Project description:The transcriptome profiles of a riboflavin-producing recombinant Bacillus subtilis RH33 and wild type Bacillus subtilis 168 were compared using DNA microarrays to identify the target genes for further enhancing riboflavin production. Transcriptome profiles of a riboflavin-producing B. subtilis RH33 were compared with those of the wild-type B. subtilis 168 as a control strain during exponentially growing period on LBG medium. These conditions corresponded to the state of high riboflavin production, which was growth related. For each comparison, two independent cultivations on LB medium with 1% glucose were performed, and exponentially growing cells (OD600 3â6) were harvested. The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).
Project description:Cappable-seq was used to map transcription start sites globally in wild type Bacillus subtilis. Total RNA was isolated from cells grown in LB media until exponential phase. RNA corresponding to transcription start sites was capped with a 5' biotin tag, which was used for enrichment via a pull down with streptavidin beads. Enriched RNA was converted to cDNA and then subjected to illumina sequencing.
Project description:First whole transcriptome assessment of a Bacillus megaterium strain. The B. megaterium DegU regulon was assessed for LB batch cultures with artificially induced degU expression. DegU is a pleiotropic regulator in B. subtilis governing adaptive responses such as secretory enzyme production.
Project description:To obtain global cellular response of Bacillus subtilis WT W168 when treated with amphotericin B, we performed RNA-seq experiments. For this, we added 10 µg ml-1 amphotericin B to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.
Project description:To obtain global cellular response of Bacillus subtilis WT W168 against the intrinsically produced antimicrobial peptide YydF, we performed RNA-seq experiments. For this, we synthesized YydF, extrinsically added 0.5µM to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.
Project description:Study the effect of single amino acid point mutations in CcpA at the transcriptome level. Cells were grown in LB with or without 1% glucose and harvested at an OD600 of 0.3 (early exponential phase). Bacillus subtilis strain ccpA::spec carrying pHT304 (empty plasmid), pWH_ccpA_M17R, pWH_ccpA_T62H, or pWH_ccpA_R304W were grown in LB with or without 1% glucose. The control in the microarray study was the strain Bacillus subtilis ccpA::spec carrying pWH_ccpA-wt. All Bacillus subtilis cultures were harvested in the early exponential growth phase at an OD600 of 0.3 from 100 ml culture. Two independent cultures of each strain per growth condition (+/- glucose) and a technical replicate (dye-swap) were used. Please note that '[A}' and '{B}' channels (in the raw data *slide.txt files) correspond to Cy3 (Ch1) and Cy5 (Ch2) in each sample record.
Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.
Project description:To obtain global cellular response of Bacillus subtilis WT W168 when treated with SynAnt 49 (BDTL049) we performed RNA-seq experiments. For this, we added 4 µg ml-1 SynAnt 49 to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.
Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress. Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays).
Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions. B subtilis Natto wild type cells were grown on the top of LB solid medium with 1.5% and 0.7% agar concentration (samples 1-4). B subtilis Natto wild type and spo0A derivative were grown on top of LB solid medium with 0.7% agar concentration (Sample 5-7). In first experiment, 4 biological replicates were used, while in the second experiment 3 biological replicates included. Dye swaps are included in both experiments.