Metabolic rearrangements causing elevated proline and polyhydroxybutyrate accumulation during the osmotic adaptation response of Bacillus megaterium
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PROVIDER: PRJNA434394 | ENA |
REPOSITORIES: ENA
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Project description:First transcriptome analyses of Bacillus megaterium DSM319 grown under mild and severe salt stress (up to 1.8 M NaCl) to analyse the addaptation of the organism on transcriptome level
2020-01-13 | GSE110712 | GEO
Project description:For many years now, Bacillus megaterium has served as a microbial industrial strain for high-level production of recombinant proteins in the g/L-scale. Nevertheless, the impact of process-related stress has only been poorly characterized so far. Taking advantage of the recent technical developments for quantifying the cell at various molecular levels, we interrogated the osmotic stress response of B. megaterium using transcriptome, proteome, metabolome and fluxome analyses. Under osmotic upshift conditions, several stress response enzymes, iron scavenging, and reactive oxygen species (ROS) fighting proteins were upregulated. The downregulation of genes of the upper part of glycolysis resulted in the activation of the pentose phosphate pathway (PPP), generating an oversupply of NADPH. The (NADH/NAD+) ratio indicating the redox state of the cell was also altered, which was partially compensated by the higher production of lactate accompanied by the reduction of acetate secretion. NADH was produced mainly within the tricarboxylic acid cycle (TCA) cycle elucidated from the higher mRNA and protein levels of enzymes involved within this pathway. This adaptation mainly focused on the massive de novo synthesis of the compatible solute proline recruiting an osmo-dependent pathway to fulfil this requirement. 13C flux analyses confirmed these findings. Giving the high flux towards acetyl-CoA and large pool of NADPH, B. megaterium cells redirected the produced acetyl-CoA to the polyhydroxybutyrate (PHB) biosynthetic pathway under non-limiting nutrient condition, amassing around 30% of the CDW as PHB. This direct relation between osmotic stress and intracellular PHB content has been evidenced for the first time, thus opening new avenues for synthesizing this valuable biopolymer using varying salt concentrations under non-limiting nutrient conditions.
2020-05-26 | PXD015605 | Pride
Project description: Not available
| S-EPMC7053513 | biostudies-literature
Project description:Plant growth promoting test in A. thaliana by using biostimulant strain P. megaterium YC4-R4 in liquid inoculant A. thaliana mRNA profiles of 13-day old wild type (WT) mock and WT treated (inoculated with P. megaterium YC4-R4)
2022-03-30 | GSE199501 | GEO
Project description:Aspergillus flavus is one of the major fungal molds that colonize peanut in the field and during storage. The impact to human and animal health and to economy in agriculture and commerce are significant since this mold produces the most potent natural toxins, aflatoxins, which are carcinogenic, mutagenic, immunosuppressive, and teratogenic. A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its effect to inhibit aflatoxin formation through down-regulating aflatoxin pathway gene expression in A. flavus as demonstrated by genechip analysis in liquid medium and peanuts. The results showed that aflatoxin accumulation in potato dextrose broth liquid medium and liquid minimal medium was almost totally (more than 98%) inhibited by B. megaterium. The expression of many of the aflatoxin biosynthetic genes in the fungus was confirmed to be turned down. Some of the target genes down-regulated by B. megaterium within the whole genome and within the aflatoxin pathway gene cluster (aflF, aflT, aflS, aflJ, aflL, aflX) were identified. These target genes could be used for controlling aflatoxin contamination in crops such as corn, cotton, and peanut. Importantly, the expression of the regulatory gene aflS was found to be significantly down-regulated. The effect of B. megaterium on aflatoxin biosynthesis and genes expression of pathogen was firstly tested in potato dextrose broth (PDB) and glucose minimal salts medium (MM). The cell suspension of B. megaterium (concentration in PDB and MM was finally adjusted to 108 CFU/ml) or sterile distilled water as a control was added into the 100 ml beaker flask containing 15 ml PDB or MM, respectively. Then 100 M-NM-<l of spore suspension (5 M-CM-^W 106 spores/ml) of A. flavus were added into each beaker flask. After 48 h of incubation at 28M-BM-0C at 200 rpm, mycelia were collected, fresh frozen with liquid nitrogen, ground to a fine powder in liquid nitrogen, and stored at -80M-BM-0C for further analysis. The effect of B. megaterium on aflatoxin biosynthesis and genes expression in the A. flavus fungal pathogen was also tested in two types of peanut kernels, UF 715133-1 and Jinhua 1012, respectively. Peanut kernels were wounded (6 mm diameter and approximately 3 mm deep) using a sterile borer and then 20 M-NM-<l of 1 M-CM-^W 108 CFU/ml cell suspension of B. megaterium was inoculated on wounded peanut kernels respectively. Sterile distilled water was also used for inoculation as control. Two hours after bacterial inoculation, 10 M-NM-<l A. flavus spore suspension was inoculated into each wound at a concentration of 106 spores/ml. The kernels were placed in artificial weather chamber to maintain high humidity (85%) and incubated at 28M-BM-0C for 7 days. Each treatment was replicated three times with 20 peanut kernels in each test. The mycelia on kernels were harvested at day 7 and fresh frozen immediately in liquid nitrogen, ground into powder, and stored at -80M-BM-0C for further analysis.
