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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Low Zn vs high Zn in CDM

ABSTRACT: Comparison of the Streptococcus pneumoniae D39 wild-type in CDM Plus 0mM Zn and CDM plus 0.2 mM Zn Two condition design comparison of Wild-type strain including a dye swap

ORGANISM(S): Streptococcus pneumoniae D39

SUBMITTER: Sulman Shafeeq

PROVIDER: E-GEOD-29235 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional response of Streptococcus pneumoniae to Zn2+-limitation and the repressor/activator function of AdcR

Project description:Zinc (Zn2+) is an important trace metal ion that has been shown to regulate the expression of several (virulence) genes in streptococci. Previously, we analyzed the genome-wide response of S. pneumoniae to Zn2+-stress. In this work, we have performed a transcriptomic analysis to identify genes that are differentially expressed under intracellular Zn2+-limitation. This revealed a number of genes that are highly upregulated in the absence of extracellular Zn2+, amongst which the genes belonging to the regulon of the Zn2+-responsive repressor AdcR, like adcBCA, encoding a Zn2+-dependent ABC-uptake system, adcAII, encoding a Zn2+-binding lipoprotein, and also virulence genes belonging to the Pht family (phtA, phtB, phtD and phtE). Using transcriptome analysis, lacZ-reporter studies, in vitro DNA binding experiments, and in silico operator predictions, we show that AdcR directly represses the promoters of adcRCBA, adcAII-phtD, phtA, phtB and phtE in the presence of Zn2+. AdcR can also function as an activator, since in the presence of Zn2+ it directly induces expression of adh that encodes a Zn2+-containing alcohol dehydrogenase. In conclusion, the genome-wide transcriptional response of S. pneumoniae to Zn2+-limitation was established, which is mainly mediated via direct regulation by the Zn2+-dependent regulator AdcR. Two condition design comparison of Wild-type strain including a dye swap Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE29234: adcR mutant vs wild type D39 GSE29235: Low Zn vs high Zn in CDM

2011-05-13 | E-GEOD-29236 | biostudies-arrayexpress

adcR mutant vs wild type D39

Project description:Comparison of the Streptococcus pneumoniae D39 adcR mutant vs D39 wild type in CDM plus 0.2mM Zn One condition design comparison of two strains including a dye swap

2011-05-13 | E-GEOD-29234 | biostudies-arrayexpress

ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae

Project description:This SuperSeries is composed of the following subset Series: GSE33033: ahrC mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine GSE33034: argR1 mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine GSE33035: argR1-ahrC mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine GSE33036: Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine Refer to individual Series

2011-11-02 | E-GEOD-33043 | biostudies-arrayexpress

CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae

Project description:This SuperSeries is composed of the following subset Series: GSE31815: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Glucose at MID-log growth phase GSE31816: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + GLucose at transition-phase of growth (TS) GSE31817: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Galactose at MID-log growth phase GSE31818: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + galactose at transition-phase of growth (TS) Refer to individual Series

2011-09-30 | E-GEOD-31819 | biostudies-arrayexpress

Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine

Project description:Comparison of Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine to define the genome-wide transcriptional response to arginine. Details described in Kloosterman TG and Kuipers OP. ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae. JBC 2011 Two condition design comparison of wild type strain

2011-11-02 | E-GEOD-33036 | biostudies-arrayexpress

High low copper

Project description:Comparison of the Streptococcus pneumoniae D39 strain with 0mM compared to 0.05 mM in CDM Two condition design comparision of one strains including a dye swap

2011-07-10 | E-GEOD-30413 | biostudies-arrayexpress

copY Mutant compared to D39 wild-type

Project description:Comparison of the Streptococcus pneumoniae D39 copY-stop mutant compared to D39 wild type in CDM without added copper One condition design comparision of two strains including a dye swap

2011-07-10 | E-GEOD-30414 | biostudies-arrayexpress

High Ni2+ vs Low Ni2+

Project description:By using the transcriptomic approach, we have elucidated the effect of Ni2+ on the global gene expression of S. pneumoniae D39 by identifying several differentially expressed genes/operons in the presence of a high extracellular concentration of Ni2+. The genes belonging to the AdcR regulon (adcRCBA, adcAII-phtD, phtA, phtB and phtE) and the PsaR regulon (pcpA, prtA and psaBCA) were highly upregulated in the presence of Ni2+. We have further studied the role of Ni2+ in the regulation of the AdcR regulon by using ICP-MS analysis, electrophoretic mobility shift assays and transcriptional lacZ-reporter studies, and demonstrate that Ni2+ is directly involved in the derepression of the AdcR regulon via the Zn2+-dependent repressor AdcR, and has an opposite effect on the expression of the AdcR regulon as compared to Zn2+. Comparison of the Streptococcus pneumoniae D39 wild-type in CDM Plus 0.5 mM Ni and CDM plus 0 mM Ni2+ Two condition design comparison of two conditions 0.5 mM Ni2+ Vs 0 mM Ni2+ including a dye swap

2015-11-20 | E-GEOD-73850 | biostudies-arrayexpress

ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Glucose at MID-log growth phase

Project description:Comparison of Streptococcus pneumoniae D39 ccpA mutant compared to D39 wild type in CDM with glucose as sole carbon source to define the regulon of carbon catabolite control protein CcpA under this condition Details described in Carvalho SM, Kloosterman TG, Neves AR, Kuipers OP. CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae. Plos One 2011 One condition design comparision of two strains including a dye swap

2011-09-30 | E-GEOD-31815 | biostudies-arrayexpress

ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + GLucose at transition-phase of growth (TS)

2011-09-30 | E-GEOD-31816 | biostudies-arrayexpress

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