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  • 1
    Online Resource
    Online Resource
    A Comprehensive Proteomics and Transcriptomics Analysis of Bacillus subtilis Salt Stress Adaptation
    American Society for Microbiology ; 2010
    In:  Journal of Bacteriology Vol. 192, No. 3 ( 2010-02), p. 870-882
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 192, No. 3 ( 2010-02), p. 870-882
    Abstract: In its natural habitats, Bacillus subtilis is exposed to changing osmolarity, necessitating adaptive stress responses. Transcriptomic and proteomic approaches can provide a picture of the dynamic changes occurring in salt-stressed B. subtilis cultures because these studies provide an unbiased view of cells coping with high salinity. We applied whole-genome microarray technology and metabolic labeling, combined with state-of-the-art proteomic techniques, to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic upshift. This combined experimental approach provided quantitative data for 3,961 mRNA transcription profiles, 590 expression profiles of proteins detected in the cytosol, and 383 expression profiles of proteins detected in the membrane fraction. Our study uncovered a well-coordinated induction of gene expression subsequent to an osmotic upshift that involves large parts of the SigB, SigW, SigM, and SigX regulons. Additionally osmotic upregulation of a large number of genes that do not belong to these regulons was observed. In total, osmotic upregulation of about 500 B. subtilis genes was detected. Our data provide an unprecedented rich basis for further in-depth investigation of the physiological and genetic responses of B. subtilis to hyperosmotic stress.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.01106-09
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2010
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 2
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    Online Resource
    Adaptation of B acillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi‐omics perspective
    Wiley ; 2014
    In:  Environmental Microbiology Vol. 16, No. 6 ( 2014-06), p. 1898-1917
    Details
    In: Environmental Microbiology, Wiley, Vol. 16, No. 6 ( 2014-06), p. 1898-1917
    Abstract: The Gram‐positive bacterium B acillus subtilis encounters nutrient limitations and osmotic stress in its natural soil ecosystem. To ensure survival and sustain growth, highly integrated adaptive responses are required. Here, we investigated the system‐wide response of B . subtilis to different, simultaneously imposed stresses. 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 of the transcriptome, proteome, metabolome and fluxome. Surprisingly, 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. Specifically, increased production of several enzymes of central carbon metabolism compensates for their reduced activity in the presence of high salt. A major response of the cell during osmotic stress is the production of the compatible solute proline. This is achieved through 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.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2014.16.issue-6
    DOI: 10.1111/1462-2920.12438
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 3
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    Online Resource
    Synthesis of the compatible solute proline by Bacillus subtilis : point mutations rendering the osmotically controlled proHJ promoter hyperactive
    Wiley ; 2017
    In:  Environmental Microbiology Vol. 19, No. 9 ( 2017-09), p. 3700-3720
    Details
    In: Environmental Microbiology, Wiley, Vol. 19, No. 9 ( 2017-09), p. 3700-3720
    Abstract: The ProJ and ProH enzymes of Bacillus subtilis catalyse together with ProA (ProJ‐ProA‐ProH), osmostress‐adaptive synthesis of the compatible solute proline. The proA ‐encoded gamma‐glutamyl phosphate reductase is also used for anabolic proline synthesis (ProB‐ProA‐ProI). Transcription of the proHJ operon is osmotically inducible whereas that of the proBA operon is not. Targeted and quantitative proteome analysis revealed that the amount of ProA is not limiting for the interconnected anabolic and osmostress‐responsive proline production routes. A key player for enhanced osmostress‐adaptive proline production is the osmotically regulated proHJ promoter. We used site‐directed mutagenesis to study the salient features of this stress‐responsive promoter. Two important features were identified: (i) deviations of the proHJ promoter from the consensus sequence of SigA‐type promoters serve to keep transcription low under non‐inducing growth conditions, while still allowing a finely tuned induction of transcriptional activity when the external osmolarity is increased and (ii) a suboptimal spacer length for SigA‐type promoters of either 16‐bp (the natural proHJ promoter), or 18‐bp (a synthetic promoter variant) is strictly required to allow regulation of promoter activity in proportion to the external salinity. Collectively, our data suggest that changes in the local DNA structure at the proHJ promoter are important determinants for osmostress‐inducibility of transcription.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2017.19.issue-9
    DOI: 10.1111/1462-2920.13870
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 4
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    Online Resource
    RsbV-Independent Induction of the SigB-Dependent General Stress Regulon of Bacillus subtilis during Growth at High Temperature
    American Society for Microbiology ; 2004
    In:  Journal of Bacteriology Vol. 186, No. 18 ( 2004-09-15), p. 6150-6158
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 186, No. 18 ( 2004-09-15), p. 6150-6158
    Abstract: General stress proteins protect Bacillus subtilis cells against a variety of environmental insults. This adaptive response is particularly important for nongrowing cells, to which it confers a multiple, nonspecific, and preemptive stress resistance. Induction of the general stress response relies on the alternative transcription factor, SigB, whose activity is controlled by a partner switching mechanism that also involves the anti-sigma factor, RsbW, and the antagonist protein, RsbV. Recently, the SigB regulon has been shown to be continuously induced and functionally important in cells actively growing at low temperature. With the exception of this chill induction, all SigB-activating stimuli identified so far trigger a transient expression of the SigB regulon that depends on RsbV. Through a proteome analysis and Northern blot and gene fusion experiments, we now show that the SigB regulon is continuously induced in cells growing actively at 51°C, close to the upper growth limit of B. subtilis . This heat induction of SigB-dependent genes requires the environmental stress-responsive phosphatase RsbU, but not the metabolic stress-responsive phosphatase RsbP. RsbU dependence of SigB activation by heat is overcome in mutants that lack RsbV. In addition, loss of RsbV alone or in combination with RsbU triggers a hyperactivation of the general stress regulon exclusively at high temperatures detrimental for cell growth. These new facets of heat induction of the SigB regulon indicate that the current view of the complex genetic and biochemical regulation of SigB activity is still incomplete and that SigB perceives signals independent of the RsbV-mediated signal transduction pathways under heat stress conditions.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.186.18.6150-6158.2004
