Ontology highlight
ABSTRACT:
PROVIDER: PRJNA908904 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22540851_1.fastq.gz | Fastqsanger.gz | |||
| SRR22540851_2.fastq.gz | Fastqsanger.gz | |||
| SRR22540852_1.fastq.gz | Fastqsanger.gz | |||
| SRR22540852_2.fastq.gz | Fastqsanger.gz | |||
| SRR22540853_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Staphylococcus aureus is a Gram-positive opportunistic pathogen, which is carried by approximately 30 % of the population at any time. In addition to being a commensal S. aureus can cause an array of infections, ranging from mild skin and soft tissue infections to life threatening endocarditis and septicemia. S. aureus encodes a variety of virulence factors that facilitate its pathogenic lifestyle. Genes encoding these virulence factors are under tight control by a complex regulatory network, which includes, sigma factors, sRNAs, and protein-based systems, such as Two-Component Systems (TCS). Previous work in our lab demonstrated that overexpression of the sRNA tsr37 leads to an increase in cellular aggregation in the absence of host serum. We determined that the clumping phenotype was dependent on a previously unannotated 88 amino acid protein encoded within the tsr37 sRNA transcript (which we named ScrA for S. aureus clumping regulator A). In addition to increased clumping, overexpression of ScrA also leads to increased biofilm formation. To investigate the mechanism of action of ScrA we performed mass spectrometry proteomics and RNA-sequencing in the ScrA overexpressing strain. A variety of virulence factors, including several surface adhesins were upregulated while several proteases were downregulated. Moreover, results showed a significant upregulation of the SaeRS two component system, suggesting that ScrA is influencing SaeRS activity. We go on to demonstrate that overexpression of ScrA in a saeR mutant abrogates the clumping/biofilm phenotypes confirming that ScrA functions via the Sae system. Finally, we identified the ArlRS TCS as a potential positive regulator of scrA expression. Collectively our results show that ScrA is an activator of the SaeRS system and suggests that ScrA may act as an intermediary between the ArlRS and SaeRS systems.
2022-08-11 | PXD028409 | Pride
Project description:Staphylococcus aureus is a Gram-positive opportunistic pathogen, which is carried by approximately 30 % of the population at any time. In addition to being a commensal S. aureus can cause an array of infections, ranging from mild skin and soft tissue infections to life threatening endocarditis and septicemia. S. aureus encodes a variety of virulence factors that facilitate its pathogenic lifestyle. Genes encoding these virulence factors are under tight control by a complex regulatory network, which includes, sigma factors, sRNAs, and protein-based systems, such as Two-Component Systems (TCS). Previous work in our lab demonstrated that overexpression of the sRNA tsr37 leads to an increase in cellular aggregation in the absence of host serum. We determined that the clumping phenotype was dependent on a previously unannotated 88 amino acid protein encoded within the tsr37 sRNA transcript (which we named ScrA for S. aureus clumping regulator A). In addition to increased clumping, overexpression of ScrA also leads to increased biofilm formation. To investigate the mechanism of action of ScrA we performed mass spectrometry proteomics and RNA-sequencing in the ScrA overexpressing strain. A variety of virulence factors, including several surface adhesins were upregulated while several proteases were downregulated. Moreover, results showed a significant upregulation of the SaeRS two component system, suggesting that ScrA is influencing SaeRS activity. We go on to demonstrate that overexpression of ScrA in a saeR mutant abrogates the clumping/biofilm phenotypes confirming that ScrA functions via the Sae system. Finally, we identified the ArlRS TCS as a potential positive regulator of scrA expression. Collectively our results show that ScrA is an activator of the SaeRS system and suggests that ScrA may act as an intermediary between the ArlRS and SaeRS systems.
