Identification of MucR regulatory targets
Ontology highlight
ABSTRACT:
ORGANISM(S): Brucella melitensis 16M
SUBMITTER: Jenni Weeks
PROVIDER: E-GEOD-13647 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Quorum sensing (QS) is a communication system in bacteria that regulates gene expression in response to a small diffusible signal indicative of the bacterial population present. QS has been shown to regulate virulence genes, biofilm formation, cell division and secretion systems in a diverse set of bacteria. Brucella melitensis produces a QS signaling molecule, N-dodecanoyl homoserine lactone (C12-HSL), that interacts with a LuxR transcriptional regulator, VjbR. Deletion of vjbR has been found to highly attenuate intracellular survival of B. melitensis. The importance of QS in the regulation of genes necessary for the establishment and maintenance of B. melitensis infection has already been described for the virB and fla operons, however, a complete description of the vjbR regulon has not been described. Genome mining revealed seven luxR-like genes in B. melitensis, only one of which, vjbR, was confirmed to be attenuated for intracellular survival using macrophage assays. Using custom B. melitensis microarrays, we compared transcripts from wild type and ∆vjbR strains in the presence and absence of exogenous C12-HSL. Comparison of the transcriptomes obtained from culture-grown bacteria revealed bi-phasic gene regulation with expression peaks during exponential and early stationary growth phase; characterized by the regulation of 226 and 246 genes (respectively) by VjbR and 349 and 146 (respectively) altered by the addition of C12-HSL. Comparison of the VjbR and C12-HSL regulated genes provided confirmation that expression of 134 genes are regulated by both conditions with all but 3 genes inversely regulated. Overall, these results indicate that VjbR is an activator of gene expression at the exponential growth phase and exerts an equal effect on gene expression at the stationary growth phase; while C12-HSL has a repressive effect on gene expression at both growth stages examined and acts as an antagonist to VjbR activity. Direct transcript analysis comparing ∆vjbR with and without the addition of C12-HSL revealed that the AHL signal is able to direct gene expression in the absence of VjbR and exclusively exerted a positive influence on the expression of 56 genes, including a 93-fold increase in the expression of BabR, a second LuxR homologue. Genes regulated by these QS components included adhesins, proteases, antibiotic and toxin resistance genes, stress survival aids, including DNA repair genes and protein chaperones, transporters and porins, cellular membrane biogenesis genes, amino acid metabolism and transport, transcriptional regulators, and energy production genes. From these data, we conclude that QS is a global regulator of gene expression, and present potential virulence genes that may provide insight into the bacteria’s ability to establish and maintain the replicative vacuole (BCV) within the host cell. Keywords: Microarray comparison of a genetic deletion mutant and the addition of an effector molecule. Samples consist of RNA isolated from Brucella melitensis grown to logarithmic or stationary phase. RNA was extracted from wild type with and without exogenously added C12-HSL, and a ∆vjbR mutant. There are three biological replicates of each sample. Every Brucella melitensis open reading frame was printed in quadruplicate on each microarray. Each replicate was normalized against labeled Brucella melitensis 16M genomic DNA.
2010-04-23 | E-GEOD-13527 | biostudies-arrayexpress
Project description:Quorum sensing (QS) is a communication system in bacteria that regulates gene expression in response to a small diffusible signal indicative of the bacterial population present. QS has been shown to regulate virulence genes, biofilm formation, cell division and secretion systems in a diverse set of bacteria. Brucella melitensis produces a QS signaling molecule, N-dodecanoyl homoserine lactone (C12-HSL), that interacts with a LuxR transcriptional regulator, VjbR. Deletion of vjbR has been found to highly attenuate intracellular survival of B. melitensis. The importance of QS in the regulation of genes necessary for the establishment and maintenance of B. melitensis infection has already been described for the virB and fla operons, however, a complete description of the vjbR regulon has not been described. Genome mining revealed seven luxR-like genes in B. melitensis, only one of which, vjbR, was confirmed to be attenuated for intracellular survival using macrophage assays. Using custom B. melitensis microarrays, we compared transcripts from wild type and ∆vjbR strains in the presence and absence of exogenous C12-HSL. Comparison of the transcriptomes obtained from culture grown bacteria revealed bi-phasic gene regulation with expression peaks during exponential and early stationary growth