Intergrative analysis of proteome and transcriptome dynamics during Bacillus subtilis spore revival
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PROVIDER: PRJNA609969 | ENA |
REPOSITORIES: ENA
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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:Background: Bacterial spores can remain dormant for decades, yet harbor the exceptional capacity to rapidly resume metabolic activity and recommence life. Although germinants and their corresponding receptors have been known for more than 30 years, the molecular events underlying this remarkable cellular transition from dormancy to full metabolic activity are only partially defined. Results: Here, we examined whether protein phospho-modifications occur during germination, the first step of exiting dormancy, thereby facilitating spore revival. Utilizing Bacillus subtilis as a model organism, we performed phosphoproteomic analysis to define the Ser/Thr/Tyr phosphoproteome of a reviving spore. The phosphoproteome was found to chiefly comprise newly identified phosphorylation sites located within proteins involved in basic biological functions, such as transcription, translation, carbon metabolism and spore-specific determinants. Quantitative comparison of dormant and germinating spore phosphoproteomes revealed phosphorylation dynamics, indicating that phospho-modifications could modulate protein activity during this cellular transition. Furthermore, by mutating select phosphorylation sites located within proteins representative of key biological processes, we established a functional connection between phosphorylation and the progression of spore revival. Conclusions: In this study we provide for the first time a phosphoproteomic view of a germinating bacterial spore. We show that the spore phosphoproteome is dynamic and present evidence that phosphorylation events play an integral role in facilitating spore revival.
2015-08-27 | PXD002559 | Pride
Project description:Description
Bacillus subtilis forms highly resistant, metabolically inactive spores upon nutrient limitation. These endospores pose challenges to the food and medical sectors. Spores reactivate their metabolism upon contact with germinants through germination and outgrowth, and then develop into vegetative cells. However, the mechanism of the activation of the molecular machinery that triggers spore germination and outgrowth is unclear. To gain further insight into spore germination and outgrowth, the transcriptome and proteome 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. For each time-point sampled, the change in the spore proteome was quantitatively monitored relative to the reference proteome of 15N metabolically labelled vegetative cells. Of the quantified proteins, 60 percent are common to vegetative cells and spores, indicating that spores have a minimal set of proteins sufficient for the resumption of metabolism upon completion of germination. The shared proteins thus represent the most basic survival kit for spore-based life. Until the phase transition, defined as the completion of germination, we observed no significant change in the proteome or the transcriptome. Our analysis identified 34 abundant mRNA transcripts in the dormant spores, at least 31 of which were rapidly degraded after the phase transition. We observed 3152 differentially expressed genes, and demonstrated with our mass spectrometry analyses the differential expression of 323 proteins. Our data show that 173 proteins from dormant spores, both proteins unique to spores and proteins shared with vegetative cells, are lost after completion of germination. Further analysis is required to functionally interpret the observed protein loss. The observed diverse timing of the synthesis of different protein sets reveals a putative core-strategy of the revival of life starting from the B. subtilis spore.
2020-04-02 | MSV000085217 | MassIVE
Project description:Bacillus subtilis spores can reactivate their metabolism through germination upon contact with germinants and can develop into vegetative cells upon outgrowth. However, the mechanisms at the basis of the molecular machinery that triggers the spore germination and outgrowth processes are still largely unclear. To gain further insights into these processes, the transcriptome and proteome changes occurring during the conversion of spores to vegetative cells were analyzed in the present study. For each time point sampled, the changes in the spore proteome were quantitatively monitored relative to the proteome of metabolically 15N-labeled vegetative cells. Of the quantified proteins, 60% are shared by vegetative cells and spores, indicating that the spores have a minimal protein set, sufficient to resume metabolism upon completion of germination. These shared proteins thus represent the most basic "survival kit" for spore-based life. We observed no significant change in the proteome or the transcriptome until the spore's completion of germination. Our analysis identified 34 abundant mRNA transcripts in the dormant spores, 31 of which are rapidly degraded after germination. In outgrowing spores, we identified 3,152 differentially expressed genes and have demonstrated the differential expression of 322 proteins with our mass spectrometry analyses. Our data also showed that 173 proteins from dormant spores, including both proteins unique to spores and proteins shared with vegetative cells, were lost after completion of germination. The observed diverse timings of synthesis of different protein sets in spore outgrowth revealed a putative core strategy underlying the revival of 'life' from the B. subtilis spore.IMPORTANCE This study demonstrated the progress of macromolecular synthesis during Bacillus subtilis spore germination and outgrowth. The transcriptome analysis has additionally allowed us to trace gene expression during this transformation process. For the first time, the basic survival kit for spore-based life has been identified. In addition, in this analysis based on monitoring of protein levels in germinating and outgrowing spores, the transition from (ribo)nucleotide and amino acid biosynthesis to the restoration of all metabolic pathways can be clearly seen. The integrative multi-omics approach applied in this study thus has helped us to achieve a comprehensive overview of the molecular mechanisms at the basis of spore germination and outgrowth as well as to identify important knowledge gaps in need of further study.
| S-EPMC7407066 | biostudies-literature
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:Analysis of differential gene expression during Bacillus subtilis spore outgrowth
| PRJNA428231 | ENA
Project description:Characterization of the putative genetic determinants of the VBNC state in a known spore-forming Gram-positive organism Bacillus subtilis 168. The VBNC state was induced under osmotic stress and aminoglycoside treatment. The transcriptome landscape of VBNC cells was compared to the viable, antibiotic sensitive B. subtilis cells and to the viable cells with no antibiotic treatment.
2022-07-02 | GSE207180 | GEO
Project description:Summary
To facilitate more accurate spore proteomic analysis, the current study focuses on inducing homogeneous sporulation by overexpressing kinA and assesses the effect of sporulation synchronization on spore resistance, structures, the germination behavior at single-spore level and the proteome. The results indicate that, in our set up, the synchronized sporulation by overexpressing kinA can generate a spore yield of 70% within 8 hours. The procedure increases spore wet heat resistance and thickness of the spore coat and cortex layers, whilst delaying the time to spore phase-darkening and burst after addition of germinant. The proteome analysis reveals that the upregulated proteins in the kinA induced spores, compared to spores without kinA induction as well as the wildtype spores, are mostly involved in spore formation. The downregulated proteins mostly belong to the categories of coping with stress, carbon and nitrogen metabolism, as well as regulation of sporulation. Thus, while kinA overexpression enhances sporulation synchronicity it also has profound effects on the central equilibrium of spore formation and spore germination through modulation of the spore molecular composition and stress resistance physiology.
2020-04-28 | MSV000085346 | MassIVE
Project description:Using RNA-seq, we cataloged messenger RNAs in highly purified dormant Bacillus subtilis spores prepared either on plates or in liquid. Almost all of the most abundant spore mRNAs are encoded by genes expressed only in the developing spore late in sporulation under control of the forespore-specific RNA polymerase sigma factor, sG. Given the levels of the ~40 most abundant mRNAs in dormant spores, we calculated the great majority of the low abundance mRNAs can be present in only a small fraction of the spore population.
2019-04-01 | GSE125530 | GEO