Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression)
Ontology highlight
ABSTRACT:
ORGANISM(S): Mycobacterium tuberculosis H37Rv
SUBMITTER: Ruben Hartkoorn
PROVIDER: E-GEOD-34922 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE34919: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip) GSE34922: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression) Refer to individual Series
2012-01-20 | E-GEOD-35080 | biostudies-arrayexpress
Project description:The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF) SigF binding sites were determined by microarray analysis of anti-sigF immunoprecipitated DNA from H37Rv(ΔrsbW/sigF)::pmySigF compared to H37Rv(ΔrsbW/sigF)::pMY769 (both cultured with pristinamycin for 3 days). 4 biological replicates were performed.
2012-01-20 | E-GEOD-34919 | biostudies-arrayexpress
Project description:Singapore grouper iridovirus (SGIV) is the major agent that causes severe iridovirus diseases in grouper maricluture. Based on the genomic information, a DNA microarray, containing probes corresponding to 162 putative SGIV open reading frames (ORFs) was constucted. The viral microarrays wereused to classify the majority of SGIV transcripts into three temporal kinetic classes (immediate-early, IE; early, E; late, L) during an in vitro infection by their dependence on de novo protein synthesis inhibitor and viral DNA replication. Keywords: drug response To map the SGIV transcripts into temporal kinetic classes during the infection in vitro, GS cells were treated with drug inhibitors as previously described with some slight modifications. Briefly, GS monolayers were treated for 1 h prior to, during and throughout the viral infection with either CHX or PAA, which inhibited de novo protein synthesis and viral DNA replication mechanisms, respectively. To distinguish between viral IE transcripts and other transcripts, cells infected with SGIV (MOI of 5) or mock infected were treated with CHX (100 µg/ml), and then harvested at 8 h p.i. Whereas, viral E and L transcripts were categorized when cells infected with SGIV (MOI of 5) in the presence and absence of PAA (200 µg/ml), respectively. Until at 36 h p.i., cells were collected for RNA extraction. In a comparison analysis, we used Significance Analysis of Microarrays (SAM) software to identify the groups of different expression genes between the drug-treated samples and untreated samples. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Significance is based on an estimated of FDRâ¤5% and a 2 fold-change cutoff. Only the genes that met the following three criteria could be categorized into various temporal kinetic classes: (i) a viral gene was considered to be a IE transcript if its expression level increased or weakly affected under CHX treatment, (ii) a viral gene was considered to be a L transcript if its median intensity ratio in the PAA-treated samples was at least two-fold lower than that in the untreated samples and (iii) a viral gene was considered to be a E transcript if it expressed higher or remained within the two- fold range after PAA treatment but was inhibited distinctly by CHX treatment. To identify the significant differences in gene expression, a criterion with at least two-fold change combined with studentâs one sample t-test p value <0.05 was adopted.
2010-06-29 | E-GEOD-7154 | biostudies-arrayexpress
Project description:The Alphaproteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metal in these sites. It has been reported that C. crescentus responds to chromium exposure by altering expression of a large number of genes. In this work, we showed that the ECF sigma factor SigF is one of the regulatory proteins involved in the control of this transcriptional response. Microarray experiments from cells under dichromate stress showed that SigF controls a small regulon consisting of seven genes. Promoter analyses revealed that a conserved SigF-dependent sequence is located upstream of all but one gene of this regulon. Surprisingly, sigF itself was not found to be strongly auto-regulated under dichromate exposure. Furthermore, we showed that the second gene (CC3252) in the sigF operon acts as a negative regulator of SigF function, as overexpression of this putative membrane protein abolishes the transcriptional activation of sigF and its regulon under dichromate stress. Additionally, we found that substitution of one or both the conserved cysteines in the protein encoded by CC3252 (C131 and C181) affects the ability of this protein in maintaining expression of SigF-dependent genes at basal levels. Interestingly, we showed that the activation of SigF is not caused by reactive oxygen species generated as a consequence of dichromate exposure. Therefore, dichromate most probably may lead to conformational changes in the putative anti-sigma factor CC3252, releasing SigF to bind RNA polymerase core and drive transcription of its regulon. Three replicates perfomed with independent biological samples
2012-10-02 | E-GEOD-32406 | biostudies-arrayexpress
Project description:The mRNA 5â² cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5â² capped mRNA. We have purified P. falciparum eIF4E as a recombinant protein and demonstrated that it has canonical mRNA 5â² cap binding activity. We used this protein to purify P. falciparum full-length 5â² capped mRNAs from total parasite RNA. Microarray analysis comparing total and eIF4E-purified 5â² capped mRNAs shows that a subset of 34 features were more than two-fold under-represented in the purified RNA sample, including 19 features representative of nuclear transcripts. The uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. Keywords: total RNA vs purified capped mRNA The microarray data were obtained from four hybridizations using RNA from two independent GST-PfeIF4E purifications from separate malaria cultures.