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2004
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 5
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    Online Resource
    Genome-Wide Transcriptional Profiling Analysis of Adaptation of Bacillus subtilis to High Salinity
    American Society for Microbiology ; 2003
    In:  Journal of Bacteriology Vol. 185, No. 21 ( 2003-11), p. 6358-6370
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 185, No. 21 ( 2003-11), p. 6358-6370
    Abstract: The gram-positive soil bacterium Bacillus subtilis often faces increases in the salinity in its natural habitats. A transcriptional profiling approach was utilized to investigate both the initial reaction to a sudden increase in salinity elicited by the addition of 0.4 M NaCl and the cellular adaptation reactions to prolonged growth at high salinity (1.2 M NaCl). Following salt shock, a sigB mutant displayed immediate and transient induction and repression of 75 and 51 genes, respectively. Continuous propagation of this strain in the presence of 1.2 M NaCl triggered the induction of 123 genes and led to the repression of 101 genes. In summary, our studies revealed (i) an immediate and transient induction of the SigW regulon following salt shock, (ii) a role of the DegS/DegU two-component system in sensing high salinity, (iii) a high-salinity-mediated iron limitation, and (iv) a repression of chemotaxis and motility genes by high salinity, causing severe impairment of the swarming capability of B. subtilis cells. Initial adaptation to salt shock and continuous growth at high salinity share only a limited set of induced and repressed genes. This finding strongly suggests that these two phases of adaptation require distinctively different physiological adaptation reactions by the B. subtilis cell. The large portion of genes with unassigned functions among the high-salinity-induced or -repressed genes demonstrates that major aspects of the cellular adaptation of B. subtilis to high salinity are unexplored so far.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.185.21.6358-6370.2003
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2003
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 6
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    Online Resource
    Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis
    Wiley ; 2020
    In:  Environmental Microbiology Vol. 22, No. 8 ( 2020-08), p. 3266-3286
    Details
    In: Environmental Microbiology, Wiley, Vol. 22, No. 8 ( 2020-08), p. 3266-3286
    Abstract: The Gram‐positive bacterium Bacillus subtilis is frequently exposed to hyperosmotic conditions. In addition to the induction of genes involved in the accumulation of compatible solutes, high salinity exerts widespread effects on B. subtilis physiology, including changes in cell wall metabolism, induction of an iron limitation response, reduced motility and suppression of sporulation. We performed a combined whole‐transcriptome and proteome analysis of B. subtilis 168 cells continuously cultivated at low or high (1.2 M NaCl) salinity. Our study revealed significant changes in the expression of more than one‐fourth of the protein‐coding genes and of numerous non‐coding RNAs. New aspects in understanding the impact of high salinity on B. subtilis include a sustained low‐level induction of the SigB‐dependent general stress response and strong repression of biofilm formation under high‐salinity conditions. The accumulation of compatible solutes such as glycine betaine aids the cells to cope with water stress by maintaining physiologically adequate levels of turgor and also affects multiple cellular processes through interactions with cellular components. Therefore, we additionally analysed the global effects of glycine betaine on the transcriptome and proteome of B. subtilis and revealed that it influences gene expression not only under high‐salinity, but also under standard growth conditions.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.v22.8
    DOI: 10.1111/1462-2920.15087
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 7
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    Online Resource
    Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal
    Microbiology Society ; 2006
    In:  Microbiology Vol. 152, No. 3 ( 2006-03-01), p. 831-853
    Details
    In: Microbiology, Microbiology Society, Vol. 152, No. 3 ( 2006-03-01), p. 831-853
    Abstract: The soil bacterium Bacillus subtilis frequently encounters a reduction in temperature in its natural habitats. Here, a combined transcriptomic and proteomic approach has been used to analyse the adaptational responses of B. subtilis to low temperature. Propagation of B. subtilis in minimal medium at 15 °C triggered the induction of 279 genes and the repression of 301 genes in comparison to cells grown at 37 °C. The analysis thus revealed profound adjustments in the overall gene expression profile in chill-adapted cells. Important transcriptional changes in low-temperature-grown cells comprise the induction of the SigB-controlled general stress regulon, the induction of parts of the early sporulation regulons (SigF, SigE and SigG) and the induction of a regulatory circuit (RapA/PhrA and Opp) that is involved in the fine-tuning of the phosphorylation status of the Spo0A response regulator. The analysis of chill-stress-repressed genes revealed reductions in major catabolic (glycolysis, oxidative phosphorylation, ATP synthesis) and anabolic routes (biosynthesis of purines, pyrimidines, haem and fatty acids) that likely reflect the slower growth rates at low temperature. Low-temperature repression of part of the SigW regulon and of many genes with predicted functions in chemotaxis and motility was also noted. The proteome analysis of chill-adapted cells indicates a major contribution of post-transcriptional regulation phenomena in adaptation to low temperature. Comparative analysis of the previously reported transcriptional responses of cold-shocked B. subtilis cells with this data revealed that cold shock and growth in the cold constitute physiologically distinct phases of the adaptation of B. subtilis to low temperature.
    Type of Medium: Online Resource
    ISSN: 1350-0872 , 1465-2080
    URL: Article
    DOI: 10.1099/mic.0.28530-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2006
    detail.hit.zdb_id: 2008736-6
    SSG: 12
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