Bacillus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA400804 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative Genomic Hybridization. Analysis of genomic content of closely related Bacillus species. Refer to individual records for strain information. Refer to platform and individual sample records for experimental protocols. Keywords: other
2004-10-28 | GSE568 | GEO
Project description:AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins that are required for the pathogenicity of Bacillus anthracis. Recent transcriptome analyses also showed that AtxA affects a large number of genes on both chromosome and plasmid, suggesting its role as a global regulator. Its mechanism of gene regulation nor binding target in vivo was, however, not well understood. In this work, we conducted ChIP-seq for cataloging binding sites of AtxA in vivo and Cappable-seq for catalogging the transcription start sites on the B. anthracis genome. For detected regulons, single knockout strains were constructed and RNA-seq was conducted for each strain.
2021-06-28 | GSE167871 | GEO
Project description:Oh2007 - Genome-scale metabolic network of
Bacillus subtilis (iYO844)
This model is described in the article:
Genome-scale reconstruction
of metabolic network in Bacillus subtilis based on
high-throughput phenotyping and gene essentiality data.
Oh YK, Palsson BO, Park SM,
Schilling CH, Mahadevan R.
J. Biol. Chem. 2007 Sep; 282(39):
28791-28799
Abstract:
In this report, a genome-scale reconstruction of Bacillus
subtilis metabolism and its iterative development based on the
combination of genomic, biochemical, and physiological
information and high-throughput phenotyping experiments is
presented. The initial reconstruction was converted into an in
silico model and expanded in a four-step iterative fashion.
First, network gap analysis was used to identify 48 missing
reactions that are needed for growth but were not found in the
genome annotation. Second, the computed growth rates under
aerobic conditions were compared with high-throughput
phenotypic screen data, and the initial in silico model could
predict the outcomes qualitatively in 140 of 271 cases
considered. Detailed analysis of the incorrect predictions
resulted in the addition of 75 reactions to the initial
reconstruction, and 200 of 271 cases were correctly computed.
Third, in silico computations of the growth phenotypes of
knock-out strains were found to be consistent with experimental
observations in 720 of 766 cases evaluated. Fourth, the
integrated analysis of the large-scale substrate utilization
and gene essentiality data with the genome-scale metabolic
model revealed the requirement of 80 specific enzymes
(transport, 53; intracellular reactions, 27) that were not in
the genome annotation. Subsequent sequence analysis resulted in
the identification of genes that could be putatively assigned
to 13 intracellular enzymes. The final reconstruction accounted
for 844 open reading frames and consisted of 1020 metabolic
reactions and 988 metabolites. Hence, the in silico model can
be used to obtain experimentally verifiable hypothesis on the
metabolic functions of various genes.
This model is hosted on
BioModels Database
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MODEL1507180013.
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2015-07-30 | MODEL1507180013 | BioModels
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
Project description:This series represents the work described in the publication Bacillus subtilis Genome Diversity by Earl et al. (Journal of Bacteriology, accepted) Keywords: comparative genomic hybridization
2006-12-13 | GSE6498 | GEO
Project description:Soybeans fermented by Bacillus subtilis BJ3-2 exhibits strong ammonia taste in medium temperature below 37℃ and prominent soy sauce-like aroma moderate temperatures above 45℃. The transcriptome sequencing of Bacillus subtilis BJ3-2 (incubating at 37°C and 45°C) has been completed, screening of differentially expressed genes (DEGs) through data analysis, and analyzing their metabolic pathways, laying a foundation for exploring the regulatory mechanism of soy sauce-like aroma formation.
2021-12-31 | GSE166082 | GEO
Project description:Examine possible association of Ssb, PolC, DnaC, PcrA with ICEBs1 in RapI-induced Bacillus subtilis
2009-10-16 | GSE18228 | GEO
Project description:Bacillus anthracis causes anthrax infections in mammals. Large-scale mortality resulting from the intentional release of B. anthracis spores represents a potential bioterrorism threat. Inhalational anthrax almost invariably proceeds to fatal systemic infection, characterized by massive bacteremia. A better understanding of host-pathogen interactions is urgently needed for effective treatment of this lethal disease. However, virulence mechanisms used by B. anthracis to survive and multiply in human blood are not completely understood. Identification of genes that are differentially expressed during the growth of B. anthracis in human serum can elucidate how this pathogen successfully colonizes the bloodstream. We compared the transcriptional profile of B. anthracis growing in heat-inactivated human serum to that in LB medium. Genes involved in the biosynthesis of purines, certain amino acids and riboflavin and lipid metabolism, genes encoding ABC transporters, respiratory enzymes and several genes with hypothetical function were identified as being upregulated during growth in serum.
2022-12-01 | GSE97567 | GEO