Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of SCOTS and standard microarray protocol

ABSTRACT: 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. To validate the use of SCOTS, we compare the expression patterns obtained by SCOTS to those obtained when a standard microarray protocol was used. RNA from bacteria in E phase was treated using SCOTS or a standard microarray protocol where the cDNA is labeled during the reverse transcription reaction as previously published. The resulting cDNA was hybridized to the microarray slides as described previously and data analysis was carried out the same way as for the SCOTS treated samples.

ORGANISM(S): Legionella pneumophila subsp. pneumophila str. Philadelphia 1

SUBMITTER: Sebastien Faucher

PROVIDER: E-GEOD-23032 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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. The aim of this work was to study the gene expression profile of Legionella during infection of macrophages infected at a low multiplicity of infection (MOI). SCOTS is a method that allows amplification of small amounts of bacterial RNA from infected host cells, while discarding host cell transcripts and ribosomal RNA. Before infection, macrophages derived from the THP-1 monocyte cell line were pre-treated with antibodies against the L. pneumophila major outer membrane protein, which increases the efficiency of bacterial entry into host cells . After 2 hours of infection, the macrophages were washed and treated with gentamicin for 1 hour, to synchronize the infection and kill extracellular bacteria, and cells were washed 3 times and fresh medium was added. Samples for the first time point (T0) were collected after the gentamicin treatment. Samples were also collected after 6h (T6) and 18h (T18). Samples from all conditions, including growth in AYE broth to exponential (E) or post exponential (PE) phase, were treated with three consecutive rounds of SCOTS and the resulting cDNA was labeled and hybridized to the microarray slides. As a reference channel, labeled gDNA was also hybridized. For each condition studied, three independent biological replicates and two technical replicates were analyzed, resulting in six replicates for each condition. The data was background subtracted and normalized by calculating the contribution of each spot to the total intensity and the ratio to gDNA was recorded. A one tailed student's T test was used for statistical analysis and the ratio between test conditions (PE, T0, T6 and T18) and the control conditions (E phase or T0) was calculated.

Project description:Legionella pneumophila (Lp) is an opportunistic pathogen and its survival in water is critical for human infection. Therefore, identifying the genes of Lp that are required for survival in water may help devise strategies to prevent Legionella outbreaks. In this study, we exposed Lp in rich medium and in an artificial freshwater medium (Fraquil) for 2, 6 and 24 hours to uncover the global transcriptomic changes of Lp in water. The repression of major metabolic pathways, such as division, transcription and translation, suggests that Lp enters a dormant state in water. The induction of the flagellar associated genes (flg, fli and mot), enhance entry genes (enh) and some Icm/Dot effectors suggests that Lp may be waiting to establish intracellular replication in suitable host. Moreover, many genes involved in resistance to antibiotic and oxidative stress were induced, suggesting that Lp may be more tolerant to environmental stresses in water. Indeed, Lp exposed to water is more resistant to erythromycin, gentamycin and kanamycin than those cultured in rich medium. Apart from this, the gene bdhA involved in the degradation of the intracellular energy storage compound poly-hydroxybutyrate is highly expressed in water. Further characterization shows that bdhA is positively regulated by RpoS during short-term exposure to water. The deletion mutant of bdhA had a survival defect in water at 37°C, demonstrating that this gene is important for maintaining the long-term survivorship of Lp in water. Other identified genes highly induced upon exposure to water could also be necessary for Lp to survive in water. Legionella pneumophila Philadelphia-1 strain JR32 was grown in AYE broth at 25°C shaking to OD600 of 1 in triplicate. Samples were taken for analysis; this is the control. Then the cultures were washed three times in Fraquil and resuspended in Fraquil to an OD600 of 1 and transfered to vessels of bioreactior (Biostat Q-plus). Samples were taken after 2h, 6h and 24h.

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. The 70-mer microarray representing all annotated ORFs of L. pneumophila has been previously described (Charpentier et al., 2008). RNA was extracted from ssrS mutant strain and the wild-type strain grown to PE phase. gDNA was used as a reference channel on each slides. Labelling of samples, hybridization strategy and data acquisition were performed as described in the Methods section. Local background was removed from spot signal intensity and normalization was carried out by calculating the fraction over the total signal intensity in both channel as previously described (Faucher et al., 2006). Signal levels that were lower than background in experiments and controls were filtered out. A total of six cDNA to reference ratios were recorded for each time point. Statistical analysis between mutant and wild-type strain was performed using unpaired one-tailed studentâs t-test. Genes were considered as differentially expressed if they demonstrated a ratio to control value of Â±2-fold with a p < 0.001.

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 Â°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 â¥ 0.95.

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Comparison of SCOTS and standard microarray protocol

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