ABSTRACT: Non-targted metabolomics from extracts from B. subtilis wildtype and SRF knock-out mutant. Data processed with MZMine2 and Ion Identity Networking.
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.
Project description:The B. subtilis transcriptome was analyzed under conditions of different growth rates, i.e. during growth in different cultivation media. Gene-level intensities were scaled based on the intensity values of 10 spike-in transcripts. This approach allowed to determine the total mRNA fraction out of the total RNA pool. The data revealed that the proportion of total mRNA in total RNA remained constant across samples which implies that total mRNA abundance in B. subtilis increases proportionally to the growth rate.
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.
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.
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. For each sample analyzed in this study three biological replicates were performed. Three different samples were taken from a strain expressing the WalR-SPA protein as well as from wild-type (168) without a tagged WalR. Samples were taken from exponentially growing cells in low phosphate medium (LPDM) as well as from phosphate-limited cells (T2). Each sample compares ChIP DNA vs. Total DNA from the same cells.
Project description:The aim of the experiments was to determine the regulon of the Bacillus subtilis alternative sigma factor SigI. Biological relevance: To expand our knowledge about Bacillus subtilis transcriptional network under unfavorable conditions. Experimental workflow overview: Bacillus subtilis 168 trp+ (BaSysBio) was used as the genetic background. (i) sigI-rsgI knock-out, (ii) rsgI knock-out, and (iii) wr strains were cultured in LB medium to mid-exponential phase at 37°C and 52°C. Total RNA was isolated from 3 ml of the culture. rRNA was depleted from the samples with RiboMinus; subsequently RNA-seq libraries were prepared (Illumina compatible NEXTflex Rapid Directional RNA-Seq Kit, Bioo Scientific) and sequenced at the EMBL GeneCore facility. The experiment was performed in three independent replicates.
Project description:The general assumption is that when bacteria run out of nutrients they become dormant or form spores. Here we show, using a new technique, that under deep starvation conditions non-sporulating Bacillus subtilis cells do not become dormant but continue to grow. B. subtilis can form (endo)spores and this has been regarded as the principal mechanism through which it survives long periods of nutrient depletion. However, in this study we demonstrate that non-sporulating B. subtilis cells can survive deep starvation conditions for many months. During this period, cells adopt an almost coccoid shape and become tolerant to antibiotics and oxidative stress. Interestingly, these cells appeared to be metabolically active, and transcriptome analyses indicated that their gene-expression profile differs substantially from both stationary phase cells, and exponentially growing cells. Surprisingly, using an inhibitor for cell division, we discovered that these coccoid-like B. subtilis cells are not dormant but actually grow and divide, albeit with a doubling time of ~4 days. It emerged that secreted proteases, allowing acquisition of nutrients from lysed brethren, are essential for this growth mode. In fact, nutrient levels comparable to 10,000 times diluted LB (Lysogeny broth) appeared to be sufficient to sustain this growth. The very slow growth provides an alternative strategy for B. subtilis to survive nutrient depletion and environmental stresses. We propose to call this the oligotrophic growth state. This state might be common among bacterial species to survive deep starvation conditions.