RNA-seq analysis of transport deficient S. pneumoniae TIGR4 mutants
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ABSTRACT:
PROVIDER: PRJEB22066 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2073920.fastq.gz | Fastqsanger.gz | |||
| ERR2073921.fastq.gz | Fastqsanger.gz | |||
| ERR2073922.fastq.gz | Fastqsanger.gz | |||
| ERR2073923.fastq.gz | Fastqsanger.gz | |||
| ERR2073924.fastq.gz | Fastqsanger.gz |
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Project description:The polyamine transport operon in Streptococcus pneumoniae TIGR4 is necessary for survival in murine models of pneumococcal pneumonia. To date, there is no description of polyamine transport dependent pneumococcal gene expression. In this study, we compared gene expression between the wild-type and transport deficient (potABCD) TIGR4 by RNA-Seq analysis.
2017-08-14 | E-MTAB-5951 | biostudies-arrayexpress
Project description:The aim of this experiment is to determine the difference in protein expression, if any, in a mouse model of pneumococcal pneumonia using wild type and a polyamine transport operon deletion mutant strain of S. pneumoniae TIGR4, using expression proteomics. Eight week old female C57bl/6 mice were used in this study. The experimental design had two groups of 3 animals each that were administered 50 µL 1 X 107 CFU wild type S. pneumoniae TIGR4 or S. pneumoniae TIGR4 ΔpotABCD strain by intranasal instillation. The control group with three animals received 50 µL PBS. Mice were euthanized 4 hr and 12 hr post infection and lung tissues were harvested. The control group animals were euthanized 12 hr post infection.
2018-10-27 | PXD002300 | Pride
Project description:The polyamine biosynthesis gene, speE, in Streptococcus pneumoniae TIGR4 is necessary for survival in murine models of pneumococcal pneumonia. To date, there is no description of polyamine biosynthesis dependent pneumococcal gene expression. In this study, we compared gene expression between the wild-type and biosynthesis deficient (speE) TIGR4 by RNA-Seq analysis.
2023-01-01 | E-MTAB-6070 | biostudies-arrayexpress
Project description:Streptococcus pneumoniae TIGR4 Epigenomics
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Project description:Previous studies have indicated that PsaR of Streptococcus pneumoniae is a manganese-dependent regulator, negatively affecting the expression of at least seven genes. Here, we extended these observations by transcriptome and proteome analysis of psaR mutants in strains D39 and TIGR4. The microarray analysis identified three shared PsaR targets: the psa-operon, pcpA, and prtA. Additionally, we found 31 genes to be regulated by PsaR in D39 only, most strikingly a cellobiose-specific PTS and a putative bacteriocin operon (sp0141-sp0146). In TIGR4, 14 PsaR gene targets were detected, with the rlrA pathogenicity islet being the most pronounced. Proteomics confirmed most of the shared gene targets. To examine the contribution of PsaR to pneumococcal virulence, we compared D39 and TIGR4 wild-type (wt) and psaR-mutants in three murine infection models. During colonization, no clear effect was observed of the psaR mutation in either D39 or TIGR4. In the pneumonia model, small but significant differences were observed in the lungs of mice infected with either D39wt or ∆psaR: D39∆psaR had an initial advantage in survival in the lungs. Conversely, TIGR4∆psaR-infected mice had significantly lower bacterial loads at 24h only. Finally, during experimental bacteremia, D39∆psaR-infected mice had significantly lower bacterial loads in the blood stream than wt-infected mice for the first 24h of infection. TIGR4∆psaR showed attenuation at 36h only. In conclusion, our results show that PsaR of D39 and TIGR4 has a strain-specific role in global gene expression and in the development of bacteremia in mice.
2008-11-19 | GSE13505 | GEO
Project description:Streptococcus pneumoniae TIGR4 Genome sequencing
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Project description:Streptococcus pneumoniae TIGR4 Genome sequencing
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Project description:Streptococcus pneumoniae TIGR4 Raw sequence reads
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Project description:Previous studies have indicated that PsaR of Streptococcus pneumoniae is a manganese-dependent regulator, negatively affecting the expression of at least seven genes. Here, we extended these observations by transcriptome and proteome analysis of psaR mutants in strains D39 and TIGR4. The microarray analysis identified three shared PsaR targets: the psa-operon, pcpA, and prtA. Additionally, we found 31 genes to be regulated by PsaR in D39 only, most strikingly a cellobiose-specific PTS and a putative bacteriocin operon (sp0141-sp0146). In TIGR4, 14 PsaR gene targets were detected, with the rlrA pathogenicity islet being the most pronounced. Proteomics confirmed most of the shared gene targets. To examine the contribution of PsaR to pneumococcal virulence, we compared D39 and TIGR4 wild-type (wt) and psaR-mutants in three murine infection models. During colonization, no clear effect was observed of the psaR mutation in either D39 or TIGR4. In the pneumonia model, small but significant differences were observed in the lungs of mice infected with either D39wt or âpsaR: D39âpsaR had an initial advantage in survival in the lungs. Conversely, TIGR4âpsaR-infected mice had significantly lower bacterial loads at 24h only. Finally, during experimental bacteremia, D39âpsaR-infected mice had significantly lower bacterial loads in the blood stream than wt-infected mice for the first 24h of infection. TIGR4âpsaR showed attenuation at 36h only. In conclusion, our results show that PsaR of D39 and TIGR4 has a strain-specific role in global gene expression and in the development of bacteremia in mice. Microarray analysis was performed essentially as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). In short, 500 ml of CDM was inoculated with 10-20 colonies from agar plates, and these cultures were statically grown at 37°C. Samples for RNA isolation were taken when the cultures reached an optical density (OD600) of 0.2 (mid-log growth). RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures. Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (Hendriksen et al., 2007; Kloosterman et al., 2006). In all cases, dye-swapping was performed with one of the three biological replicates. Microarrays used in this study were constructed as described (Hendriksen et al., 2007; Kloosterman et al., 2006) and contain amplicons representing 2,087 ORFs of S. pneumoniae TIGR4 and 184 ORFs unique for S. pneumoniae R6, all spotted in duplicate.
2010-05-15 | E-GEOD-13505 | biostudies-arrayexpress
Project description:Purpose: We recently reported that isogenic deletion of lysine decarboxylase (ΔcadA/SP_0916), an enzyme that catalyzes the biosynthesis of polyamine cadaverine in Streptococcus pneumoniae TIGR4 results in loss of capsular polysaccharide (CPS), which constitutes a novel mechanism of regulation of CPS. Here, we conducted RNA-Seq to elucidate molecular mechanisms of CPS regulation in polyamine synthesis impaired pneumococci. Result: Significantly differentially expressed genes in ΔcadA represent pneumococcal pathways involved in the biosynthesis of precursors for CPS and peptidoglycan. Conclusion: We establish a possible link and interchange between two cellular processes such as high energy demanding capsule production and oxidative stress responses in polyamine synthesis impaired pneumococci (ΔcadA).
2019-09-30 | GSE130511 | GEO