Brucella melitensis global gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Brucella melitensis
PROVIDER: GSE11192 | GEO | 2009/05/14
SECONDARY ACCESSION(S): PRJNA106781
REPOSITORIES: GEO
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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:Brucellosis, an important bacterial zoonosis caused by Brucella species, has drawn increased attention around the world. As an intracellular pathogen, the ability of Brucella to deal with stress within the host cell is closely related to its virulence. The survival pressure on Brucella within a phagosome is considered similar to that during the stationary phase. Here, label-free proteomics approach was used to study the adaptive response of Brucella abortus (B. abortus) in the stationary stage. 182 down-regulated and 140 up-regulated proteins were found in the stationary-phase B. abortus. B. abortus adapted to adverse environmental changes by regulating virulence, reproduction, transcription, translation, stress response, and energy production. In addition, both logarithmic and stationary-phase B. abortus were treated with short-term starvation. The logarithmic-phase B. abortus restricted cell reproduction and energy utilization in response to nutritional stress. Additionally, the expression levels of some virulence-related proteins were identified as being significantly regulated during the transition from logarithmic to stationary phase or under starvation treatment, such as Type IV secretion system protein (T4SS), VjbR, and integration host factor (IHF). Altogether, we outlined adaptive mechanisms that B. abortus could employ during the growth and compared the differences between logarithmic and stationary-phase B. abortus in response to starvation.
2021-09-09 | PXD020869 | Pride
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:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Experiment Overall Design: E.coli cells were were grown and samples were taken at different times during growth: 90 min (early logarithmic phase), 150 min (mid-logarithmic phase), 240 min (late logarithmic phase), and 360 min (early stationary phase) for RNA extraction and hybridization on Affymetrix microarrays. This was done in triplicate and the raw data was analyzed using Microarray Analysis Suite version 5.0 (Affymetrix).
2008-06-15 | E-GEOD-7379 | biostudies-arrayexpress
Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Experiment Overall Design: E.coli cells were were grown and samples were taken at different times during growth: 90 min (early logarithmic phase), 150 min (mid-logarithmic phase), 240 min (late logarithmic phase), and 360 min (early stationary phase) for RNA extraction and hybridization on Affymetrix microarrays. This was done in triplicate and the raw data was analyzed using Microarray Analysis Suite version 5.0 (Affymetrix).
2008-06-15 | E-GEOD-7380 | biostudies-arrayexpress
Project description:Transcription analysis of ΔpknK mutant (LIX11) versus wild type H37Rv during logarithmic and stationary phase growth. This will elucidate the genes regulated by PknK during transition from logarithmic growth to stationary phase growth.
2012-06-02 | GSE37823 | GEO
Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Keywords: time course
2007-08-15 | GSE7380 | GEO
Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Keywords: time course
2007-08-15 | GSE7379 | GEO
Project description:Brucella type strains (B. abortus 544 and B. melitensis 16 M), field-isolates (B. abortus T and B. melitensis C) were independently cultivated six times on Tryptic Soy Broth at 37 °C in the presence of 5% CO2 until mid-logarithmic phase. The cells were harvested by brief centrifugation and the bacteria was inactivated using recommended ethanol precipitation procedure. Following which the cells were lysed, proteins quantified and the differentially expressed proteins among B. abortus and B. melitensis were identified using liquid chromatography-mass spectrometry (LC/MS) based label free quantitative proteomics analysis.
2020-06-11 | PXD006348 | Pride