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Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and
Christine Eymann1, Georg Homuth, Christian Scharf
1Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany.
Journal of Bacteriology
|April 12, 2002
Summary
The stringent response in Bacillus subtilis involves complex regulation of protein synthesis, with some proteins being downregulated and others upregulated, depending on the RelA protein. Transcriptome analysis provides a more comprehensive view than proteomics for understanding gene expression during this response.
Area of Science:
- Microbiology
- Molecular Biology
- Bacterial Physiology
Background:
- The stringent response is a crucial survival mechanism in bacteria, triggered by nutrient deprivation or stress.
- This response involves the accumulation of guanosine tetraphosphate (ppGpp) and its effect on gene expression.
- Understanding the stringent response in Bacillus subtilis is vital for comprehending bacterial adaptation and survival strategies.
Purpose of the Study:
- To comprehensively characterize the stringent response in Bacillus subtilis using integrated proteome and transcriptome analyses.
- To identify and classify proteins and genes affected by the stringent response and the RelA protein.
- To compare the effectiveness of proteomic and transcriptomic approaches in mapping gene expression changes.
Main Methods:
- Proteome analysis comparing wild-type and relA mutant Bacillus subtilis under stringent conditions.
- Transcriptome analysis using DNA macroarrays to assess global gene expression.
- DL-norvaline was used to induce the stringent response.
Main Results:
- Significant differences in protein synthesis patterns were observed between wild-type and relA mutant cells.
- Proteins were categorized into four classes based on their regulation: negative stringent control (decreased synthesis), positive stringent control (induced synthesis), and RelA-independent regulation.
- Transcriptome analysis revealed comparable gene expression patterns to proteomic data but offered a more comprehensive global profile, detecting a broader subset of RelA-dependent genes.
- The study mapped protein-encoding genes affected by (p)ppGpp, revealing that negative control targets growth-related processes, while positive control involves RelA-dependent induction.
Conclusions:
- The stringent response in Bacillus subtilis is a multifaceted process involving both repression and induction of gene expression, significantly influenced by the RelA protein.
- Proteomics and transcriptomics are complementary approaches, with transcriptomics providing a more global view of gene expression changes.
- A passive model involving RNA polymerase redistribution is proposed to explain the positive stringent control mechanism mediated by (p)ppGpp.