Analysis of the messenger RNAs in Spores of Bacillus subtilis
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ABSTRACT:
PROVIDER: PRJNA516686 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8478961_1.fastq.gz | Fastqsanger.gz | |||
| SRR8478961_2.fastq.gz | Fastqsanger.gz | |||
| SRR8478962_1.fastq.gz | Fastqsanger.gz | |||
| SRR8478962_2.fastq.gz | Fastqsanger.gz | |||
| SRR8478963_1.fastq.gz | Fastqsanger.gz |
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Project description:Using RNA-seq, we cataloged messenger RNAs in highly purified dormant Bacillus subtilis spores prepared either on plates or in liquid. Almost all of the most abundant spore mRNAs are encoded by genes expressed only in the developing spore late in sporulation under control of the forespore-specific RNA polymerase sigma factor, sG. Given the levels of the ~40 most abundant mRNAs in dormant spores, we calculated the great majority of the low abundance mRNAs can be present in only a small fraction of the spore population.
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Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.
2012-06-01 | GSE37124 | GEO
Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.
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Project description:Bacillus subtilis strain R0179 is found in a number of commercially-available probiotic products. The mechanism(s) of action of B. subtilis in the host are poorly understood, but may involve the immune system response to switching between spore and vegetative forms. In order to help elucidate this mechanism, we challenged the immune response of a human colonic epithelial HT-29 cell model for 3 hours with the two forms of B. subtilis. The cellular response was evaluated using a custom-designed two-color expression microarray targeting 1354 genes of the human immune system. The data obtained in this study indicates that the vegetative cell form of the strain moderately induced TH1 pro-inflammatory response through IL-17C and TNF signaling pathway while down-regulating anti-inflammatory response genes IL-10 and TGFβ-2. The spore form had an opposite effect and acted primarily by down-regulating the Mitogen-Activated Protein Kinase pathway. The overall design consisted of 2 samples of HT-29 cells treated with Bacillus subtilis R0179 spores or vegetative states versus unchallenged HT-29 cells. A minimum of four dye-swap hybridizations (4 biological replicates) were performed for each of the 2 samples analyzed. Unchallenged HT-29 cells were controls and challenged HT-29 cells with Bacillus subtilis R0179 spores or vegetative were treated samples.
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Project description:Two wide type strains of Bacillus subtilis, S-2 and 312, were selected to study their genic differences treated by L-alanine through comparative transcriptomics analysis. The spores of B. subtilis S-2 were selected because of their high germination potential to L-alanine. The spores of B. subtilis 312 without a response to L-alanine were used as the control. The spores with or without L-alanine (100 mm) pretreatment were both cultured in the synthetic medium for 9 h, and then collected for sequencing.
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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: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.
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Project description:Spores of Bacillales and Clostridiales species contain 100s of different mRNAs, and their major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. In new work, RNA was isolated from spores of five Bacillales and one Clostridioides species and relative spore mRNA levels were determined by RNA-seq. Determination of RNA levels in single spores allowed calculation of RNA nt/spore, and assuming mRNA is 3% of spore RNA allowed calculation that only ~6% of spore mRNAs were present at ≥ 1/spore. Bacillus subtilis, Bacillus atrophaeus and Clostridioides difficile spores had 49, 42 and 51 mRNAs at >1/spore, respectively. Numbers of mRNAs at ≥1/spore were ~10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores, respectively, and ~ 4-fold higher in Bacillus megaterium spores. Notably, in all species: i) many of the 60 most abundant spore mRNAs were transcribed by RNA polymerase with forespore-specific s factors; ii) some to many of the most abundant spore mRNAs encoded orthologs of those encoded by abundant B. subtilis spore mRNAs and proteins present in dormant spores ; and iii) some spore mRNAs were likely transcribed in the mother cell compartment of the sporulating cell. Indeed , analysis of the coverage of RNA-seq reads on mRNAs from all six species suggested that abundant spore mRNAs were at least somewhat fragmented. This observation was confirmed by RT-qPCR analysis of three abundant mRNAs each from B. subtilis and C. difficile spores. These data add to a growing body of evidence indicating that the great majority of mRNAs in spores of Firmicutes are degradation and function as a ribonucleotide depot for new RNA synthesis when spores germinate.
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