserved across organisms, and to a greater extent than the abundances of the corresponding mRNAs. However, such studies have not distinguished between evolutionary (e.g., sequence divergence) and environmental (e.g., growth condition) effects on the regulation of steady-state protein and mRNA abundances. Here we systematically investigated the transcriptome and proteome of two closely related Pseudomonas aeruginosa strains, PAO1 and PA14, under identical experimental conditions, thus controlling for environmental effects. For 703 genes observed by both shotgun proteomics and microarray experiments, we find that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains, to an extent comparable to protein and mRNA abundances. In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level. Our data demonstrate that post-transcriptional regulation is important for understanding the discordance between mRNA and protein abundance.
2018-08-29 | MSV000082863 | MassIVE
Project description:We have tested the effect of deletion of Topoisomerase I on genes transcription of the bacteria Pseudomonas. aeruginosa. Topoisomerase I is a conserved protein that modulate the topology state of the DNA from super-coiled to relaxed. To this end we have compared the transcription profile of a topA::GentR mutant to that of the wild-type strain. The topA mutant contains in topA gene a Mariner transposon with a gentamicin resistance cassette. It is part of the non-redundant mutant library of P. aeruginosa PA14 strains.
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Project description:Genomic DNA from Pseudomonas aeruginosa strains PAO1 and PA14
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Project description:Our understanding of bacterial physiology during human infection is limited by the difficulty in assessing bacterial function in the infection site. Recent studies have begun to address this question by quantifying bacterial mRNA levels in human-derived samples using transcriptomics. One challenge for these studies is the poor predictivity of mRNA for protein levels for some genes. Here, we used carefully controlled chemostat experiments to examine the relationship between mRNA and protein levels across four growth rates (3hr, 6hr, 14hr, 25hr doubling times) in the bacterial pathogen Pseudomonas aeruginosa PA14.
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Project description:To further determine the origin of the increased virulence of Pseudomonas aeruginosa PA14 compared to Pseudomonas aeruginosa PAO1, we report a transcriptomic approach through RNA sequencing. Next-generation sequencing (NGS) has revolutioned sistems-based analsis of transcriptomic pathways. The goals of this study are to compare the transcriptomic profile of all 5263 orthologous genes of these nearly two strains of Pseudomonas aeruginosa.
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Project description:We have tested the effect of deletion of Topoisomerase I on genes transcription of the bacteria Pseudomonas. aeruginosa. Topoisomerase I is a conserved protein that modulate the topology state of the DNA from super-coiled to relaxed. To this end we have compared the transcription profile of a topA::GentR mutant to that of the wild-type strain. The topA mutant contains in topA gene a Mariner transposon with a gentamicin resistance cassette. It is part of the non-redundant mutant library of P. aeruginosa PA14 strains. WT and mutant cells were grown to OD 2.0 in LB 200rpm shaking at 37C.
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Project description:We report RNA-seq data of Pseudomonas aeruginosa PA14 (UCBPP-PA14) and an isogenic rpoS-STOP mutant generated using CRISPR/Cas9 base editing. Transcriptomic profiling during exponential growth in rich medium highlights the regulatory influence of RpoS. These data enable exploration of RpoS-dependent responses in the virulent PA14 strain.
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Project description:Extremely slow growth imposed by energy limitation is a ubiquitous but poorly understood physiological state for microbes. We used oxygen limitation to impose this state on Pseudomonas aeruginosa and measured newly synthesized proteins using a time-selective proteome labeling method (BONCAT) to identify relevant regulators and metabolic pathways. We further characterized one upregulated protein that has no homology to any known protein domains. This small, acidic protein is post-transcriptionally regulated and physically interacts with RNA polymerase, binding near the secondary channel during transcription elongation, and leading to widespread effects on gene expression. For some genes, the impacts on transcript and protein levels are different, suggesting possible modulation of translation as well. These effects have phenotypic consequences, as deletion of the gene affects biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. Based on these phenotypes, we have designated the protein SutA (survival under transitions).
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