CLIP-seq of Salmonella ProQ in intracellular-like conditions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1051606 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27194264_1.fastq.gz | Fastqsanger.gz | |||
| SRR27194264_2.fastq.gz | Fastqsanger.gz | |||
| SRR27194265_1.fastq.gz | Fastqsanger.gz | |||
| SRR27194265_2.fastq.gz | Fastqsanger.gz | |||
| SRR27194266_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The aim of the project is to identify transcriptome-wide binding sites for the global RNA-binding protein ProQ in Salmonella during intracellular-like conditions.
2024-02-13 | GSE250014 | GEO
Project description:IP (as previously described Chao et al., 2012; Smirnov et al., 2016) of ProQ-3xFLAG and FinO-3xFLAG in Salmonella SL1344 at different growth conditions.
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Project description:FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. Comparison with Hfq, Salmonella’s other major RNA chaperone, reinforces the notion that these two global RNA binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs, we show that STnc540 represses a virulence-related magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella infection and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
2018-11-28 | GSE117255 | GEO
Project description:FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. Comparison with Hfq, Salmonella’s other major RNA chaperone, reinforces the notion that these two global RNA binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs, we show that STnc540 represses a virulence-related magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella infection and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
2018-11-28 | GSE117252 | GEO
Project description:FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. Comparison with Hfq, Salmonella’s other major RNA chaperone, reinforces the notion that these two global RNA binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs, we show that STnc540 represses a virulence-related magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella infection and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
2018-11-28 | GSE117236 | GEO
Project description:While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset includes representative RIP experiments carried out to characterize the in vivo interactome of the bacterial global RNA-binding protein ProQ. They include a series of RIPs performed on a Salmonella Typhimurium SL1344 ProQ-3xFLAG strain grown to the exponential (OD600=0.5), transition (OD600=2.0) or stationary (6 hours after cells reached OD600=2.0) phases; a RIP perfomed on an Escherichia coli W3110 ProQ-3xFLAG strain grown to the transition phase; a control series of RIPs performed on Salmonella Typhimurium SL1344 ProQ-3xFLAG and PhoP-3xFLAG strains grown to the transition phase. The first series shows how the ProQ RNA interactome evolves over growth in Salmonella, the second reveals ProQ targets in Escherichia, the third illustrates the lack of RNA-binding activity in a negative control, DNA-binding transcription regulator PhoP.
2016-08-29 | GSE62987 | GEO
Project description:Role of ProQ in Salmonella virulence
| PRJNA481543 | ENA
Project description:Salmonella invasion of non-phagocytic cells is a dynamic process that requires the translocation of effector proteins into host cells by a type III secretion system (T3SS1) encoded on Salmonella pathogenicity island 1 (SPI1). The signals involved in T3SS1 induction in vivo are not known, but SPI1-induced invasive Salmonella can be prepared by growth in synthetic media. Here we compared two different methods of preparing SPI1-induced bacteria by using a combination of transcriptome analysis, a single-cell reporter assay and intracellular gene expression analysis to reveal clear differences between these two bacterial populations that are reflected in their ability to interact with cultured epithelial cells. Invasion efficiency and intracellular replication were greater for bacteria grown with aeration to late-log phase compared to those grown without aeration to stationary phase. No significant differences in SPI1 regulon expression were revealed by transcriptome analysis. By contrast, surface appendage and stress response genes were considerably changed. Single cell analyses of gene expression revealed variation in the frequency of SPI1-induced bacteria and a correlation between SPI1-induction and the presence of flagella. The expression of virulence genes following invasion of cultured epithelial cells was also found to be predetermined by pre-invasion growth conditions. Key words: epithelial, flagella, invasion, motility, Salmonella-containing vacuole, treatment of shaking versus treatment of static growth conditions for St-SL1344
2010-04-19 | E-GEOD-13343 | biostudies-arrayexpress
Project description:Salmonella invasion of non-phagocytic cells is a dynamic process that requires the translocation of effector proteins into host cells by a type III secretion system (T3SS1) encoded on Salmonella pathogenicity island 1 (SPI1). The signals involved in T3SS1 induction in vivo are not known, but SPI1-induced invasive Salmonella can be prepared by growth in synthetic media. Here we compared two different methods of preparing SPI1-induced bacteria by using a combination of transcriptome analysis, a single-cell reporter assay and intracellular gene expression analysis to reveal clear differences between these two bacterial populations that are reflected in their ability to interact with cultured epithelial cells. Invasion efficiency and intracellular replication were greater for bacteria grown with aeration to late-log phase compared to those grown without aeration to stationary phase. No significant differences in SPI1 regulon expression were revealed by transcriptome analysis. By contrast, surface appendage and stress response genes were considerably changed. Single cell analyses of gene expression revealed variation in the frequency of SPI1-induced bacteria and a correlation between SPI1-induction and the presence of flagella. The expression of virulence genes following invasion of cultured epithelial cells was also found to be predetermined by pre-invasion growth conditions. Key words: epithelial, flagella, invasion, motility, Salmonella-containing vacuole,
2010-04-19 | GSE13343 | GEO