FurB knockout
Ontology highlight
ABSTRACT:
ORGANISM(S): Mycobacterium tuberculosis
PROVIDER: GSE5815 | GEO | 2006/09/15
SECONDARY ACCESSION(S): PRJNA97199
REPOSITORIES: GEO
Similar Datasets
Project description:We used DNA microarrays to define the M. tuberculosis whiB5 regulon and to study the variation of the global transcription profile in response of its induction. For this purpose we constructed a M. tuberculosis strain in which whiB5 was transcribed from an pristinamycin-inducible promoter and its transcriptional profile was compared on DNA microarray with the transcriptional profile of its control strain (empty vector-containing clone). WhiB5 induction for 15’ resulted in the induction of 26 genes, while induction for 3 h resulted in the induction of 58 genes. Interestingly, all of the 26 genes induced after 15 minutes of incubation with pristinamycin were still induced after 3 h of incubation. No repressed genes were identified. Among the induced genes we found the alternative sigma factor SigM and at least 12 genes previously shown to be regulated by this sigma factor, including those encoding the ESX-4 type VII secretion system. Interestingly, also the genes encoding ESX-2 type VII secretion system were strongly induced together with an operon probably involved in hydrogen metabolism in anaerobiosis. 10 representative genes were chosen from the microarray experiments and their expression was measured by quantitative RT-PCR using sigA as invariant internal control. In support to the gene expression profiling data, the mRNA levels of all selected genes was clearly higher in the whiB5 mutant strain relative to control.
2011-08-15 | GSE30299 | GEO
Project description:Comparison of gene expression profile of the whiB4 mutant strain of Mycobacterium tuberculosis with the wild type Mycobacterium tuberculosis H37RV Mtb WhiB4 mutant mRNA was compared with the mRNA of wtMtb H37RV under aerobic conditons
2012-07-24 | GSE37840 | GEO
Project description:We used DNA microarrays to define the M. tuberculosis whiB5 regulon and to study the variation of the global transcription profile in response of its induction. For this purpose we constructed a M. tuberculosis strain in which whiB5 was transcribed from an pristinamycin-inducible promoter and its transcriptional profile was compared on DNA microarray with the transcriptional profile of its control strain (empty vector-containing clone). WhiB5 induction for 15’ resulted in the induction of 26 genes, while induction for 3 h resulted in the induction of 58 genes. Interestingly, all of the 26 genes induced after 15 minutes of incubation with pristinamycin were still induced after 3 h of incubation. No repressed genes were identified. Among the induced genes we found the alternative sigma factor SigM and at least 12 genes previously shown to be regulated by this sigma factor, including those encoding the ESX-4 type VII secretion system. Interestingly, also the genes encoding ESX-2 type VII secretion system were strongly induced together with an operon probably involved in hydrogen metabolism in anaerobiosis. 10 representative genes were chosen from the microarray experiments and their expression was measured by quantitative RT-PCR using sigA as invariant internal control. In support to the gene expression profiling data, the mRNA levels of all selected genes was clearly higher in the whiB5 mutant strain relative to control. We compared the global gene expression of the whiB5 overexpressing strain and the control strain of Mtb in different conditions: after 15 min of induction or after 3 hours of induction. Hybridizations were performed using RNA extracted from three different biological samples. Each sample was hybridized twice through swap labeling of the respective cDNAs.
2011-08-14 | E-GEOD-30299 | biostudies-arrayexpress
Project description:Comparison of gene expression profile of the whiB4 mutant strain of Mycobacterium tuberculosis with the wild type Mycobacterium tuberculosis H37RV Mtb WhiB4 mutant mRNA was compared with the mRNA of wtMtb H37RV under aerobic conditons Aerbic conditions OD600 nm of 0.4, MtbWhiB4KO vs wtMtb, biological replicates: 3 wt Mtb H37RV and 3 MtbWhiB4 KO
2012-07-23 | E-GEOD-37840 | biostudies-arrayexpress
Project description:We report the effects of VapC21 overexpression on Mycobacterium tuberculosis H37Rv strain. The total RNA was isolated from M. tuberculosis harboring either pTetR-int or pTetR-Int-vapC21 the expression was induced with 50 ng/ml anhydrotetracycline for 24 hrs. We report the effect of deletion VapC21 on the transciptional profile of Mycobacterium tuberculosis Erdman strain. For RNA-seq analysis, total RNA was isolated from mid-log phase culture of either parental or △vapC21 mutant strain.
