Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of genome-reduced Bacillus subtilis strains

ABSTRACT: 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.

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

PROVIDER: GSE82249 | GEO | 2016/11/30

SECONDARY ACCESSION(S): PRJNA324431

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mini-Bacillus - Large-scale reduction of the Bacillus subtilis genome: Consequences for the transcriptional network, resource allocation, and metabolism

Project description:In this study, we have applied the top-down approach to reduce the genome of B. subtilis in order to obtain minimal strains with robust growth on complex medium at 37°C. For this purpose, we have evaluated the function of each gene of the B. subtilis genome and identified essential, important and dispensable genomic regions. Using an efficient markerless and scarless deletion method and a system allowing induction of genetic competence in the complete cell population, we have constructed two genome-reduced strains lacking about 36% of dispensable genetic information. Multi-omics analyses with the genome-reduced strains revealed substantial changes in the transcriptome, the proteome and in the metabolome. The massive reorganization of metabolism in the two genome-reduced strains can be explained by the underlying genotypes that were determined by genome re-sequencing. Moreover, the transcriptome and proteome analyses uncovered novel dispensable genomic regions that can be removed to further streamline the B. subtilis genome. In conclusion, both minimal strains show interesting metabolic features and they serve as excellent starting points to generate an ultimate reduced-genome B. subtilis cell containing only genes required for robust growth on complex medium.

2016-12-06 | PXD004565 | Pride

Transcriptome analysis of glucose starved Bacillus subtilis cells

2010-12-01 | GSE24058 | GEO

Transcriptome analysis of glucose starved Bacillus subtilis cells

Project description:In this study, temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation were monitored. For proteomic profiling, a combination of in vivo metabolic labeling and shot gun mass spectrometric analysis was carried out for five different proteomic subfractions (i. cytosolic, ii. extracellular, iii. membrane, iv. integral membrane, and v. surface proteome fraction) leading to the identification of about 52% of the predicted proteome of B. subtilis. Acquired proteomic and transcriptomic data were analyzed using Voronoi treemaps which link functional classifications and relative expression changes of gene products according to their fate in the stationary phase. The data obtained enables for in-depth analysis of major physiological processes including protein degradation and is the first comprehensive profiling of changes in the membrane subfraction. Cells were grown in a minimal medium with glucose and L-malate (0.05 % each) to induce glucose starvation after growth to an OD500 of 1.0. Samples were taken at different time points along the growth curve (exponential growth, transition phase, transition phase +30, +60 and +120 minutes). Microarray hybridizations were performed with RNA from two biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.

2010-12-01 | E-GEOD-24058 | biostudies-arrayexpress

Transcriptional profiling of Bacillus subtilis WT (ABS2005) and ydcH mutant (ASEC56)

Project description:With these experiments we investigate the impact of the deletion of the ydcH gene on the transcriptomes of Bacillus subtilis strains ABS2005.

2017-11-06 | GSE104816 | GEO

Bacillus subtilis

Project description:Bacillus subtilis Proteome

| PRJNA1058701 | ENA

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

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

Transcriptome-wide effects of NusA on RNA polymerase pausing in Bacillus subtilis

Project description:In this work we conducted RNET-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this data we analysed the transcriptome-wide effects of NusA on RNA polymerase pausing and found that NusA has modest pause stimulating as well as suppressing effects throughout the genome.

2021-10-22 | GSE186285 | GEO

Bacillus subtilis WalR (YycF) ChIP-chip Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Project description:Identification of the specific WalR (YycF) binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the WalRK regulon in Bacillus subtilis and its role in cell wall metabolism, as well as implying a role in several other cellular processes.

2015-01-26 | GSE65272 | GEO

The conserved WhiA protein influences the fatty acid composition of the Bacillus subtilis cell membrane

Project description:The conserved WhiA protein family is present in most Gram-positive bacteria and plays a role in cell division. WhiA contains a DNA-binding motive and has been identified as a transcription factor in the actinomycetes. In Bacillus subtilis, a deletion of whiA influences cell division and chromosome segregation. However, WhiA does not seem to function as a transcription factor in this organism, and it is still unclear how WhiA influences these processes. The B. subtilis whiA gene is part of an operon and flanked by two metabolic genes, including yvcK required for growth under gluconeogenic conditions, and the gene encoding the catabolite repressor Crh. Therefore, B. subtilis WhiA might play a role in carbon metabolism which could indirectly affect cell division and chromosome maintenance. To study this, we followed a metabolomics approach and measured exo-metabolome flux during growth on different carbon sources, using nuclear magnetic resonance spectroscopy. The carbon utilization of wild type and whiA mutant cells was similar, however, the whiA mutant exhibited depleted pools of branched-chain fatty acid precursors and higher levels of acetate and 2-oxoglutarate. Transcriptome data could not link these effects to gene regulatory differences, but the reduction in branched-chain fatty acid precursors influenced the fatty acid composition of the cell membrane. In conclusion, WhiA does not participate in carbon catabolite regulation, but affects fatty acid composition of the membrane by an as yet unknown mechanism. We speculate that the effect on the membrane might be related to the pleiotropic phenotype of the B. subtilis whiA mutant.

2019-10-18 | GSE121479 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data