Analysis of differential gene expression during Bacillus subtilis spore outgrowth in high-salinity environments using RNA sequencing
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168
PROVIDER: GSE81238 | GEO | 2016/05/09
SECONDARY ACCESSION(S): PRJNA321031
REPOSITORIES: GEO
Similar Datasets
Project description:Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30 % of the B. subtilis genome. Keywords: time course, spore outgrowth
2007-03-27 | GSE6865 | GEO
Project description:In its natural habitat, the soil bacterium Bacillus subtilis often has to cope with fluctuating osmolality and nutrient availability. Upon nutrient depletion it can form dormant spores, which can revive to form vegetative cells when nutrients become available again. While the effects of salt stress on spore germination have been analyzed previously, detailed knowledge on the salt stress response during the subsequent outgrowth phase is lacking. In this study, we investigated the changes in gene expression during B. subtilis outgrowth in the presence of 1.2 M NaCl using RNA sequencing. In total, 402 different genes were upregulated and 632 genes were downregulated during 90 min of outgrowth in the presence of salt. The salt stress response of outgrowing spores largely resembled the osmospecific response of vegetative cells exposed to sustained high salinity and included strong upregulation of genes involved in osmoprotectant uptake and compatible solute synthesis. The σB-dependent general stress response typically triggered by salt shocks was not induced, whereas the σW regulon appears to play an important role for osmoadaptation of outgrowing spores. Furthermore, high salinity induced many changes in the membrane protein and transporter transcriptome. Overall, salt stress seemed to slow down the complex molecular reorganization processes ("ripening") of outgrowing spores by exerting detrimental effects on vegetative functions such as amino acid metabolism.
| S-EPMC5052260 | biostudies-literature
Project description:The germination of spore-forming bacteria in high-salinity environments is of applied interest for food microbiology and soil ecology. It has previously been shown that high salt concentrations detrimentally affect Bacillus subtilis spore germination, rendering this process slower and less efficient. The mechanistic details of these salt effects, however, remained obscure. Since initiation of nutrient germination first requires germinant passage through the spores' protective integuments, the aim of this study was to elucidate the role of the proteinaceous spore coat in germination in high-salinity environments. Spores lacking major layers of the coat due to chemical decoating or mutation germinated much worse in the presence of NaCl than untreated wild-type spores at comparable salinities. However, the absence of the crust, the absence of some individual nonmorphogenetic proteins, and the absence of either CwlJ or SleB had no or little effect on germination in high-salinity environments. Although the germination of spores lacking GerP (which is assumed to facilitate germinant flow through the coat) was generally less efficient than the germination of wild-type spores, the presence of up to 2.4 M NaCl enhanced the germination of these mutant spores. Interestingly, nutrient-independent germination by high pressure was also inhibited by NaCl. Taken together, these results suggest that (i) the coat has a protective function during germination in high-salinity environments; (ii) germination inhibition by NaCl is probably not exerted at the level of cortex hydrolysis, germinant accessibility, or germinant-receptor binding; and (iii) the most likely germination processes to be inhibited by NaCl are ion, Ca(2+)-dipicolinic acid, and water fluxes.
| S-EPMC4561714 | biostudies-literature
Project description:The transcriptome of 8 strains were studied during 7 stages of the Morphological phases of sporulation P0 = Resuspention of cells in sporulation medium; P1 = Onset of sporulation before asymmetric division; P2 = Visible asymmetric septum; P3 = Ongoing engulfment of the forespore compartment by the mother cell compartment of sporulating cells; P4 = Completed engulfment (engulfed phase-dark forespores are surrounded by the mother-cell cytoplasm); P5 = Maturation (ongoing dehydration of the forespore core seen as a transition of phase-dark forespores into phase-bright foresppores); P6 = Phase-bright forespores (sporulation almost completed, mother-cells contain phase-bright dehydrated forespores).
2018-03-08 | GSE108659 | GEO
Project description:Germination and outgrowth of endospores of the Gram-positive bacterium Bacillus subtilis involves the degradation and conversion to free amino acids of abundant proteins located in the spore core known as small acid-soluble proteins (SASP). This degradation is mediated primarily by the germination protease Gpr. Here we show that YmfB, a distant homologue of ClpP serine proteases that is highly conserved among endospore-forming bacteria, contributes to SASP degradation but that its function is normally masked by Gpr. Spores from a ymfB gpr double mutant were more delayed in spore outgrowth and more impaired in SASP degradation than were spores from a gpr single mutant. The activity of YmfB relied on three putative active-site residues as well as on the product of a small gene ylzJ located immediately downstream of, and overlapping with, ymfB. We propose that YmfB is an orphan ClpP protease that is dedicated to the degradation of a specialized family of small protein substrates.
| S-EPMC3808192 | biostudies-literature
Project description:To gain insight into spore germination and outgrowth, the transcriptome changes during Bacillus subtilis spore conversion to vegetative cells were analyzed. The transcriptome analysis also allowed us to trace the different functional groups of genes expressed during this conversion. . Our analysis identified 34 abundant mRNA transcripts in the dormant spores, at least 31 of which were rapidly degraded after the phase transition and observed 3152 differentially expressed genes during spore germination and outgrowth.
