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
and identified by:
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:Examine possible association of Ssb, PolC, DnaC, PcrA with ICEBs1 in RapI-induced Bacillus subtilis
2009-10-16 | GSE18228 | 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:Coordination of chromosome segregation and cytokinesis is crucial for efficient cell proliferation. In Bacillus subtilis the nucleoid occlusion protein Noc protects chromosomes by associating with the chromosome and preventing cell division in its vicinity. Using protein localization, ChAP-on-Chip and bioinformatics, we have identified a consensus Noc-binding DNA sequence (NBS), and show that Noc is targeted to about 70 discrete regions scattered around the chromosome, though absent from a large region around the replication terminus. Purified Noc bound specifically to an NBS in vitro. NBSs inserted near the replication terminus bound Noc-YFP and caused a delay in cell division. An autonomous plasmid carrying an NBS recruited Noc-YFP and conferred a severe Noc-dependent inhibition of cell division. This shows that Noc is a potent inhibitor of division but that its activity is strictly localized by interaction with NBS sites in vivo. We propose that Noc not only serves as a spatial regulator of cell division to protect the nucleoid, but also a timing device with an important role in the co-ordination of chromosome segregation and cell division.
2009-07-01 | E-MEXP-2133 | biostudies-arrayexpress