GEO DataSets

(Submitter supplied) Two wide type strains of Bacillus subtilis, S-2 and 312, were selected to study their genic differences treated by L-alanine through comparative transcriptomics analysis. The spores of B. subtilis S-2 were selected because of their high germination potential to L-alanine. The spores of B. subtilis 312 without a response to L-alanine were used as the control. The spores with or without L-alanine (100 mm) pretreatment were both cultured in the synthetic medium for 9 h, and then collected for sequencing.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29318

8 Samples

Download data: TXT

(Submitter supplied) Like other functional RNAs, ribozymes contain a conserved catalytic center supported by peripheral domains that vary among ribozyme sub-families. To understand how core-peripheral interactions contribute to ribozyme fitness, we compared the cleavage kinetics of all single base substitutions at 152 sites across the Bacillus subtilis glmS ribozyme by high-throughput sequencing (ClvSeq). The in vitro activity map mirrored phylogenetic sequence conservation in glmS ribozymes, indicating that biological fitness reports all biochemically important positions. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL29318

12 Samples

Download data: TXT

(Submitter supplied) In a previous study we used RNA-seq to identify cellular stresses related to the overexpression of xylanase XynA, and found that upregulation of the CtsR regulon improves the yield of XynA production in B. subtilis. In this study, we compared the transcriptomes of B. subtilis cells overexpressing either the xylanase XynA or the heterologous amylase AmyM, to identify general and enzyme-specific stress responses. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28092

16 Samples

Download data: FASTA, GFF3, XLSX

(Submitter supplied) The glycopeptide vancomycin is a drug of choice for the treatment of severe non-gastrointestinal infections with members of Bacillus cereus sensu lato. Recently, sporadic detection of vancomycin resistant phenotypes emerged, mostly for agar diffusion testing. The food packaging isolate BC70 displayed a pseudo-resistant phenotype for vancomycin in both Etest and disk diffusion. In this work, we used RNA-Seq on the nanopore platform to study differentially expressed genes in BC70 cells, which were able to actively move into the inhibition zone during vancomycin susceptibility testing using Etest and therefore appeared to be resistant. more...

Organism:

Bacillus cereus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34081

4 Samples

Download data: CSV

(Submitter supplied) To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.

Organism:

Bacillus thuringiensis

Type:

Expression profiling by array

Platform:

GPL17384

6 Samples

Download data: TXT

(Submitter supplied) This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.

Organism:

Bacillus sp. (in: firmicutes)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34384

4 Samples

Download data: TXT

(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) Antibiotic resistance (AR) is one of the greatest threats to global health and is associated with higher treatment costs, longer hospital stays, and increased mortality. Current gold standard antibiotic susceptibility tests (AST) are dependent on organism growth rates resulting in prolonged diagnostic answers for slow growing organisms. Changes in the cellular transcriptome can be instantaneous in the presence of stressors such as antibiotic pressure. more...

Organism:

Yersinia pestis; Bacillus anthracis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33703 GPL29781

48 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28092

6 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL28092

4 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28092

2 Samples

Download data: BIGWIG, TXT

(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) The transcriptional control of sporulation in Bacillus subtilis is reasonably well understood, but its translational control is underexplored. Here, we use RNA-seq, ribosome profiling and fluorescence microscopy to study the translational dynamics of B. subtilis sporulation. We identify two events of translation silencing and describe spatiotemporal changes in subcellular localization of ribosomes during sporulation. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24109

64 Samples

Download data

(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