2021-10-01 | GSE184753 | GEO
Project description:In bacterial two-component regulatory systems (TCSs), dephosphorylation of phosphorylated response regulator is essential for resetting the activated systems to the pre-activation state. However, in the SaeRS TCS, a major virulence TCS of Staphylococcus aureus, the mechanism for dephosphorylation of the response regulator SaeR has not been identified. Here we report that two auxiliary proteins from the sae operon, SaeP and SaeQ, form a ternary complex with the sensor kinase SaeS and activate the sensor kinase’s phosphatase activity. Efficient activation of the phosphatase activity of SaeS required the presence of both SaeP and SaeQ. When SaeP and SaeQ were expressed, the expression of coagulase, a sae target with low affinity to phosphorylated SaeR, was greatly reduced, while the expression of alpha-hemolysin, a sae target with high affinity to phosphorylated SaeR, was not, demonstrating a differential effect of SaePQ on sae target gene expression. When expression of SaePQ was abolished, most sae target genes were induced at an elevated level. Since the expression of SaeP and SaeQ is induced by SaeRS TCS, these results suggest that the SaeRS TCS returns to pre-activation state by a negative feedback mechanism.
2012-03-09 | GSE36230 | GEO
Project description:In bacterial two-component regulatory systems (TCSs), dephosphorylation of phosphorylated response regulator is essential for resetting the activated systems to the pre-activation state. However, in the SaeRS TCS, a major virulence TCS of Staphylococcus aureus, the mechanism for dephosphorylation of the response regulator SaeR has not been identified. Here we report that two auxiliary proteins from the sae operon, SaeP and SaeQ, form a ternary complex with the sensor kinase SaeS and activate the sensor kinase’s phosphatase activity. Efficient activation of the phosphatase activity of SaeS required the presence of both SaeP and SaeQ. When SaeP and SaeQ were expressed, the expression of coagulase, a sae target with low affinity to phosphorylated SaeR, was greatly reduced, while the expression of alpha-hemolysin, a sae target with high affinity to phosphorylated SaeR, was not, demonstrating a differential effect of SaePQ on sae target gene expression. When expression of SaePQ was abolished, most sae target genes were induced at an elevated level. Since the expression of SaeP and SaeQ is induced by SaeRS TCS, these results suggest that the SaeRS TCS returns to pre-activation state by a negative feedback mechanism. To examine the global effect of SaePQ on sae target gene expression, we treated the wild type strain of USA300-P23 and its P1 promoter mutant with HNP-1 and analyzed the transcription of sae target genes by microarray assays. WT and P1 cells were compared against a each other at the same time point and against a T=0 reference.
2012-03-09 | E-GEOD-36230 | biostudies-arrayexpress
Project description:Background: Staphylococcus epidermidis (SE) has emerged as one of the most important causes of nosocomial infections. The SaeRS two-component signal transduction system (TCS) influences virulence and biofilm formation in Staphylococcus aureus. The deletion of saeR in S. epidermidis results in impaired anaerobic growth and decreased nitrate utilization. However, the regulatory function of SaeRS on biofilm formation and autolysis in S. epidermidis remains unclear. Results: The saeRS genes of SE1457 were deleted by homologous recombination. The saeRS deletion mutant, SE1457DsaeRS, exhibited increased biofilm formation that was disturbed more severely (a 4-fold reduction) by DNase I treatment compared to SE1457 and the complementation strain SE1457saec. Compared to SE1457 and SE1457saec, SE1457DsaeRS showed increased Triton X-100-induced autolysis (approximately 3-fold) and decreased cell viability in planktonic/biofilm states; further, SE1457DsaeRS also released more extracellular DNA (eDNA) in the biofilms. Correlated with the increased autolysis phenotype, the transcription of autolysis-related genes, such as atlE and aae, was increased in SE1457DsaeRS. Whereas the expression of accumulation-associated protein was up-regulated by 1.8-fold in 1457DsaeRS, the expression of an N-acetylglucosaminyl transferase enzyme (encoded by icaA) critical for polysaccharide intercellular adhesion (PIA) synthesis was not affected by the deletion of saeRS. Conclusions: Deletion of saeRS in S. epidermidis resulted in an increase in biofilm-forming ability, which was associated with increased eDNA release and up-regulated Aap expression. The increased eDNA release from SE1457DsaeRS was associated with increased bacterial autolysis and decreased bacterial cell viability in the planktonic/biofilm states. Comparision between SE1457 wild type strain and SA1457 SaeRS mutant strain after 4 hours and 12 hours of growth