phase; characterized by the regulation of 226 and 246 genes (respectively) by VjbR and 349 and 146 (respectively) altered by the addition of C12-HSL. Comparison of the VjbR and C12-HSL regulated genes provided confirmation that expression of 134 genes are regulated by both conditions with all but 3 genes inversely regulated. Overall, these results indicate that VjbR is an activator of gene expression at the exponential growth phase and exerts an equal effect on gene expression at the stationary growth phase; while C12-HSL has a repressive effect on gene expression at both growth stages examined and acts as an antagonist to VjbR activity. Direct transcript analysis comparing ∆vjbR with and without the addition of C12-HSL revealed that the AHL signal is able to direct gene expression in the absence of VjbR and exclusively exerted a positive influence on the expression of 56 genes, including a 93-fold increase in the expression of BabR, a second LuxR homologue. Genes regulated by these QS components included adhesins, proteases, antibiotic and toxin resistance genes, stress survival aids, including DNA repair genes and protein chaperones, transporters and porins, cellular membrane biogenesis genes, amino acid metabolism and transport, transcriptional regulators, and energy production genes. From these data, we conclude that QS is a global regulator of gene expression, and present potential virulence genes that may provide insight into the bacteria’s ability to establish and maintain the replicative vacuole (BCV) within the host cell. Keywords: Microarray comparison of a genetic deletion mutant and the addition of an effector molecule. Samples consist of RNA isolated from Brucella melitensis grown to logarithmic or stationary phase. RNA was extracted from a ∆vjbR mutant with and without exogenously added C12-HSL. There are three biological replicates of each sample. Every Brucella melitensis open reading frame was printed in quadruplicate on each microarray. Each replicate was normalized against labeled Brucella melitensis 16M genomic DNA.
2010-04-23 | E-GEOD-13633 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE13527: Expt 1: The contribution of vjbR and N-dodecanoyl homoserine lactone on gene regulation in Brucella melitensis GSE13633: Expt 2: The contribution of vjbR and N-dodecanoyl homoserine lactone on gene regulation in Brucella melitensis Refer to individual Series
2010-04-23 | E-GEOD-13634 | biostudies-arrayexpress
Project description:Brucella spp. is an intracellular pathogen in vivo. The intracellular B. melitensis transcriptome was determined by initially enriched and then amplified B. melitensis RNA from total RNA of B. melitensis-infected HeLa cells. Analysis of microarray results identified 161 and 115 genes differentially expressed at 4 and 12 h p.i., respectively. Most of the genes (78%) differentially expressed were down-regulated at the earliest time point, but up-regulated (75%) at 12 h p.i. The analysis of the results indicates that Brucella undergo an adaptation period during the first 4 h p.i. that is overcome by 12 h p.i., permitting Brucella to replicate intracellularly. Specific genes and biological processes identified in this study will further help elucidate how Brucella act during the early infectious process to their eventual benefit and to the detriment of the naM-CM-/ve host. Keywords: Time course study of intracellular B. melitensis gene expression Gene expression of the intracellular Brucella melitensis was determined at 4 and 12 h p.i. We generated the following samples: A) B. melitensis total RNA enriched and amplified from total RNA of B. melitensis-infected HeLa cells at 4 h p.i.; B) Total RNA isolated from B. melitensis-infected HeLa cells at 4 h p.i.; C) B. melitensis total RNA enriched and amplified from total RNA of B. melitensis-infected HeLa cells at 12 h p.i.; D) Total RNA isolated from B. melitensis-infected HeLa cells at 12 h p.i. B. melitensis total RNA was initially enriched and then amplified from total RNA of B. melitensis-infected HeLa cells at 4 and 12 h p.i. in quadruplicate, indirectly labeled and co-hybridized against B. melitensis gDNA to a custom 3.2K B. melitensis oligo-array (n = 8). As there was a possibility that some HeLa transcripts cross-hybridize with probes on B. melitensis microarrays, the original total RNA from B. melitensis-infected HeLa cells were also co-hybridized against B. melitensis gDNA to B. melitensis oligo-arrays (n = 8), and any oligospots with signals were considered non-specific and eliminated from all analysis to avoid false positive gene detection. The intracellular B. melitensis gene expression was compared to the gene expression of the inoculum (n = 2). Every Brucella melitensis open reading frame was printed in triplicate on each microarray, thereby providing three technical replicates for each biological replicates. Each replicate was normalized against labeled Brucella melitensis genomic DNA.
