The YmdB phosphodiesterase is a global regulator of biofilm-specific mRNA levels in Bacillus subtilis
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ABSTRACT:
ORGANISM(S): Bacillus subtilis
PROVIDER: GSE39142 | GEO | 2013/12/11
SECONDARY ACCESSION(S): PRJNA170132
REPOSITORIES: GEO
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Project description:Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper. GSM956794-GSM956801: Bacillus subtilis 168 wild type and its ymdB derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationary phase. Dye swaps are included in both experiments. GSM1011025-GSM1011032: Bacillus subtilis GP966 antibiotic tagged synthetic wild type and its ymdB E39Q point mutant strain GP969 were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationer phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationer phase. Dye swaps are included in both experiments.
2013-12-11 | E-GEOD-39142 | biostudies-arrayexpress
Project description:Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper.
2012-11-26 | GSE36877 | GEO
Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper.
2014-09-09 | GSE46682 | GEO
Project description:Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper. Bacillus subtilis 168 wild type and its cshA derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used and 2 were mixed after cDNA labeling, resulting 2 slides for both exponential and stationary phase. Dye swaps are included in both experiments.
2012-11-26 | E-GEOD-36877 | biostudies-arrayexpress
Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper. B subtilis NCIB3610 cells were grown in the presence of Aspergillus niger CB 119.1 hyphae for 3 hours. The mycelium and the attached bacteria were separated from the non-attached B. subtilis cells via filtration through Miracloth. The mycelia and attached bacteria were briefly rinsed with TY medium, dried, and the sample was frozen in liquid nitrogen. Bacterial cells in the flow-through medium fraction were harvested by centrifugation at 10.397 g for 1 min. To extract RNA mainly from the bacterial cells, lysozyme solution and RiboLock (Thermo Scientific) was added followed by incubation at 37 C for 30 minutes. Further RNA extraction was performed with the Macaloid/Roche method as described before (van Hijum et al., 2005, Kovács and Kuipers, 2011) but omitting the bead beater treatment and using RiboLock.
2014-09-09 | E-GEOD-46682 | biostudies-arrayexpress
Project description:Genome-wide comparative transcriptome analysis of the Bacillus subtilis parent strain PY79 and its yvfI derivative with yvfI::T10::spc (TEK1) grown in PA medium Detailed description of sample preparation and microarray conditions can be also found in Irigul et al to be submitted
2013-12-11 | GSE34414 | GEO
Project description:Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number of known signals that trigger biofilm formation do so through the activation of one or more sensory histidine kinases, it was discovered that biofilm activation is also coordinated by sensing intracellular metabolic signals, including serine starvation. Serine starvation causes ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR, which encodes a master repressor for biofilm matrix genes and ultimately triggers biofilm induction. How serine levels change in different growth stages, how B. subtilis regulates intracellular serine levels, and how serine starvation triggers ribosomes to pause on selective serine codons remain unknown. Here, we show that serine levels decrease as cells enter stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine biosynthesis genes decreases upon the transition into stationary phase. The deletion of the gene for a serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm formation, further supporting the idea that serine levels are a critical intracellular signal for biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are decreased in stationary phase compared with exponential phase. However, the three isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two that recognize AGC and AGU serine codons. Our findings provide evidence for a link between serine homeostasis and biofilm development in B. subtilisIMPORTANCE In Bacillus subtilis, biofilm formation is triggered in response to environmental and cellular signals. It was proposed that serine limitation acts as a proxy for nutrient status and triggers biofilm formation at the onset of biofilm entry through a novel signaling mechanism caused by global ribosome pausing on selective serine codons. In this study, we reveal that serine levels decrease at the biofilm entry due to catabolite control and a serine shunt mechanism. We also show that levels of five serine tRNA isoacceptors are differentially decreased in stationary phase compared with exponential phase; three isoacceptors recognizing UCN serine codons are reduced much more than the two recognizing AGC and AGU codons. This finding indicates a possible mechanism for selective ribosome pausing.
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Project description:Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report a surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm-associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following these results, we demonstrate that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This study represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful roadmap for future studies on biofilm physiology.
2019-03-27 | GSE128875 | GEO
Project description:Bacillus subtilis is a plant-beneficial Gram-positive bacterium widely used as a biofertilizer. However, relatively little is known regarding the molecular processes underlying this bacterium's ability to colonize roots. In contrast, much is known about how this bacterium forms matrix-enclosed multicellular communities (biofilms) in vitro. Here, we show that, when B. subtilis colonizes Arabidopsis thaliana roots it forms biofilms that depend on the same matrix genes required in vitro. B. subtilis biofilm formation was triggered by certain plant polysaccharides. These polysaccharides served as a signal for biofilm formation transduced via the kinases controlling the phosphorylation state of the master regulator Spo0A. In addition, plant polysaccharides are used as a source of sugars for the synthesis of the matrix exopolysaccharide. The bacterium's response to plant polysaccharides was observed across several different strains of the species, some of which are known to have beneficial effects on plants. These observations provide evidence that biofilm genes are crucial for Arabidopsis root colonization by B. subtilis and provide insights into how matrix synthesis may be triggered by this plant.
| S-EPMC3637697 | biostudies-literature
Project description:Biofilms of Bacillus subtilis consist of long chains of cells that are held together in bundles by an extracellular matrix of exopolysaccharide and the protein TasA. The exopolysaccharide is produced by enzymes encoded by the epsA-O operon and the gene encoding TasA is located in the yqxM-sipW-tasA operon. Both operons are under the control of the repressor SinR. Derepression is mediated by the antirepressor SinI, which binds to SinR with a 1:1 stoichiometry. Paradoxically, in medium promoting derepression of the matrix operons, the overall concentration of SinR in the culture greatly exceeded that of SinI. We show that under biofilm-promoting conditions sinI, which is under the control of the response regulator Spo0A, was expressed only in a small subpopulation of cells, whereas sinR was expressed in almost all cells. Activation of Spo0A is known to be subject to a bistable switch, and we infer that SinI reaches levels sufficient to trigger matrix production only in the subpopulation of cells in which Spo0A is active. Additionally, evidence suggests that sinI is expressed at intermediate, but not low or high, levels of Spo0A activity, which may explain why certain nutritional conditions are more effective in promoting biofilm formation than others.
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