Subpopulation array data, Veening et al.
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacillus subtilis
PROVIDER: GSE9266 | GEO | 2007/10/23
SECONDARY ACCESSION(S): PRJNA102897
REPOSITORIES: GEO
Similar Datasets
Project description:The transcriptome profiles of sporulating vs non-sporulating cells, within an isogenic culture were compared. RNA was isolated from endospore containing cells which were separated from non-spore forming cells using buoyant density gradient centrifugation within an isogenic culture (details in Veening et al, submitted).
2010-05-25 | E-GEOD-9266 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in sporulating Bacillus subtilis 168 delta-prpE mutant, compared to the wild-type strain. The mutation engineered into this strain results in impaired germination of spores. A six chip study using total RNA extracted from three separate wild-type cultures of sporulating Bacillus subtilis 168 and three separate cultures of sporulating mutant strain, Bacillus subtilis 168 delta-prpE, in which prpE (yjbP BSU11630) gene coding for a protein phosphatase is deleted entirely. Each chip consists of four fields able to measure the expression level of 4,104 genes from Bacillus subtilis subsp. subtilis strain 168 NC_000964 with eight 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.
2013-07-08 | E-GEOD-44125 | biostudies-arrayexpress
Project description:This series of experiments was designed to identify the program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. The mother cell is one of two cell types generated by asymmetric division of sporulating cells approximately two hours after initiation of sporulation. The program is governed by a hierarchical cascade consisting of the transcription factors: sigmaE, sigmaK, GerE, GerR (YlbO) and SpoIIID. The characterization of the sigmaE regulon was reported in Eichenberger et al. (2003), J. Mol. Biol. 327, 945-972. Here we report the data for sigmaK, GerE, GerR and SpoIIID.
2004-09-01 | GSE1620 | GEO
Project description:This series of experiments was designed to identify the program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. The mother cell is one of two cell types generated by asymmetric division of sporulating cells approximately two hours after initiation of sporulation. The program is governed by a hierarchical cascade consisting of the transcription factors: sigmaE, sigmaK, GerE, GerR (YlbO) and SpoIIID. The characterization of the sigmaE regulon was reported in Eichenberger et al. (2003), J. Mol. Biol. 327, 945-972. Here we report the data for sigmaK, GerE, GerR and SpoIIID.
2010-06-06 | E-GEOD-1620 | biostudies-arrayexpress
Project description:This a model from the article:
Transient heterogeneity in extracellular protease production by Bacillus subtilis.
Veening JW, Igoshin OA, Eijlander RT, Nijland R, Hamoen LW, Kuipers OP
Mol. Syst. Biol. 2008 ; Volume: 4 : 184
18414485,
Abstract:
The most sophisticated survival strategy Bacillus subtilis employs is the differentiation of a subpopulation of cells into highly resistant endospores. To examine the expression patterns of non-sporulating cells within heterogeneous populations, we used buoyant density centrifugation to separate vegetative cells from endospore-containing cells and compared the transcriptome profiles of both subpopulations. This demonstrated the differential expression of various regulons. Subsequent single-cell analyses using promoter-gfp fusions confirmed our microarray results. Surprisingly, only part of the vegetative subpopulation highly and transiently expresses genes encoding the extracellular proteases Bpr (bacillopeptidase) and AprE (subtilisin), both of which are under the control of the DegU transcriptional regulator. As these proteases and their degradation products freely diffuse within the liquid growth medium, all cells within the clonal population are expected to benefit from their activities, suggesting that B. subtilis employs cooperative or even altruistic behavior. To unravel the mechanisms by which protease production heterogeneity within the non-sporulating subpopulation is established, we performed a series of genetic experiments combined with mathematical modeling. Simulations with our model yield valuable insights into how population heterogeneity may arise by the relatively long and variable response times within the DegU autoactivating pathway.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.For more information see the terms of use.To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2024-09-02 | BIOMD0000000240 | BioModels
Project description:Sporulation as a typical bacterial differentiation process has been studied for decades. However, two crucial aspects of sporulation, (i) the energy sources supporting the process, and (ii) the maintenance of spore dormancy throughout sporulation, are scarcely explored. Here, we reported the crucial role of RocG-mediated glutamate catabolism in regulating mother cell lysis, a critical step for successful sporulation of Bacillus subtilis, likely by providing energy metabolite ATP. Notably, rocG overexpression resulted in an excessive ATP accumulation in sporulating cells, leading to adverse effects on future spore properties, e.g. increased germination efficiency, reduced DPA content, and lowered heat resistance. Additionally, we revealed that Ald-mediated alanine metabolism was highly related to the inhibition of premature germination and the maintenance of spore dormancy during sporulation, which might be achieved by decreasing the typical germinant L-alanine concentration in sporulating environment. Our data inferred that sporulation of B. subtilis was a highly orchestrated biological process requiring a delicate balance in diverse metabolic pathways, hence ensuring both the completion of sporulation and production of high-quality spores.
2024-06-07 | PXD052983 |
Project description:Investigation of whole genome gene expression level changes in sporulating Bacillus subtilis 168 delta-prpE mutant, compared to the wild-type strain. The mutation engineered into this strain results in impaired germination of spores.
2013-07-08 | GSE44125 | GEO
Project description:The aim of the project was to investigate polysome profiles and analyse ribosomes of sporulating Bacillus subtilis strains, WT and a triple knock-out (3KO) strain lacking three paralogs of ribosomal proteins, by mass spectrometry, depending on the sample preparation conditions. B. subtilis, a gram positive spore forming bacterium, was induced to sporulate and harvested three hours post sporulation induction, approximately soon after asymmetric septation, respectively. Three conditions were analysed: 1) proteins were cross-linked by addition of DSP to the culture just before harvesting, and the cells were lysed by membrane solubilisation with digitonin, 2) cell lysis was performed by membrane solubilisation with digitonin with no prior cross-linking, 3) cell lysis was performed by grinding with pestle and mortar with addition of aluminium oxide. To provide additional comparisons, analogous experiments were performed for the cultures collected in logarithmic growth phase and two hours post sporulation induction, before asymmetric septation (lysis by membrane solubilisation with digitonin and grinding respectively). For the 3KO strain, cultures were harvested 3hours post sporulation induction and lysates were prepared by grinding.
2024-07-17 | PXD047497 | Pride
Project description: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. We investigate the potential regulatory role of ribosomes during sporulation using a strain lacking zinc-independent paralogs of three zinc-dependent ribosomal proteins (L31, L33 and S14). The mutant strain exhibits delayed sporulation, reduced germination efficiency, dysregulated translation of metabolic and sporulation-related genes, and disruptions in translation silencing, particularly in late sporulation. This SuperSeries is composed of the SubSeries listed below.
2023-12-06 | GSE249450 | GEO
Project description: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. Using a triple knock-out strain (3KO) of zinc-independents paralogs of three zinc-dependent ribosomal proteins L31, L33 and S14, we investigated the potential regulatory role of ribosome during sporulation. The 3KO strain exhibited delayed sporulation, reduced germination efficiency, and dysregulated translation including expression of key metabolic and sporulation-related genes as well as disruptions in translation silencing, particularly in late sporulation.
2023-12-06 | GSE249449 | GEO