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Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation [RNA-seq]

ABSTRACT: Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. Using a triple knock-out strain (3KO) of zinc-independents paralogs of three zinc-dependent ribosomal proteins L31, L33 and S14, we investigated the potential regulatory role of ribosome during sporulation. The 3KO strain exhibited delayed sporulation, reduced germination efficiency, and dysregulated translation including expression of key metabolic and sporulation-related genes as well as disruptions in translation silencing, particularly in late sporulation.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE249449 | GEO | 2023/12/06

REPOSITORIES: GEO

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Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation [Ribo-seq]

Project description:Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. Using a triple knock-out strain (3KO) of zinc-independents paralogs of three zinc-dependent ribosomal proteins L31, L33 and S14, we investigated the potential regulatory role of ribosome during sporulation. The 3KO strain exhibited delayed sporulation, reduced germination efficiency, and dysregulated translation including expression of key metabolic and sporulation-related genes as well as disruptions in translation silencing, particularly in late sporulation.

2023-12-06 | GSE249448 | GEO

Elongation Factor P is important for sporulation initiation

Project description:The universally conserved protein Elongation Factor P facilitates translation at amino acids that form peptide bonds with low efficiency, particularly poly-proline tracts. Despite its wide conservation, it is not essential in most bacteria and its physiological role remains unclear. Here, we show that EF-P affects the process of sporulation initiation in the bacterium Bacillus subtilis. We observe that lack of EF-P delays expression of sporulation-specific genes. Using ribosome profiling, we observe that expression of spo0A, encoding a transcription factor that functions as the master regulator of sporulation, is lower in a ∆efp strain as compared to the wildtype. Ectopic expression of Spo0A rescues the sporulation initiation phenotype, indicating that reduced spo0A expression explains the sporulation defect in ∆efp cells. Since Spo0A is the earliest sporulation transcription factor, these data suggest that sporulation initiation can be delayed when protein synthesis is impaired.

2023-01-04 | GSE222121 | GEO

Sporulation in Bacillus subtilis (mother cell)

Project description:This series of experiments was designed to identify the program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. The mother cell is one of two cell types generated by asymmetric division of sporulating cells approximately two hours after initiation of sporulation. The program is governed by a hierarchical cascade consisting of the transcription factors: sigmaE, sigmaK, GerE, GerR (YlbO) and SpoIIID. The characterization of the sigmaE regulon was reported in Eichenberger et al. (2003), J. Mol. Biol. 327, 945-972. Here we report the data for sigmaK, GerE, GerR and SpoIIID.

2004-09-01 | GSE1620 | GEO

RNA-seq of four Bacillus subtilis mutants during sporulation

Project description:Endospore (hereafter called spore) is a dormant, tough, and non-reproductive structure produced in a lack of nutrients by certain species of bacteria from the Firmicute phylum. Sporulation is tightly linked to cell cycle and involving by temporal and spatial regulation of hundreds genes. It has been suggested more than 500 genes are contributed to sporulation in B. subtilis, and there are certainly more. In our study, we identified four new sporulation genes and their mutants exhibited sporulation abnormal. RNA-seq of mutants compared to wild type during sporulation will reveal the regulation of sporulation related genes in the four mutants, and therefore shed the light to the functional role of the four new sporulation genes.

2020-03-18 | E-MTAB-8124 | biostudies-arrayexpress

High resolution time-lapse proteomic analysis of sporulation

Project description:Bacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome changeover during sporulation, a time-lapse proteomic analysis was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules. Modules brown and green are upregulated during sporulation and are annotated as associated with sporulation. Module blue, which is negatively correlated with modules brown and green, comprised ribosomal and metabolic proteins, and module yellow is co-expressed with module blue and modules brown & green. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green. We speculate that they may also play roles during sporulation. Finally, amounts of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation. While we speculate on their possible role in guiding or helping assembly of other coat proteins, after which they can be disposed of, such a hypothesis remains to be experimentally addressed.

