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Evaluation of gene expression changes in tcs09 single and double mutants in the pneumococcal strain D39

ABSTRACT: Evaluation of gene expression changes in tcs09 single and double mutants in the pneumococcal strain D39

PROVIDER: PRJNA695258 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13563519_1.fastq.gz	Fastqsanger.gz
	SRR13563519_2.fastq.gz	Fastqsanger.gz
	SRR13563520_1.fastq.gz	Fastqsanger.gz
	SRR13563520_2.fastq.gz	Fastqsanger.gz
	SRR13563521_1.fastq.gz	Fastqsanger.gz

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Evaluation of gene expression changes in tcs09 single and double mutants in the pneumococcal strain D39

Project description:In order to elucidate the regulatory role of pneumococcal TCS09, a transcriptomic approach was performed using RNA-seq from bacterial cultures in chemical defined medium of single and double tcs09 mutants. A total of 69 genes presenting significant expression changes were selected for further evaluation and discussion. These 69 genes were classified accordingly to their biochemical function.

2021-02-22 | GSE165642 | GEO

Evaluation of gene expression changes in tcs08 single and double mutants in the pneumococcal strain TIGR4

Project description:In order to elucidate the regulatory role of pneumococcal TCS08, a transcriptomic approach was performed using microarray from bacterial cultures in chemical defined medium of single and double tcs08 mutants. A total of 159 genes presenting significant expression changes were selected for further evaluation and discussion. These 159 genes were classified accordingly to their biochemical function.

2018-05-01 | GSE108874 | GEO

Evaluation of gene expression changes in tcs08 single and double mutants in the pneumococcal strain TIGR4

Project description:Evaluation of gene expression changes in tcs08 single and double mutants in the pneumococcal strain TIGR4

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Global transcription pattern of virulent S. pneumoniae strain D39 (NCTC) compared to that of strains R6 and D39 (Lilly)

Project description:Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenicity. To date, the complete genome sequences have been reported for only two S. pneumoniae strains; TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report herein the genome sequences of two different isolates of strain D39 and the corrected sequence and updated annotation of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only 5 relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single base pair changes, 6 deletions, 4 insertions, and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed. Keywords: bacterial strain comparison, bacterial isolate comparison

2006-10-09 | GSE5375 | GEO

Streptococcus pneumoniae D39 spxB- mutant vs. D39 wild-type

Project description:Comparison of the Streptococcus pneumoniae D39 spxB- mutant vs D39. For DNA microarray analysis, D39 wild-type and two independently obtained D39spxB- mutants were grown as four, two and two biological replicates, respectively, in Glc-M17 under semi-aerobic conditions and harvested at an OD595 of approximately 0.25 (mid-exponential). The RNA of both D39spxB- strains was compared to D39 and the combined data was analyzed. All other procedures regarding microarray analyses were done as described before. A gene was considered differentially expressed when the fold change was ≥ 2, ≤ 0.5, with a Bayes p ≤ 0.00001 and when at least 7 measurements were available.

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Role of PsaR of Streptococcus pneumoniae D39 and TIGR4 in global gene expression and virulence

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

Double-strand breaks in spo11 mutants

Project description:Double-strand breaks in spo11 mutants

| PRJNA631751 | ENA

Investigation of pneumococcal two-component signal transduction system RR/HK06 in D39

Project description:We wanted to identify genes regulated by the two-component signal transduction system RR/HK06 in Streptococcus pneumoniae. We used microarray in order to discover regulated genes, investigating the effects of the over-expression of RR06 in D39 (serotype 2). Keywords: Gene Regulation

2006-12-23 | GSE5322 | GEO

Roles of relSpn in Stringent Response, Global Regulation, and Virulence of Serotype 2 Streptococcus pneumoniae D39

Project description:Transcriptome analysis of D39 rel+Spn and delta-relSpn strains treated with mupirocin revealed relSpn-independent (translation stress), relSpn-dependent (stringent response), and delta-relSpn-dependent changes suggesting that relSpn and (p)ppGpp amount play wide-ranging homeostatic roles in pneumococcal physiology, besides adjusting macromolecular synthesis and transport in response to nutrient availability.

2010-01-11 | GSE14750 | GEO

Streptococcus pneumoniae D39 spxB- mutant vs. D39 wild-type

Project description:Comparison of the Streptococcus pneumoniae D39 spxB- mutant vs D39. For DNA microarray analysis, D39 wild-type and two independently obtained D39spxB- mutants were grown as four, two and two biological replicates, respectively, in Glc-M17 under semi-aerobic conditions and harvested at an OD595 of approximately 0.25 (mid-exponential). The RNA of both D39spxB- strains was compared to D39 and the combined data was analyzed. All other procedures regarding microarray analyses were done as described before. A gene was considered differentially expressed when the fold change was M-bM-^IM-% 2, M-bM-^IM-$ 0.5, with a Bayes p M-bM-^IM-$ 0.00001 and when at least 7 measurements were available. One condition design comparision of two strains including a dye swap.

2013-08-08 | E-GEOD-45971 | biostudies-arrayexpress

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