2010-06-10 | E-GEOD-6356 | biostudies-arrayexpress
Project description:The sRNA F6 in M.tb is under the control of SigF, a non essential sigma factor known to be induced during nutrient starvation. We knocked out this sRNA in M. tb and subjected the strain to 24 hours starvation. RNA/RNA microarrays were then used in order to look at effects in gene expression between wildtype H37Rv and F6 knockout.
2021-01-17 | E-MTAB-9327 | biostudies-arrayexpress
Project description:The experiment was performed to search for genes regulated by the UV RESISTANT LOCUS (UVR8) under solar ultraviolet radiation (UV).
2013-01-15 | E-MTAB-1093 | biostudies-arrayexpress
Project description:Transcriptional profile comparison among PDIM positive and negative isolates. Standard in vitro exponential phase cultures of M. tuberculosis H37Rv ATCC27294 were plated on 7H11 plates. Individual colonies were sub-cultured in 7H9 broth and metabolically labeled with [14C] propionic acid. The apolar lipid fraction was then extracted from those cultures and assayed for PDIM (phthiocerol dimycocerosate) content via TLC. Individual isolates producing and deficient in PDIM were selected for performing transcriptional profile comparisons. Four M. tuberculosis clones derived from the same parental strain were compared. Two of them were PDIM producers while the other two were PDIM deficient. Two or four replicates were performed for each comparison using two different biological samples.
2010-05-16 | E-GEOD-17234 | biostudies-arrayexpress
Project description:GAS is a highly virulent Gram-positive bacterium. For the successful infection GAS express many virulence factors, which are clustered together with transcriptional regulators in distinct genomic regions. Ralp3 is a central regulator of the ERES region. In this study, we investigated the role of Ralp3 in GAS pathogenesis. To characterize the Ralp3 regulatory function on the whole genome level, GAS M49 wild type and Äralp3 mutant strains were comprehensively compared by two colour microarray analysis. Samples were taken from cultures in the transition phase. One condition experiment, wild type vs Δralp3. Biological replicates: 4 wild type and 4 mutant replicates per array.
2011-07-05 | E-GEOD-30397 | biostudies-arrayexpress
Project description:Following fertilisation, translation of stored, but previously translationally repressed transcripts, is instrumental in shaping the proteome of the early embryo of multicellular eukaryotes; further development relies on de novo transcription of the zygotic genome. A related process was evidenced in the unicellular protozoa Plasmodium berghei during transmission to the mosquito host where fertilisation and zygote development result in the formation of an entirely new cell type, the ookinete. DOZI and CITH are mRNP components that maintain mRNAs silent in the female precursor cell. In the absence of DOZI or CITH, hundreds of transcripts are destabilised, which does not block fertilization upon transmission to the mosquito host, but impairs further development of the malaria parasite. However, how many transcripts are bound by DOZI/CITH in these mRNPs and what are they remain unknown. Here, we investigated the extent of maternal contribution during post-fertilization development of P. berghei by RNA immunoprecipitation (RIP)-Chip data mining and provided further functional significance using gene tagging and gene knockout approaches. We provide conclusive evidence that in the rodent malaria parasite Plasmodium berghei 50% of the transcriptome of the female sexual precursor cell is stably associated with the translational repressors DOZI and CITH allowing morphogenesis of the zygote into the ookinete to proceed in the absence of RNA polymerase II transcription. Using in situ tagging with GFP we find for the first time novel genes that rely on translational repression on the 5' UTR. This maternal repressome provides the developing ookinete with coding potential for key molecules required during developmental progression: a near complete set of factors required for the gliding motility apparatus, but also protein trafficking, adhesins, proteases and other factors.
2014-10-23 | E-MTAB-2900 | biostudies-arrayexpress