Comprehensive subcellular topologies of polypeptides in Streptomyces

Area of Science:

• Microbiology
• Proteomics
• Bioinformatics

Background:

• Streptomyces are Gram-positive bacteria, crucial as cell factories for metabolites and protein secretion.
• Their large genomes and proteomes present complex challenges for metabolic regulation and genetic engineering.

Purpose of the Study:

• To comprehensively annotate the subcellular localization of the Streptomyces lividans TK24 proteome.
• To develop and provide public access to the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb).

Main Methods:

• Introduced uniform nomenclature, re-annotating approximately 4000 proteins.
• Assigned protein localization de novo using prediction tools and manual curation for 7494 proteins.
• Linked S. lividans proteome with Streptomyces coelicolor and Escherichia coli via homology, accessible via a web interface.

Main Results:

• Developed SToPSdb, a comprehensive resource for S. lividans protein localization.
• Included 183 proteins from recent genome re-annotation not found in other databases.
• Incorporated experimental proteomics data for 579 proteins, validating protein existence and topology, and identified vesicle-released proteins.

Conclusions:

• SToPSdb is an updated, comprehensive annotation resource for S. lividans and other streptomycetes.
• It serves as a foundation for integrating experimental proteomics, genomics, and metabolomics data.