2012-01-12 | E-GEOD-29309 | biostudies-arrayexpress
Project description:Background: Staphylococcus epidermidis (SE) has emerged as one of the most important causes of nosocomial infections. The SaeRS two-component signal transduction system (TCS) influences virulence and biofilm formation in Staphylococcus aureus. The deletion of saeR in S. epidermidis results in impaired anaerobic growth and decreased nitrate utilization. However, the regulatory function of SaeRS on biofilm formation and autolysis in S. epidermidis remains unclear. Results: The saeRS genes of SE1457 were deleted by homologous recombination. The saeRS deletion mutant, SE1457DsaeRS, exhibited increased biofilm formation that was disturbed more severely (a 4-fold reduction) by DNase I treatment compared to SE1457 and the complementation strain SE1457saec. Compared to SE1457 and SE1457saec, SE1457DsaeRS showed increased Triton X-100-induced autolysis (approximately 3-fold) and decreased cell viability in planktonic/biofilm states; further, SE1457DsaeRS also released more extracellular DNA (eDNA) in the biofilms. Correlated with the increased autolysis phenotype, the transcription of autolysis-related genes, such as atlE and aae, was increased in SE1457DsaeRS. Whereas the expression of accumulation-associated protein was up-regulated by 1.8-fold in 1457DsaeRS, the expression of an N-acetylglucosaminyl transferase enzyme (encoded by icaA) critical for polysaccharide intercellular adhesion (PIA) synthesis was not affected by the deletion of saeRS. Conclusions: Deletion of saeRS in S. epidermidis resulted in an increase in biofilm-forming ability, which was associated with increased eDNA release and up-regulated Aap expression. The increased eDNA release from SE1457DsaeRS was associated with increased bacterial autolysis and decreased bacterial cell viability in the planktonic/biofilm states.
2012-01-12 | GSE29309 | GEO
Project description:Methicillin resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen chief amongst bloodstream infecting pathogens. MRSA produces an array of human specific virulence factors that may contribute to immune suppression. Here, we defined the response of primary human phagocytes to infection with MRSA using RNA-Seq. We found that the overall transcriptional response to MRSA was weak both in the number of genes and the magnitude of response. Using an ex vivo bacteremia model with fresh human blood, we found that infection with live MRSA resulted in the down-regulation of genes related to innate immune response, and cytokine and chemokine signaling. This muted transcriptional response was conserved across diverse S. aureus clones but absent in heat-killed MRSA or blood infected with live Staphylococcus epidermidis. Importantly, the muted signature was also present in patients with S. aureus bacteremia. We next identified the master regulator SaeRS and the SaeRS-regulated pore-forming toxins as key mediators of transcriptional suppression. The impaired chemokine and cytokine responses were reflected by circulating protein levels in the plasma. MRSA elicits a soluble milieu that is restrictive in the recruitment of human neutrophils compared to strains lacking saeRS. Thus, MRSA blunts the inflammatory response resulting in impaired neutrophil recruitment, which could promote the survival of S. aureus during invasive infection.
2022-07-20 | GSE193219 | GEO
Project description:Streptococcus agalactiae (Group B Streptococcus, GBS) can colonize the human vaginal tract leading to both superficial and serious infections in adults and neonates. To study bacterial colonization of the reproductive tract in a mammalian system, we employed a murine vaginal carriage model. Using RNASeq, the transcriptome of GBS growing in vivo during vaginal carriage was determined. Over one-quarter of the genes in GBS were found to be differentially regulated during in vivo colonization as compared to laboratory cultures. A two-component system (TCS) homologous to the staphylococcal virulence regulator SaeRS was identified as being up-regulated in vivo. One of the SaeRS targets, pbsP, a proposed GBS vaccine candidate, was shown to be important for colonization of the vaginal tract. A component of vaginal lavage fluid acted as a signal to turn on pbsP expression via SaeRS. These data demonstrate the ability to quantify RNA expression directly from the murine vaginal tract and identify novel genes involved in vaginal colonization by GBS. They also provide more information about the regulation of an important virulence and colonization factor of GBS, pbsP, by the TCS SaeRS.
