Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA123683 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE19196: Detection of predicted small RNA of Legionella pneumophila GSE19200: Gene affected by deletion of 6S RNA in post-exponential phase Refer to individual Series
2010-06-24 | E-GEOD-19451 | biostudies-arrayexpress
Project description:Legionella pneumophila is a gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to test the hypothesis that sRNAs play a similar role in L. pneumophila. We used computational prediction followed by experimental verification to identify and characterize sRNAs encoded in the L. pneumophila genome. A 50-mer probe microarray was constructed to test the expression of predicted sRNAs in bacteria grown under a variety of conditions. This strategy successfully identified 22 expressed RNAs, out of which six were confirmed by northern blot and RACE. One of the identified sRNAs is highly expressed when the bacteria enter post exponential phase and computational prediction of its secondary structure reveals a striking similarity to the structure of 6S RNA, a widely distributed prokaryotic sRNA, known to regulate the activity of σ70-containing RNAP. A 70-mer probe microarray was used to identify genes affected by L. pneumophila 6S RNA in stationary phase. The 6S RNA encoded by the ssrS gene positively regulates expression of genes encoding type IVB secretion system effectors, stress response genes such as groES and recA as well as many genes with unknown or hypothetical functions. Deletion of 6S RNA significantly reduced L. pneumophila intracellular multiplication in both protist and mammalian host cells, but had no detectable effect on growth in rich media.
2010-01-01 | GSE19196 | GEO
Project description:Legionella pneumophila transcriptomic response of hfq mutant during post-exponential phase
| PRJNA183836 | ENA
Project description:Legionella pneumophila is a gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to test the hypothesis that sRNAs play a similar role in L. pneumophila. We used computational prediction followed by experimental verification to identify and characterize sRNAs encoded in the L. pneumophila genome. A 50-mer probe microarray was constructed to test the expression of predicted sRNAs in bacteria grown under a variety of conditions. This strategy successfully identified 22 expressed RNAs, out of which six were confirmed by northern blot and RACE. One of the identified sRNAs is highly expressed when the bacteria enter post exponential phase and computational prediction of its secondary structure reveals a striking similarity to the structure of 6S RNA, a widely distributed prokaryotic sRNA, known to regulate the activity of Ï70-containing RNAP. A 70-mer probe microarray was used to identify genes affected by L. pneumophila 6S RNA in stationary phase. The 6S RNA encoded by the ssrS gene positively regulates expression of genes encoding type IVB secretion system effectors, stress response genes such as groES and recA as well as many genes with unknown or hypothetical functions. Deletion of 6S RNA significantly reduced L. pneumophila intracellular multiplication in both protist and mammalian host cells, but had no detectable effect on growth in rich media. A microarray was designed for the detection of 101 predicted sRNAs by using OligiWiz version 2.1.3 (Nielsen et al., 2003, Wernersson & Nielsen, 2005). The prokaryotic setting was used to design 50-mers probes located, when possible, at the 3â end of the predicted genes. Probes for 10 negative controls, representing 10 genes of the L. pneumophila Paris plasmid, were also designed. Probes (Illumina) were dissolved in 50% DMSO to a final concentration of 30 uM and printed in triplicate on UltraGAPS coated glass slides (Corning) using a PerkinElmer SpotArray microarray printer. Fifteen micrograms of total RNA was labelled during cDNA synthesis using Superscript II reverse transcriptase (Invitrogen) and amino-allyl dUTP (Sigma). Bacterial genomic DNA was used as the reference channel on each slide to allow comparison of each time point and different samples (Talaat et al., 2002). Five micrograms of genomic DNA (gDNA) was labelled with amino-allyl dUTP by using Klenow fragment and random primers (Invitrogen) at 37 °C for 18 h. DNA was subsequently coupled to the succinimidyl ester fluorescent dye AlexaFluor 546 (for cDNA) or Alexa Fluor 647 (for gDNA) (Invitrogen) following manufacturerâs protocols. Hybridization and data acquisition were performed as previously described (Hovel-Miner et al., 2009).Very low density array, like the sRNA microarray used here, cannot be normalised with common procedure like total intensity or lowess. Local background was removed from spot signal intensity and the noise signal was estimated by recording the average signal intensity of 10 negative controls printed on the chip. Normalisation of signal intensity was carried out by calculating the fold increase over the noise signal value. Correlation of replicates using this normalisation procedure was ⥠0.95.
