GEO DataSets

(Submitter supplied) The spontaneous mutation rate is a crucial parameter in molecular evolution which is maintained very low. To better characterize how proofreading activity of the DNA polymerase and Mismatch repair (MMR) which are ubiquitous in all kingdoms of life shape a mutational landscape we built B. subtilis 168-derived strains allowing conditional inactivation of either one or both of these two error reparation mechanisms. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30358

12 Samples

Download data: CSV

(Submitter supplied) Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19910

20 Samples

Download data: CSV

(Submitter supplied) Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, particularly polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Other

Platform:

GPL23473

6 Samples

Download data: XLSX

(Submitter supplied) Protein synthesis is a major energy-consuming process of the cell, which requires controlled production and turnover of ribosomes. While the last years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3’ to 5’ exonuclease, RNase R. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21373

9 Samples

Download data: BEDGRAPH

(Submitter supplied) Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24109

32 Samples

Download data: XLSX

(Submitter supplied) Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL24109

32 Samples

Download data: XLSX

(Submitter supplied) Objective: to compare and contrast the effects of exogenous application of strigolatone analogue rac-dGR24, on gene expression in bacillus subtilis. The experiment compared the effects on three genotypes: wild type and two mutant lines, a ∆rsbQ and RsbQS96A.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30886

18 Samples

Download data: XLSX

(Submitter supplied) Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). In many bacteria, a surface-exposed domain inserted into the catalytic trigger loop (TL) of RNAP, called SI3 in Escherichia coli, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ∆SI3*). ∆SI3* increased transcription rate in vitro relative to ∆SI3, possibly explaining its viability, but retained both positive and negative effects of ∆SI3 on pausing. more...

Organism:

Escherichia coli; Bacillus subtilis

Type:

Other

Platform:

GPL33390

2 Samples

Download data: TXT

(Submitter supplied) N-terminal coding sequences (NCS) are key regulatory elements for fine-tuning gene expression during translation initiation, the rate-limiting step of translation. However, due to complex combinatory effects of NCS biophysical factors and endogenous regulation, designing NCS remains challenging. Herein, we implemented multi-view learning strategy for model-driven generation of synthetic NCS for Saccharomyces cerevisiae and Bacillus subtilis, which are model microorganisms widely used in the laboratory and industry.

Organism:

Saccharomyces cerevisiae; Bacillus subtilis

Type:

Other

Platforms:

GPL30886 GPL27812

4 Samples

Download data: CSV

(Submitter supplied) Bacterial cell envelope is the first and the major line of defense against threats from the environment. Because of its crucial roles in bacterial cell life, cell envelope is a prime target for numerous antibiotics. In this study, by treating Gram-positive model strain Bacillus subtilis with numbers of cell wall targeted antibiotics, we aimed to obtain a global comprehensive transcriptional profile of cell envelope stress response in B. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29318

27 Samples

Download data: BW, TSV, XLSX

(Submitter supplied) Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB’s DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. more...

Organism:

Bacillus subtilis PY79

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28115 GPL23088

8 Samples

Download data: CSV

(Submitter supplied) PNPase is the primary RNA turnover enzyme in Bacillus subtilis and plays a crucial role in regulating gene expression. To investigate the life activities that PNPase participated in Bacillus subtilis 9407, RNA immunoprecipitation-sequencing (RIP-seq) analysis was performed to pinpoint the direct RNA targets of PNPase using 6×his-tagged PNPase (PNPase group) and PNPaseD493A (D493A group) constructs that were driven by the IPTG-induced Pgrac promoter. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL30886

3 Samples

Download data: TSV

(Submitter supplied) Using transcriptomics, we studied the spatiotemporal dynamics of B. subtilis swarming colonies on soft-agar surface and identified functional subpopulations.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30886 GPL29318

317 Samples

Download data: CSV

(Submitter supplied) SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and further increase flagellar density to swarm over solid surfaces. Here we perform ChIP-seq and demonstrate that SwrA interacts with many sites on the chromosome indirectly through the response regulator DegU. We identify a DegU-specific inverted repeat and show that SwrA increased DegU DNA binding affinity in parallel to phosphorylation. more...

Organism:

Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL33660

42 Samples

Download data: CSV

(Submitter supplied) M3-Seq is a single-cell RNA-sequencing platform for bacteria that pairs combinatorial cell indexing with post hoc rRNA depletion. We use M3-Seq to profile hundreds of thousands of bacterial cells and reveal rare populations of bacteria that include bet-hedging strategies, prophage induction, and phage-infected cells in E. coli and B. subtilis.

Organism:

Pseudomonas aeruginosa; Bacillus subtilis; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33391 GPL33390

4 Samples

Download data: CSV

(Submitter supplied) Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown at four different temperatures. We show that increases in reactivity with increasing temperature follow non-monotonic trends. Focusing on subregions of the transcriptome led to the discovery of two novel RNA thermometers that control expression of glpF and glpT.

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL32426

24 Samples

Download data: TXT

(Submitter supplied) Analysis of B. subtilis biofilm metabolism at gene expression level. The hypothesis tested in the present study was that extracellular pH and environmental buffer influence the biofilm development. Results provide important information of the response of biofilms to changes in extracellular pH.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29515

24 Samples

Download data: XLSX

(Submitter supplied) Regulation of gene activity during the cell cycle is fundamental to bacterial replication but is challenging to study in unperturbed, asynchronous bacterial populations. Using single cell RNA-sequencing of heterogeneous Staphylococcus aureus populations, we uncovered a global gene expression pattern dominated by chromosomal position. We show that this pattern results from the effect of DNA replication on gene expression, and in Escherichia coli, changes under different growth rates and modes of replication. more...

Organism:

Bacillus subtilis; Escherichia coli; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24034 GPL21222 GPL24109

88 Samples

Download data: TXT

(Submitter supplied) To identify RoxS targets and do the comparison with RoxS targets identified by pulsed SILAC experiment

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19910

6 Samples

Download data: TXT

(Submitter supplied) We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum.

Organism:

Thermofilum adornatum; Escherichia coli; Bacillus subtilis

Type:

Other

Platforms:

GPL32512 GPL30886 GPL25368

6 Samples

Download data: TSV