2021-04-03 | MSV000087154 | MassIVE

Sporulation in Bacillus subtilis (mother cell)

2010-06-06 | E-GEOD-1620 | biostudies-arrayexpress

Global analysis of genes induced during sporulation of Clostridium difficile

Project description:Purpose: The goal of this study was to identify genes whose expression is induced during sporulation in a Spo0A-, σF-, σE-, σG-, and σK-dependent manner. Methods: Whole genome RNA sequencing was performed on wildtype, spo0A-, sigF-, sigE-, sigG-, and sigK- C. difficile strains (strain 630 background; JIR8094 = parent strain), and the transcriptional profiles of the different mutants during growth on 70:30 agar plates were determined using an Illumina HiSeq1000. Results: This analysis identified 185 genes whose expression is collectively activated by sporulation sigma factors: 150 were σF-dependent, 150 were σE-dependent, 30 were σG-dependent, and 31 were σK-dependent. A total of 237 genes were identified as requiring Spo0A for their expression when sporulation was induced on the 70:30 plates. Conclusions: These results provide the first genome-wide transcriptional analysis of genes whose expression is induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. For example, in contrast with the B. subtilis sporulation pathway, C. difficile σE was not required to fully activate σG, and σG was not required to activate σK.

2013-08-10 | GSE45977 | GEO

Regulation of σK activity and function by SpoIIID during Clostridium difficile sporulation

Project description:Purpose: A goal of this study was to identify genes induced in the mother cell during Clostridium difficile sporulation (specifically in a σE-, σK-, and SpoIIID-dependent manner). Methods: Whole genome RNA sequencing was performed on wildtype, sigE-, sigK- and spoIIID- C. difficile strains (strain 630 background; JIR8094 = parent strain), and the transcriptional profiles of the different mutants during growth on 70:30 agar plates were determined using an Illumina MiSeq1000. Results: This analysis identified 200 genes whose expression is collectively activated by sporulation sigma factors: 159 were σF-dependent, 162 were σE-dependent, 28 were σG-dependent, and 36 were σK-dependent. A total of 254 genes were identified as requiring Spo0A for their expression when sporulation was induced on the 70:30 plates. Conclusions: These results provide the first genome-wide transcriptional analysis of genes whose expression is induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. For example, in contrast with the B. subtilis sporulation pathway, C. difficile σE was not required to fully activate σG, and σG was not required to activate σK.

2014-12-02 | GSE63777 | GEO

RNA-seq of four Bacillus subtilis mutants during sporulation

Project description:RNA-seq of four Bacillus subtilis mutants during sporulation

| PRJEB33371 | ENA

PrkA regulates Bacillus subtilis sporulation through a Lon protease activity

Project description:In Bacillus subtilis, sporulation is a sequential and highly regulated process. Phosphorylation events by Histidine or Serine/Threonine kinases are key points in this regulation. PrkA has been proposed to be an essential Serine kinase for the initiation of sporulation but its kinase activity has not been clearly demonstrated so far. Indeed, neither its autophosphorylation nor identification of a B. subtilis phosphorylated substrate was unambiguously established. Bioinformatic homology searches revealed sequence similarities with the AAA+ ATP-dependent Lon protease family. Here, we showed that PrkA is indeed able to hydrolyse the α-casein, an exogenous substrate of Lon proteases, in an ATP-dependent manner. We also showed that this ATP-dependent protease activity is essential for PrkA function in sporulation since mutation in the Walker A motif leads to a sporulation defect. Furthermore, we found that PrkA protease activity is tightly regulated by phosphorylation events involving one of the Ser/Thr kinases of B. subtilis, PrkC, as characterized by mass spectrometry from 3 in vitro independent experiments (1: PrkA+PrkC/2:PrKA-S219E+PrkC/3: PrKA-T217E+PrkC). We finally demonstrated that PrkA regulation of the transcriptional factor σK via the transition phase regulator ScoC is certainly indirect.

2022-10-15 | PXD032931 | Pride

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