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) 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) 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) Our study showed that optimizing ncRNA expression can increase or lower the yield of alpha-amylase enzyme production in Bacillus subtilis while revealing a range of potentially novel ncRNAs.

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21796

8 Samples

Download data: FNA, GFF, TSV

(Submitter supplied) 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. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL15150

12 Samples

Download data: PAIR

(Submitter supplied) The universally conserved protein Elongation Factor P facilitates translation at amino acids that form peptide bonds with low efficiency, particularly poly-proline tracts. Despite its wide conservation, it is not essential in most bacteria and its physiological role remains unclear. Here, we show that EF-P affects the process of sporulation initiation in the bacterium Bacillus subtilis. We observe that lack of EF-P delays expression of sporulation-specific genes. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21344

4 Samples

Download data: WIG

(Submitter supplied) DNA replication is essential for all living organisms. Several events can disrupt replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and so-called “roadblocks” (e.g., DNA-binding proteins or transcription). Bacteria have several well-characterized mechanisms for repairing damaged DNA and then restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of chemical alterations to DNA. more...

Organism:

Bacillus subtilis subsp. subtilis

Type:

Other

Platform:

GPL32956

10 Samples

Download data: WIG

(Submitter supplied) By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates Bacillus subtilis division frequency without affecting growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media and in domesticated and undomesticated strains. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24119

6 Samples

Download data: TXT

(Submitter supplied) We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of Bacillus subtilis growing in the presence of Tse1, a T6SS effector of Pseudomonas chlororaphis

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31125

4 Samples

Download data: XLSX

(Submitter supplied) In our study, we found that lack of tmRNA affects the biofilm formation in Bacillus subtilis, which has important research significance. Then, we obtained a revertant strain MB from tmRNA mutant strain. And MB strain could restore biofilm production capacity. Therefore, the transcriptomes of the three strains were sequenced. Based on the statistical analysis of gene expression (P < 0.05), there were 756 genes up regulated while 992 genes down regulated by at least two folds when comparing TM to WT. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32075

9 Samples

Download data: TXT

(Submitter supplied) In an evolutionary experiment on high hemin concentrations, a frameshift mutation in the ChrS gene was figured out to be striking in survival at high hemin concentrations (Ala245fs). Apart from high upregulation of heme exporter hrtB, microarrays should reveal further different controlled genes compared to the WT.

Organism:

Corynebacterium glutamicum; Bacillus subtilis subsp. subtilis str. 168; Gluconobacter oxydans 621H; Escherichia coli str. K-12 substr. MG1655; Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL32387

3 Samples

Download data: GPR

(Submitter supplied) The production of alpha-amylase (AMY) enzyme in Bacillus subtilis at a high rate leads to accumulation of unfolded AMY, which causes secretion stress. The over-expression of the PrsA chaperon aids the enzyme folding and thus reduces stress. Stress pathways are complex and intertwined in regulation of a variety of cellular mechanism; for instance, PrsA over-expression leads to reduced cell growth. To capture an overview over the impacted mechanisms, we analyze the transcriptomic changes during fed-batch AMY fermentation between a PrsA over-expressing strain and a control in a time-series RNA-seq experiment (n=3, 6 timepoints). more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30999

41 Samples

Download data: BED, FNA, GFF, TSV

(Submitter supplied) Sequencing technologies, in particular RNASeq, have become critical tools in the design, build, test, learn cycle for synthetic biology. They provide a better understanding of synthetic designs and they help identify ways to improve and select designs. While this data is beneficial to design, its collection and analysis is a complex, multi-step process that has implications both on discovery and reproducibility of experiments. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26592 GPL30358

1344 Samples

Download data: CSV

(Submitter supplied) miniBacillus PG10 lacks ~36% of dispensible genentic material and has been derived from B. subtilis 168 (Reuß et al. 2017; PMID: 27965289). We performed RNA-seq analysis on mid-to-late exponential cultures and stationary phase cultures that were grown in LB medium. We specifically analyzed differential gene expression levels of lipid metabolic genes to compare to the lipidomic profiles of the two strains.

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21796

12 Samples

Download data: WIG

(Submitter supplied) In nature, bacteria reside in biofilms - multicellular differentiated communities held together by extracellular matrix. In this work, we identified a novel subpopulation essential for biofilm formation – mineral-forming cells in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31125

28 Samples

Download data: TXT

(Submitter supplied) The nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria by binding to the RNA polymerase. Here we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes from soil bacteria to pathogens: (p)ppGpp directly binds to the transcription factor PurR to downregulate purine biosynthesis. more...

Organism:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30809

25 Samples

Download data: RDATA, TXT

(Submitter supplied) 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. more...

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL21981

7 Samples

Download data: TXT

(Submitter supplied) The transcriptional profiling and global gene expression analysis revealed a higher globally gene expression level in BS-F91L or BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes categorized by GO, KEGG and COG analysis, highlighted the crucial roles of Bsu06560 in regulating N6-methyladenosine metabolism and further influenced a myriad of biological processes in multiple layers, including transcription, translation, metabolites regulations, and cellular signal transduction.

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30358

12 Samples

Download data: TXT

(Submitter supplied) In the cell, stalled ribosomes are rescued through ribosome-associated protein quality-control (RQC) pathways. We demonstrate that RqcH is responsible for tRNAAla selection during RQC elongation, whereas RqcP lacks any tRNA specificity. The ribosomal protein uL11 is crucial for RqcH, but not RqcP, recruitment to the 50S subunit, and B. subtilis lacking uL11 are RQC-deficient. Through mutational mapping, we identify critical residues within RqcH and RqcP that are important for interaction with the P-site tRNA and/or the 50S subunit. more...

Organism:

Enterococcus faecalis; Bacillus subtilis subsp. subtilis str. 168

Type:

Non-coding RNA profiling by array

Platform:

GPL30116

19 Samples

Download data: TXT

(Submitter supplied) Investigation of the impact of an overexpression of cg1978 on gene expression under standard conditions (CGXII-Glucose)

Organism:

Escherichia coli; Corynebacterium glutamicum; Corynebacterium glutamicum ATCC 13032; Pseudomonas putida KT2440; Gluconobacter oxydans; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL26911

3 Samples

Download data: GPR