2020-10-05 | GSE154320 | GEO
Project description:We previously showed that increased expression of the principal sigma factor, SigA, mediates the capacity of Mycobacterium tuberculosis 210 strains to grow more rapidly in human monocytes, compared to other strains. To identify SigA-regulated genes that favor intracellular mycobacterial growth, we used microarray analysis to compare gene expression between a recombinant M. tuberculosis 210 strain bearing a sense sigA construct and a vector control during growth in MonoMac6 cells. The most strongly upregulated gene in the sense sigA transformant was Rv2416c, which has previously been shown to enhance intracellular survival of M. smegmatis, and has been designated as eis. Real-time PCR confirmed marked upregulation of eis mRNA by the intracellular sense sigA transformant, and lysates of this transformant contained high concentrations of the Eis protein. Chromatin immunoprecipitation demonstrated that SigA bound the eis promoter region in live bacteria. Deletion of the eis gene reduced growth of M. tuberculosis in macrophages, and complementation of eis reversed this effect. We conclude that SigA regulates eis expression, which in turn contributes to the enhanced capacity of the M. tuberculosis 210 strain to grow in human macrophages. The M. tuberculosis DNA microarray consisted of 4,295 70-mer oligonucleotides representing the 3,924 predicted open reading frames of the H37Rv strain (http://www.sanger.ac.uk) and 371 probes designed to detect sequences in the CDC1551 strain (http://www.tigr.org). The arrays were prepared by spotting oligonucleotides (Tuberculosis Genome set version 1.0, Operon Biotechnologies) onto poly-L-lysine coated glass microscope slides, as described (Pang et al., 2007). Total RNA from two independent experiments was prepared from M. tuberculosis harvested from infected MonoMac6 cells, as described above. cDNA synthesis, labeling, hybridization, scanning, image acquisition and normalization were performed, as described (Pang et al., 2007), and for each experiment, a dye flip was performed. Data were filtered by removing all spots that were below the background noise or flagged as âbadâ. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest mean background of the chip. The ratio of the average median intensity of Cy5 over the average median intensity of Cy3 was determined for each spot and the fold change values were calculated. Expression changes were considered significant if there was at least a 2-fold or higher change in expression between TB294-pSigA and TB294-pCV in three of the four array experiments.
2010-10-08 | E-GEOD-13780 | biostudies-arrayexpress
Project description:We used DNA microarrays to define the physiological roles of the Tap efflux pump in M. bovis BCG during the exponential and the stationary phase of in vitro growth. For this purpose we constructed a M. bovis BCG strain in which the tap gene was inactivated by the insertion of a hygromycin resistance cassette (Ω-hyg). When the gene expression patterns of the tap mutant were compared to the wild-type strain, almost no differences were observed during exponential growth; only seven genes slightly increased their expression. In contrast, more that 100 genes showed a variation in their level of expression during stationary growth. More than ten representative genes were chosen from the microarray experiments and their expression was measured by quantitative RT-PCR using sigA as invariant internal control. In support to the gene expression profiling data, the mRNA levels of all selected genes was significantly different in the tap mutant strain relative to control. A functional category analysis (http://tuberculist.epfl.ch/index.html) of the genes differentially expressed revealed a high proportion belonging to the Virulence, Detoxification, Adaptation (VDA), Intermediary Metabolism and Respiration (IMR), Conserved Hypotheticals (CH), and Cell Wall and Cell Processing (CWCP) categories suggesting a major adaptation to a stress generated by inactivation of the tap efflux pump gene.