2010-06-24 | E-GEOD-19196 | biostudies-arrayexpress
Project description:The intracellular pathogen Legionella pneumophila (Lp) is a strict aerobe, surviving and replicating in environments where it frequently encounters reactive oxygen species, such as the nutrient-poor water environment and inside host cells. In many proteobacteria, the oxidative stress response is regulated by the LysR-type regulator OxyR; however, the role played by the OxyR homologue in Lp is still unclear. Therefore, we undertook the characterisation of the phenotypes associated with the deletion of OxyR in Lp. OxyR is dispensable for growth in rich broth, in amoeba and in human cultured macrophages, and for the survival of Lp in water. Nevertheless, the mutant was found to be more sensitive to hydrogen peroxide than the wild-type when grown to post-exponential phase, but not when grown to exponential phase. Moreover, the mutant is defective in forming isolated colonies on charcoal yeast extract (CYE) agar plates, but supplementation with anti-ROS molecules, such as pyruvate, α-ketoglutarate and catalase, rescued this defect. Further characterisation of this phenotype using a transcriptional reporter fusion and microarray analysis revealed that the deletion mutant is not defective for the expression of known anti-ROS genes which suggests that the growth defect on agar plates and the higher susceptibility to hydrogen peroxide are due to a broad change in the transcriptional response. Furthermore, the growth defect is suppressed when the mutant is grown on CYE plates made with agarose, suggesting that a compound present in typical agar is toxic for the oxyR mutant.
2021-07-20 | GSE87029 | GEO
Project description:The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. In this dataset we identified proteins regulated by CsrA in the human bacterial pathogen Legionella pneumophila by labelfree shotgun proteomics. WT and ∆csrA bacteria were grown to exponential phase in three biological replicates. Bacteria were lysed by sonication and extracted proteins were reducted, alkylated and digested with trypsin. The resulting peptide mixtures were analyzed by LC-MS/MS and proteins were identified by the MaxQuant software. In total of 1,448 proteins were quantified by the MaxLFQ algorithm in a labelfree approach. Cluster analysis showed that expression of almost all proteins was affected by the mutation of CsrA as about half of the identified proteins were up and half were down regulated. About 15% of the proteome (238 proteins) was strongly affected with 132 proteins significantly up and 109 significantly down regulated dependent on CsrA.
2017-02-13 | PXD004730 | Pride
Project description:Legionella pneumophila wild-type and hfq mutant were grown to post-exponential. The wild-type strain is used as the control.
2013-05-21 | GSE42905 | GEO
Project description:Legionella pneumophila is the causative agent of Legionnaires’ disease, an acute pulmonary infection. L. pneumophila is able to infect and multiply in both phagocytic protozoan, such as Acanthamoeba castellanii, and mammalian professional phagocytes. The best-known virulence determinant used by L. pneumophila to infect host cells is a Type IVb translocation system named Icm/Dot, which is used to modify the host cell functions to the benefit of the bacteria. To date the Icm/Dot systeme is known to translocate more than 100 effectors. While the transcriptional response of Legionella to the intracellular environement of A. castelannii as already been investigated, much less is known of how Legionella reacts transcriptionnally inside human macrophages. In this study, the transcriptome of L. pneumophila was monitored during exponential and post-exponential phase in rich AYE broth and during infection of human cultured macrophages by using microarray and a RNA amplification procedure called SCOTS to allow for the study of conditions of low bacterial loads. Among the genes induced intracellularly are those involved in amino acid synthesis pathway leading to L-arginine, L-histidne and L-proline as well as many transport system involved in amino acid and iron uptake. The Icm/Dot systems is not differentially expressed inside cells compare to the E phase control but the effectors are strongly induced. The intracellular transcriptome was further used to identify putative new Icm/Dot effectors and translocation was show to occur for 3 of them. This study provides a comprehensive view of how L. pneumophila react to the human macrophages intracellular environment.
2011-01-01 | GSE23029 | GEO
Project description:Transcriptomic change of Legionella pneumophila in water.
| PRJNA268489 | ENA
Project description:The LetA/S two-component system is essential for the survival of Legionella pneumophila in water
| PRJNA386103 | ENA