2012-12-27 | E-GEOD-14704 | biostudies-arrayexpress
Project description:In a time course study, we characterized global gene expression profile of B. melitensis-infected bovine Peyer patches in the first 4 h p.i. Microarray analysis revealed that 2,916 bovine genes were detected as differentially expressed (z-score p < 0.025) in loops inoculated with virulent B. melitensis 16M compared with controls between 15 min and 4 h post-infection. From these genes, 2,286 (78%) were up- and 630 (22%) were down-regulated. Specific genes and biological processes identified in this study will further help elucidate how both host and Brucella interact during the early infectious process to the eventual benefit of the pathogen and to the detriment of the naM-CM-/ve host. Microarrays were used to examine the transcriptional profiles of bovine intestinal Peyer patches infected with wild type Brucella melitensis 16M across five time points (15 min, 30 min, 1, 2 and 4 hours). Intestinal loops inoculated with cell culture medium were used as a control. Experiments were performed in quadruplicate (bovine ligated ileal loops surgeries were performed with four calves), generating a total of 40 arrays.
2013-10-15 | E-GEOD-41835 | biostudies-arrayexpress
Project description:A whole genome expression comparision between wild type B. melitensis 16M and M-NM-^TBM-LOV-HK (M-NM-^TBMEII0679) B. melitensis strains grown in broth culture to determine genes directly and indirectly regulated by BM-LOV-HK. 6 samples, 3 wild type B. melitensis 16M replicates, 3 M-NM-^TBM-LOV-HK B. melitensis replicates
2013-06-15 | E-GEOD-42599 | biostudies-arrayexpress
Project description:Brucella ovis causes an important disease characterized by decreased fertility in rams, sporadic abortions in ewes and increased lamb mortality. The live attenuated B. melitensis Rev.1 vaccine is considered the best vaccine available against this infection. However, this vaccine shows variable protective efficacy ranging from 40% to 100%.The objective of this study was to identify possible correlates of protective response to B. ovis infection through the characterization by microarray hybridization and real-time RT-PCR of inflammatory and immune response genes upregulated in rams previously immunized with the B. melitensis Rev 1 vaccine strain and experimentally challenged with B. ovis. Gene expression profiles were compared before and after challenge with B. ovis between rams protected and those vaccinated but found infected after challenge. The genes upregulated in vaccinated and protected rams provide possible correlates of protective response to B. ovis infection in rams immunized with the B. melitensis Rev 1 vaccine. Gene expression profiles were compared before and after vaccination and challenge with B. ovis between rams protected with the B. melitensis Rev 1 vaccine strain and those vaccinated but infected after challenge. Total RNA was isolated from buffy coat samples before vaccination (T0), after vaccination and before challenge (T1) and 60 days post challenge (T2) using TriReagent (Sigma, St. Louis, MO, USA)
2010-06-25 | E-GEOD-13202 | biostudies-arrayexpress
Project description:The four-carbon sugar erythritol is an important component of B. melitensis pathogenesis. To determine the transcriptional response to erythritol, B. melitensis strain 16M was grown in the presence of either glucose or erythritol as a sole carbon source. Two control samples (glucose) and two experimental samples (erythritol) were analyzed on Nimblegen B. melitensis microarray chips.
2013-03-01 | E-GEOD-37819 | biostudies-arrayexpress
Project description:In this study we report that B. melitensis at the late logarithmic phase of growth are more invasive for HeLa cells than at mid logarithmic or stationary growth phases. Microarray analysis of B. melitensis gene expression identified 414 up- and 40 down-regulated genes in late-log growth phase compared to the stationary growth phase. The vast majority of the up-regulated genes in late-log cultures were those associated with DNA replication, transcription and translation, intermediate metabolism, energy production and conversion, membrane transport and cell envelope, biogenesis and outer membrane, while the down-regulated genes were distributed among several functional categories. This first Brucella global gene expression study provides novel information on growth phase-specific gene regulation important not only for understanding Brucella physiology but also the initial molecular interactions between Brucella and its host. Keywords: Comparison bacterial growth phase normalized to genomic DNA There are two kind of samples consisting of RNA isolated from Brucella melitensis grown logarithmically or at stationary phase. There are four biological replicates of each sample. Every Brucella melitensis open reading frame was printed in triplicate on each microarray, thereby providing three technical replicates for each biological replicates. Each replicate was normalized against labeled Brucella melitensis genomic DNA.
2010-05-19 | E-GEOD-11192 | biostudies-arrayexpress
Project description:Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic. No identified bacterial factors or mechanisms account for this difference in virulence. To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth. Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport. Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens. Comparison of total bacterial RNA from Brucella melitensis infected murine macrophages to broth grown bacteria
2012-12-01 | E-GEOD-34495 | biostudies-arrayexpress