2018-02-06 | GSE109680 | GEO
Project description:Staphylococcus aureus is a significant Gram-positive human pathogenic bacterium that can give rise to skin and soft tissue infections and may also result in lethal diseases such as sepsis, pneumonia, endocarditis, osteomyelitis, etc. The cell wall of Staphylococcus aureus is a crucial immunogenic substance and participates in physiological processes like antibiotic resistance and virulence. The previous studies in the laboratory have indicated that the deletion of LCPB can upregulate the virulence of Staphylococcus aureus. However, the specific mechanisms by which LCPB regulates the virulence system of Staphylococcus aureus and its interaction with the host remain unclear. To explore the specific signal pathways by which lcpb regulates the interaction between Staphylococcus aureus and the host, we conducted proteomic experiments. This research discovered that both the knockout of LCPB and the application of WTA synthesis inhibitors can prevent the synthesis of the main component of the cell wall, wall teichoic acid (WTA), and upregulate the expression of excreted virulence factors such as HlgA, LukAB, and hla in Staphylococcus aureus. Subsequently, it was found that the central virulence regulation system agr of Staphylococcus aureus can respond to the reduction of WTA content, and the activation of agr is dependent on the expression of the two-component signal system saeRS.
2024-12-25 | PXD059233 |
Project description:Staphylococcus aureus is a Gram-positive human pathogen causing a variety of human diseases in both hospital and community settings. This bacterium is so closely associated with prophages that it is rare to find S. aureus isolates without prophages. Two phages are known to be important for staphylococcal virulence: the beta-hemolysin (hlb) converting phage and the Panton-Valentine Leukocidin (PVL) converting phage. The hlb-converting phage is found in more than 90% of clinical isolates of S. aureus. This phage produces exotoxins and immune modulatory molecules, which inhibit human innate immune responses. The PVL-converting phage produces the two-component exotoxin PVL, which can kill human leucocytes. This phage is wide-spread among community-associated methicillin resistant S. aureus (CA-MRSA). It also shows strong association with soft tissue infections and necrotizing pneumonia. Several lines of evidence suggest that staphylococcal prophages increase bacterial virulence not only by providing virulence factors but also by altering bacterial gene expression: 1) Transposon insertion into prophage regulatory genes, but not into the genes of virulence factors, reduced S. aureus killing of Caenorhabditis elegans.; 2) Although the toxins and immune modulatory molecules encoded by the hlb- converting phages do not function in the murine system, deletion of ϕNM3, the hlb-converting phage in S. aureus Newman, reduced staphylococcal virulence in the murine abscess formation model. 3) In a preliminary microarray experiment, prophages in S. aureus Newman altered the expression of more than 300 genes. In this research proposal, using microarray and high-throughput quantitative RT-PCR (qRT-PCR) technologies, we will identify the effects of the two important staphylococcal phages on the gene expression of S. aureus in both in vitro and in vivo conditions. This project is intended to be completed within one year. All the data – microarray, qRT-PCR and all the primer sequences- will be made available to public 6 month after completion. Data from this project will help us to understand the role of prophages in the S. aureus pathogenesis and can lead to development of a strategy to interfere with the pathogenesis process. Following strains were grown in TSA broth: Staphylococcus aureus USA300 (reference) Staphylococcus aureus USA300 with deletion of ϕSa2usa (Query) Staphylococcus aureus USA300 with deletion of ϕSa3usa (Query) Staphylococcus aureus USA300 Prophage-free mutant (Query) Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa2mw (Query) Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa3usa (Query) strain: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa (Query) RNA samples were harvested at early log, midlog and stationary phase.Samples were hybridized on aminosilane coated slides with 70-mer oligos.
2011-02-28 | E-GEOD-26623 | biostudies-arrayexpress