2013-10-22 | E-GEOD-51469 | biostudies-arrayexpress
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.
2011-08-15 | GSE31083 | GEO
Project description:Aspergillus flavus is one of the major fungal molds that colonize peanut in the field and during storage. The impact to human and animal health and to economy in agriculture and commerce are significant since this mold produces the most potent natural toxins, aflatoxins, which are carcinogenic, mutagenic, immunosuppressive, and teratogenic. A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its effect to inhibit aflatoxin formation through down-regulating aflatoxin pathway gene expression in A. flavus as demonstrated by genechip analysis in liquid medium and peanuts. The results showed that aflatoxin accumulation in potato dextrose broth liquid medium and liquid minimal medium was almost totally (more than 98%) inhibited by B. megaterium. The expression of many of the aflatoxin biosynthetic genes in the fungus was confirmed to be turned down. Some of the target genes down-regulated by B. megaterium within the whole genome and within the aflatoxin pathway gene cluster (aflF, aflT, aflS, aflJ, aflL, aflX) were identified. These target genes could be used for controlling aflatoxin contamination in crops such as corn, cotton, and peanut. Importantly, the expression of the regulatory gene aflS was found to be significantly down-regulated.
2013-10-22 | GSE51469 | GEO
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. 8 x 15 K customer made microarrays for gene expression analysis of B. megaterium were obtained from Agilent (Agilent Technologies, USA) with up to three probes per open reading frame of the B. megaterium DSM319 genome. Finally, the hybridization and final washing steps of the microarrays occurred as described in the Agilent manual for two color microarrays. The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA). For scanning and feature extraction the software Agilent Scan Control 8.4.1 and Feature Extraction 10.7.3.1 (Agilent Technologies, USA), respectively, was used according to the instruction. The analysis of the raw data occurred with the programming language R and Bioconductor as described in Yang and Paquet (2005). Finally, in consequence of the microarray design three different probes belonging to one gene were matched performing mean and median summarization of the logarithmic fold changes (logFC). Nevertheless, the p-values and also the logFC values were given for each probe separately, to account for different hybridization behavior of the different probes (Bunk, 2010). Only genes with a p-value < 0.01 in all replicates and an absolute |logFC| > 1 were considered as to be differentially expressed. Samples from degU expressing cells (xylose induction) of a degSU deletion mutant were compared to samples obtained from the likewise induced empty vector control strain, two time points, biological replicates: 3-5
2011-08-14 | E-GEOD-31083 | biostudies-arrayexpress
Project description:Here, we investigated for the first time the systems-wide response of B. subtilis to different simultaneous stresses, i.e. nutrient limitation and high osmolarity. To address the anticipated complexity of the cellular response networks, we combined chemostat experiments under conditions of carbon limitation, salt stress and osmoprotection with multi-omics analyses at the transcriptome, proteome, metabolome and fluxome levels. Our results indicate that the flux through central carbon and energy metabolism is very robust under all conditions studied. The key to achieve this robustness is the adjustment of the biocatalytic machinery to compensate for solvent-induced impairment of enzymatic activities during osmotic stress. The accumulation of the exogenously provided osmoprotectant glycine betaine helps the cell to rescue enzyme activities in the presence of high salt. A major effort of the cell during osmotic stress is the production of the compatible solute proline. This is achieved by the concerted adjustment of multiple reactions around the 2-oxoglutarate node, which drives metabolism towards the proline precursor glutamate. The fine-tuning of the transcriptional and metabolic networks involves functional modules that overarch the individual pathways.
2014-03-31 | GSE53333 | GEO