Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis

Area of Science:

• Microbiology and Molecular Biology
• Systems Biology
• Bacterial Physiology

Background:

• Bacillus subtilis is a key Gram-positive model organism for studying bacterial cell physiology.
• Understanding cellular responses to nutrient limitation is crucial for basic science and biotechnology.

Purpose of the Study:

• To comprehensively profile temporal changes in the proteome, transcriptome, and extracellular metabolome of B. subtilis during glucose starvation.
• To investigate the fate of gene products and major physiological processes, including protein degradation, in the stationary phase.

Main Methods:

• Utilized in vivo metabolic labeling and shotgun mass spectrometry for quantitative proteomic analysis across five subfractions (cytosolic, integral membrane, membrane, surface, extracellular).
• Analyzed ~52% of the predicted B. subtilis proteome.
• Integrated quantitative proteomic and transcriptomic data using Voronoi treemaps for functional classification and expression analysis.

Main Results:

• Detailed profiling of changes in the membrane proteome subfraction during glucose starvation.
• Identification of ~52% of the B. subtilis proteome, providing a broad quantitative overview.
• Linked gene product expression changes to functional classifications and their roles in stationary phase adaptation.

Conclusions:

• Glucose starvation induces significant temporal changes across the proteome, transcriptome, and extracellular metabolome of B. subtilis.
• The study provides the first comprehensive analysis of membrane proteome dynamics under starvation.
• Integrated multi-omics data offer deep insights into bacterial adaptation strategies and protein turnover.