Staphylococcus aureus HG001
Ontology highlight
ABSTRACT:
ORGANISM(S): Staphylococcus aureus
SUBMITTER: Pierre Nicolas
PROVIDER: E-GEOD-70043 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Transcriptomic analysis of Bacillus subtilis hfq mutant in exponential phase of growth. Wild-type strain and hfq mutant cells in exponentially growth phase were subjected to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. Hfq does not appear to influence B.subtilis RNA patterns during the exponential phase to any significant extent, at least in cells grown in rich medium. This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ?hfq mutant were examined at OD ~0.5 in LB medium. Two biological replicates were analyzed.
2015-06-22 | E-GEOD-66891 | biostudies-arrayexpress
Project description:Transcriptomic analysis of Bacillus subtilis wild-type strain and hfq mutant in stationary phase of growth using to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. 97 transcription units (representing 134 genes) were found significantly different between the wild-type and the ?hfqBs strains in the stationary cultures performed in rich LB medium. This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ?hfq mutant were examined 5 h after the onset of stationary phase in LB medium. Two biological replicates were analyzed.
2015-06-22 | E-GEOD-66892 | biostudies-arrayexpress
Project description:We report the condition-dependent transcriptome of S. aureus HG001, a derivative of strain NCTC 8325, by strand-specific tiling array hybridizations. More than 40 experimental conditions were investigated ranging from optimal in vitro growth to interaction with host cells. Analyses included the systematic mapping of transcription units, annotation of non-coding RNAs, the classification of promoters according to their dependency on SigA and SigB, and the prediction of potentially new transcription factor target sites. Antisense RNAs being of particular interest because of the small number of alternative sigma factors used by S. aureus were found to be relatively rare, overlapping only 6% of the annotated coding genes. RNA samples prepared from S. aureus HG001 grown in shake flask or cell culture infection experiments were reverse transcribed, labeled and hybridized to tiling arrays. Hybridizations were performed in triplicate using RNA isolated from independent cultures.
2016-03-08 | E-GEOD-70040 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-06-22 | E-GEOD-66893 | biostudies-arrayexpress
Project description:AbrB is a global gene regulator involved in transition phase phenomena in Bacillus subtilis. It participates in a complex regulatory network governing the expression of stationary phase functions. AbrB was previously found to be phosphorylated on serine 86 located close to its C-terminal oligomerization domain. Here we report that AbrB can be phosphorylated by three B. subtilis serine/threonine kinases expressed during the transition and stationary phase: PrkC, PrkD and YabT. Our in vitro findings suggest that AbrB phosphorylation impedes its DNA binding and abolishes binding cooperativity. In vivo we established that a phospho-mimetic mutation abrB S86D leads to a significant loss of AbrB control over several key target functions: exoprotease production, competence development and sporulation. A wider transcriptome analysis of abrB S86D and S86A mutant strains revealed deregulation of a large number of target genes. We therefore propose that AbrB phosphorylation serves as an additional input for fine-tuning the activity of this ambiactive gene regulator. A 6 arrays study of the transcriptome profiles of B. subtilis strain 168, abrB-S86A and abrB-S86D mutant strains. Compared to the wild-type strain the mutant strains were used to test the effect of the phosphorylation of AbrB on ser-86 (using a phosphomimetic of AbrB (abrB-S86D strain) or its absence (abrB-S86A strain) on transcript profiles.
2014-04-11 | E-GEOD-56723 | biostudies-arrayexpress
Project description:Bacillus subtilis mutants lacking the SMC-ScpAB complex are severely impaired for chromosome condensation and partitioning, DNA repair, and cells are not viable under standard laboratory conditions. We isolated suppressor mutations that restored the capacity of a smc deletion mutant (Δsmc) to grow under standard conditions. These suppressor mutations reduced chromosome segregation defects and abrogated hypersensitivity to gyrase inhibitors of Δsmc. Three suppressor mutations were mapped in genes involved in tRNA aminoacylation and maturation pathways. A transcriptomic survey of isolated suppressor mutations pointed to a potential link between suppression of Δsmc and induction of the stringent response. This link was confirmed by (p)ppGpp quantification which indicated a constitutive induction of the stringent response in multiple suppressor strains. Furthermore, sublethal concentrations of arginine hydroxamate (RHX), a potent inducer of stringent response, restored growth of Δsmc under non permissive conditions. We showed that production of (p)ppGpp alone was sufficient to suppress the thermosensitivity exhibited by the Δsmc mutant. Our findings shed new light on the coordination between chromosome dynamics mediated by SMC-ScpAB and other cellular processes during rapid bacterial growth. A 7 array study of the transcriptome profiles of B. subtilis strain 168, CB167 and CB169: ylbM and ywlC mutant strains. Compared to the wild-type strain the mutant strains were used to characterize the effect of the mutation on transcript profiles in order to understand the suppression of the SMC deletion.
2015-09-23 | E-GEOD-73315 | biostudies-arrayexpress
Project description:Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an excellent coverage of the transcriptome of this bacterium. In addition to the Genbank annotation 1583 new segments of the chromosome were identified as transcribed and have transcription levels reported in the data matrix. RNA samples prepared from B. subtilis 168 grown under 104 experimental conditions were reverse transcribed, labeled and hybridized to tiling arrays. Most hybridizations were performed in duplicate or triplicate using RNA isolated from independent cultures. All experiments were performed with strain BSB1 which is a tryptophan-prototrophic (trp+) derivative of the 168 trpC2 strain.
2012-03-07 | E-GEOD-27219 | biostudies-arrayexpress
Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus. delta rho and wild type
2016-03-08 | E-GEOD-70041 | biostudies-arrayexpress
Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift. genomic DNA from wild type
2016-03-08 | E-GEOD-70042 | biostudies-arrayexpress
Project description:Comprison of the transcriptome of wild type Bacillus subtilis to the mutants sigW, rasP and prsW to select all candidate sigW regulated genes. We identified 89 genes as being sigW regulated, including several non-coding RNA's. The effects of rasP and prsW mutations on sigW regulated genes were relatively mild, implying that RasP or PrsW are not strictly required for sigW activation. The rasP mutant has a peliotropic phenotype, affecting competence development, protein secretion and membrane protein production. We show that these are not mirrored in the transcriptome, suggesting that RasP exerts its effects at the post transcriptional level. RNA samples prepared from B. subtilis 168 and mutants sigW, rasP, and prsW were grown in Luria Bertani broth to O.D 600nm 1.0 were reverse transcribed, labeled and hybridized to tiling arrays. All hybridizations (except prsW which was in duplicate) were performed in triplicate using RNA isolated from independent cultures.
2013-01-02 | E-GEOD-35236 | biostudies-arrayexpress