2011-12-30 | GSE32249 | GEO
Project description:Tuberculosis (TB) is still a major life-threatening infectious disease, within which especially the rise of multidrug resistant TB (MDR-TB) is currently worrying. This study focuses on mechanisms of development of rifampicin resistance, since rifampicin seems to play an important role in the development of MDR-TB. To provide further insight in rifampicin resistance, we performed a genome-wide transcriptional profile analysis for Mycobacterium tuberculosis (M. tuberculosis) using microarray technology and qRT-PCR analysis. We exposed a rifampicin-susceptible H37Rv wild type (H37Rv-WT) and a rifampicin-resistant progeny H37Rv strain with a H526Y mutation in the rpoB gene (H37Rv-H526Y) to several concentrations of rifampicin, to define the effect of rifampicin on the transcription profile. Our study showed that there are resistance-dependant differences in response between both M. tuberculosis strains. Gene clusters associated with efflux, transport and virulence were altered in the rifampicin-resistant H37Rv mutant compared to the rifampicin-susceptible H37Rv-WT strain after exposure to rifampicin. We conclude that the small gene cluster Rv0559c-Rv0560c in the H37Rv-H526Y strain was remarkably up-regulated in the microarray analysis and qRT-PCR results and appeared to be dependent on rifampicin concentration and time of exposure. Therefore this study suggests that Rv0559c and Rv0560c play a pivotal role in rifampicin resistance of M. tuberculosis. Further investigation of Rv0559c and Rv0560c is needed to reveal function and mechanism of both genes that were triggered upon rifampicin exposure. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-139]
2013-04-21 | E-BUGS-139 | biostudies-arrayexpress
Project description:We previously showed that increased expression of the principal sigma factor, SigA, mediates the capacity of Mycobacterium tuberculosis 210 strains to grow more rapidly in human monocytes, compared to other strains. To identify SigA-regulated genes that favor intracellular mycobacterial growth, we used microarray analysis to compare gene expression between a recombinant M. tuberculosis 210 strain bearing a sense sigA construct and a vector control during growth in MonoMac6 cells. The most strongly upregulated gene in the sense sigA transformant was Rv2416c, which has previously been shown to enhance intracellular survival of M. smegmatis, and has been designated as eis. Real-time PCR confirmed marked upregulation of eis mRNA by the intracellular sense sigA transformant, and lysates of this transformant contained high concentrations of the Eis protein. Chromatin immunoprecipitation demonstrated that SigA bound the eis promoter region in live bacteria. Deletion of the eis gene reduced growth of M. tuberculosis in macrophages, and complementation of eis reversed this effect. We conclude that SigA regulates eis expression, which in turn contributes to the enhanced capacity of the M. tuberculosis 210 strain to grow in human macrophages.
2009-03-31 | GSE13780 | GEO
Project description:HupB is a 28 kDa in Mycobacterium tuberculosis that is co-expressed with the siderophores mycobactin and carboxymycobactin upon iron limitation. High levels of all the three components are seen in low iron (LI; 0.02 µg Fe / mL) organisms, with negligible expression in high iron organisms (HI; 8 µg Fe / mL). We generated a hupB knock out mutant of M. tuberculosis (H37Rv ∆ hupB) and studied the differential expression of genes upon iron limitation in the WT H37Rv and the mutant. The RNA transcripts of the WT H37Rv, grown under high and low iron conditions of growth were isolated and subjected to microarray analysis to identify the iron-regulated genes and second, the differential expression of genes in iron-limited H37Rv ∆ hupB vs iron-limited WT H37Rv was analysed. Microarray analysis was done commercially by Genotypic Technology (Bangalore, India), an authorised service provider for Agilent Technologies. The study revealed the up-regulation of all the mbt genes of the mycobactin biosynthetic machinery in LI - H37Rv and several other reported iron-regulated genes. The salient feature of this study is the failure of LI - H37Rv ∆ hupB to show any up-regulation of the mbt genes as compared to LI - H37Rv. Among several other genes influenced by HupB, the mutant strain showed low levels of mmpL5 and mmpS5 transcripts, whose expressed products are reported to be associated with siderophore transport and biosynthesis.
2014-03-18 | GSE53254 | GEO