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Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

ABSTRACT: Comparing the transcriptional responses of Bacillus subtilis strains WN624 and WN1106 at 5 kPa and 101 kPa. WN1106 is a 5 kPa-evolved strain with increased fitness compared to ancestor-WN624 strain at 5 kPa. This experiment probed the difference in response when the strains are grown at 5 kPa.

ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168

PROVIDER: GSE50653 | GEO | 2014/03/14

SECONDARY ACCESSION(S): PRJNA218207

REPOSITORIES: GEO

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Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

Project description:Comparing the transcriptional responses of Bacillus subtilis strains WN624 and WN1106 at 5 kPa and 101 kPa. WN1106 is a 5 kPa-evolved strain with increased fitness compared to ancestor-WN624 strain at 5 kPa. This experiment probed the difference in response when the strains are grown at 5 kPa. Two-condition experiment, 5 kPa vs. 101 kPa, for both strains. And two component condition of WN1106 compared to WN624 at either 5 kPa or 101 kPa. 4 pressure comparisons.

2014-03-14 | E-GEOD-50653 | biostudies-arrayexpress

Bacillus subtilis subsp. subtilis str. 168

Project description:Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

| PRJNA218207 | ENA

Transcriptional profiling along lineages of Bacillus subtilis strains with increasingly reduced genomes.

Project description:To investigate which cellular functions may be perturbed along the branches of a synthetic evolutionary tree obtained by incremental deletions of large genomic regions, we subjected six Bacillus subtilis strains to transcriptome profiling. These six strains are : MS (~3.98 Mbp), which is already a genome-reduced derivative of the B. subtilis 168 (~4.22 Mbp) and the root of our evolutionary tree; MGP254 (~2.73 Mbp), the farthest genome-reduced strain; MGP234 (~2.81 Mbp), another terminal leaf in our tree; MGP181 (~2.87 Mb) and MGP192 (~2.85 Mbp), two intermediate strains in the ancestor lineage common to MGP254 and MGP234; and finally MGP229 (2.82 Mbp), an intermedidate strain between MGP192 and MGP254 (i.e. an ancestor of MGP254 but not MGP234). The vast majority of genes conserved in the six strains displayed no differential expression, showing the robustness of the cell transcriptional network against massive genome reduction. Among deregulated genes, more than half could be explained by loss of known functions and aberrant transcription at deletion boundaries. An unexpected common feature in genome-reduced strains was the upregulation of genes involved in cell responses to oxidative stresses.

2023-02-15 | GSE207089 | GEO

Trancriptional profiling of Bacillus subtilis BsB1 and NCIB3610 rho-deletion mutant

Project description:With these experiments we investigate the impact of the deletion of the gene encoding transcription termination Rho on the transcriptomes of two different Bacillus subtilis strains, BsB1 and NCIB3610. The results confirm massive increase of antisense transcription initially observed with tiling arrays in B. subtilis strain 1012 (Nicolas et al. 2012; PMID:22383849; GSE27303).

2017-07-10 | GSE94303 | GEO

Comparison of the transcription profile of B. subtilis clpX strain with B. subtilis clpX spx strain, reporting on Spx activity

Project description:In B. subtilis the unusual transcription factor Spx controls the thiol stress response regulon (Nakano et al 2003 PNAS 100:13603; Rochat et a. 2012 NAR 40:9751). Under normal growth conditions Spx is constantly degraded by the AAA+ protease complex ClpXP (Nakano et al 2001 MolMi 42:383). Comparing a B. subtilis clpX strain, where Spx levels are high, with a B. subtilis clpX spx double mutant strain which lacks Spx, will report on Spx dependent transcriptional control. We prepared total RNA of exponentially grown B. subtilis clpX and of B. subtilis clpX spx cells.

2014-09-01 | GSE50102 | GEO

Membrane protein overproduction stress in Bacillus subtilis

Project description:Comparison of the transcriptome of Bacillus subtilis under going membrane protein overproduction in the wild type, sigW and cssRS deletion strains. We demonstrate that the dynamics of the stress systems involved in membrane overproduction are far more complicated than was first hypothesised and that many more systems than SigW and CssRS are involved in membrane protein overexpression stress. Interestingly the cssRS genes are repressed in the sigW deletion strain.

2018-12-30 | GSE35916 | GEO

Transcriptome analysis of genome-reduced Bacillus subtilis strains

Project description:In this study two genome-reduced Bacillus subtilis strains lacking about 36% of dispensable genetic information were constructed using a markerless and scarless deletion method. In order to analyze the consequences of the deletions for the bacteria, a multi-omics characterization of the reference strain Δ6 (Westers et al., 2003; PMID 12949151) and the two deletion strains was carried out. Bacteria were cultivated in complex medium supplemented with glucose, and samples of the same cultures were subjected to metabolome, proteome, and transcriptome analyses.These revealed a massive re-organization of metabolism as well as substantial changes in the transcriptome and the proteome.

2016-11-30 | GSE82249 | GEO

Sliding of Bacillus subtilis Natto

Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions.

2015-08-04 | GSE43840 | GEO

Temporal transcriptome analysis of Bacillus subtilis NDmed in the submerged biofilm model

Project description:Investigation of the kinetics of whole genome gene expression level changes in Bacillus subtilis NDmed strain during formation of submerged biofilm and pellicle. The Bacillus subtilis NDmed strain analyzed in this study is able to form thick and highly structured submerged biofilms as described in Bridier et al., (2011) The Spatial Architecture of Bacillus subtilis Biofilms Deciphered Using a Surface-Associated Model and In Situ Imaging. PLoS ONE 6(1):e16177.

2021-12-09 | GSE190460 | GEO

Phosphorylation of Bacillus subtilis gene regulator AbrB modulates its DNA-binding properties

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

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