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A proteomic view on genome-based signal peptide predictions
H Antelmann1, H Tjalsma, B Voigt
1Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universiät Greifswald, D-17487 Greifswald, Germany.
Genome Research
|September 7, 2001
Summary
Genome predictions for Bacillus subtilis secretomes are only 50% accurate. Proteomic analysis revealed many extracellular proteins lack predicted signal peptides or are lipoproteins, highlighting limitations in current bioinformatics tools for exported proteins.
Area of Science:
- Microbiology
- Proteomics
- Bioinformatics
Background:
- Genome sequencing enables prediction of exported proteins.
- Previous studies predicted Bacillus subtilis signal peptides but lacked proteomic verification.
- Genome-based predictions often lack experimental validation.
Purpose of the Study:
- To proteomically define the extracellular proteome of Bacillus subtilis.
- To verify genome-based predictions of secreted and lipoprotein signal peptides.
- To investigate the role of signal peptidases (SPases) in protein secretion.
Main Methods:
- Utilized two-dimensional (2D) gel electrophoresis to visualize extracellular proteins.
- Employed mass spectrometry for protein identification.
- Analyzed extracellular proteomes of wild-type and mutant Bacillus subtilis strains, including SPase mutants.
Main Results:
- Visualized ~200 extracellular proteins, identifying 82 by mass spectrometry.
- 41 identified proteins possessed signal peptides, while 41 lacked them or had retention signals.
- SPase mutants showed limited impact, except for polytopic membrane protein YfnI processing; lipoprotein processing mutants released ~23 lipoproteins.
Conclusions:
- Genome-based predictions for extracellular proteomes are only ~50% accurate.
- Significant challenges exist in predicting extracellular proteins lacking signal peptides and lipoproteins.
- Proteomic verification is crucial for accurate secretome analysis.