2020-03-04 | GSE146277 | GEO
Project description:Spores are of high interest to the food and health sectors because of their extreme resistance to harsh conditions especially against heat. Earlier research has shown that spores prepared on solid agar plates have a higher heat resistance than those prepared in a liquid medium. It has also been shown that the more mature a spore is the higher is its heat resistance contributed most likely by the progressive cross-linking of coat proteins. The current study for the first time enlightens the effect of sporulation medium on spore proteins. The 14N spores prepared on solid agar medium and 15N metabolically labelled spores prepared in liquid medium differ in their coat protein composition as revealed by LC-FT-MS/MS analyses. The 14N:15N isotopic ratio of the 1:1 mixture of liquid and solid medium cultured spores exposes that most of the identified inner coat and crust proteins are significantly upregulated while most of the outer coat proteins are significantly downregulated for the spores prepared on solid medium relative to the spores prepared in the liquid medium. Medium specific differences in isotopic ratios between the tryptic peptides of expected cross-linked proteins suggest that also the coat protein cross-linking may be medium specific. The spores prepared on solid medium show a higher thermal resistance than the spores prepared in liquid medium. Since the core DPA content is found to be similar in both the spore populations, it appears that the difference in wet heat resistance is connected to the differences in the coat protein composition and assembly. Supporting the proteomic analyses, the electron microscopy analyses show a significantly thinner outer coat layer of the spores cultures on the solid medium.
2017-09-20 | PXD004473 | Pride
Project description:Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites, and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, the results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30% of the B. subtilis genome.
| S-EPMC1855883 | biostudies-other
Project description:Pathogenic species belonging to Bacillus cereus sensu lato group possess a high evolutionary advantage in the environment and in food matrices thanks to their capacity to survive as silent spores to harsh environmental insults and grow at relatively low temperatures. Ready to re-heat products are at severe risk for contamination by members of Bacillus cereus s.l. group if not stored at proper conditions. In this work, the goal was to assess, by means of a genome-wide transcriptional assay, the isolated strain Bacillus cereus UC10070 gene expression behind the process of spore germination and consequent outgrowth in an artificially contaminated vegetable-based food model. A vegetable food model subjected to a heat treatment was determined to present favourable conditions for spores germination. Microscopic analyses together with OD measurements were applied to select the key steps of B. cereus cell cycle to be used for the microarray analysis. Using this approach we found a total of 1,646 probe sets differentially expressed and modulated during the entire B. cereus life cycle in the vegetable foodstuff. RNA was isolated from the dormant spores (DS), germinating spores at 40 minutes (GSP), early-log phase at 2h (C2h) and late log phase cells at 12 hours (C12h) after thermal treatment of B. cereus UC10070 previously isolated froma biofilm on a spoiled vegetable-based puree. There were 3 biological replicates (independent cultures) for each condition. Complete genome sequence of B. thuringiensis sv konkukian str. 97-27 (NCBI Reference Sequence: NC_005957.1) was chosen for its high homology with B. cereus s.l. UC10070, to design probes corresponding to 5,197 genes spotted in duplicates onto ElectraSenseH 12K microarrays chip.
2015-01-26 | E-GEOD-65259 | biostudies-arrayexpress
Project description:Bacterial endospores (spores) are among the most resistant living forms on earth. Spores of Bacillus subtilis A163 show extremely high resistance to wet heat compared to spores of laboratory strains. In this study, we found that spores of B. subtilis A163 were indeed very wet heat resistant and released dipicolinic acid (DPA) very slowly during heat treatment. We also determined the proteome of vegetative cells and spores of B. subtilis A163 and the differences in these proteomes from those of the laboratory strain PY79, spores of which are much less heat resistant. This proteomic characterization identified 2011 proteins in spores and 1901 proteins in vegetative cells of B. subtilis A163.
2021-03-21 | MSV000087080 | MassIVE