Dataset Information

High resolution time-lapse proteomic analysis of sporulation

ABSTRACT: 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.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Bacillus Subtilis

SUBMITTER: Gertjan Kramer

PROVIDER: MSV000087154 | MassIVE | Sat Apr 03 03:02:00 BST 2021

SECONDARY ACCESSION(S): PXD025157

REPOSITORIES: MassIVE

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Publications

High Resolution Analysis of Proteome Dynamics during <i>Bacillus subtilis</i> Sporulation.

Tu Zhiwei Z Dekker Henk L HL Roseboom Winfried W Swarge Bhagyashree N BN Setlow Peter P Brul Stanley S Kramer Gertjan G

International journal of molecular sciences 20210828 17

<i>Bacillus subtilis</i> vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome dynamics during sporulation, high-resolution time-lapse proteomics 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-ex ...[more]

PMID: 34502250

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Project description:During development, the human brain orchestrates the generation of hundreds of diverse cell types, and recent transcriptomic atlases of the developing human cortex provide new opportunities to identify novel regulators of cell fate specification. We have conducted an integrated meta-analysis of seven recently published single-cell transcriptomic profiles of the developing human cortex, generating a meta-atlas of 225 meta-modules. By tracking the activity of these meta-modules throughout development and comparing this to datasets from the adult human as well as the developing and adult mouse, we identified modules with potential roles in the transition from neurogenesis to gliogenesis and neuronal subtype maturation. The cell type and developmental state at which these modules exist was validated in primary samples from the developing human brain. Of particular interest, we identified and validated a module associated with both developing human deep layer neurons and human adult deep layer neuronal subtypes expressing the terminal differentiation marker FEZF2. Though FEZF2 is neither a member of nor co-expressed with our deep layer-associated gene module, almost half of module genes are putative FEZF2 targets, including TSHZ3, a transcription factor associated with neurodevelopmental disorders such as autism. Knockdown experiments in human cortical organoid models confirm that both FEZF2 and TSHZ3 are necessary for deep layer neuron specification. Importantly, we observe that subtle manipulations of these transcription factors result in slight changes in module activity, but together yield strong differences in cell fate. Our analyses therefore reveal a gene network that required to generate deep layer neuronal subtypes, demonstrating the ability of our meta-atlas to engender further mechanistic analyses of cortical fate specification. We anticipate this resource being useful for the study of co-expression programs across diverse biological questions related to the developing neocortex.

Dataset Information

High resolution time-lapse proteomic analysis of sporulation

Publications

High Resolution Analysis of Proteome Dynamics during <i>Bacillus subtilis</i> Sporulation.

Similar Datasets

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