Comprehensive subcellular topologies of polypeptides in Streptomyces.

BACKGROUND: Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. RESULTS: Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known. CONCLUSIONS: SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism.

Development of mass spectrometric methods for detecting arsenic-glutathione complexes.

It has been suggested recently that arsenic-glutathione (As-GSH) complexes play an important role in the methylation of arsenic. The present study describes the development of high-performance liquid chromatography (HPLC)-electrospray tandem mass spectrometry (ES-MS/MS), operated in the selected reaction monitoring (SRM) mode, and HPLC-inductively coupled plasma mass spectrometry (ICP-MS) methods suitable for the sensitive and selective identification of four As-GSH complexes. Method optimization was carried out using a series of synthetically prepared standards, i.e., three As-GSH species containing trivalent arsenic: tri(glutamyl-cysteinyl-glycinyl)trithio-arsenite (ATG), di(glutamyl-cysteinyl-glycinyl)methyl-dithio-arsonite (MADG), and (ã-glutamyl-cysteinyl-glycinyl) dimethyl-thio-arsinite (DMAG), as well as one As-GSH species containing pentavalent As: dimethylthioarsinic acid-glutathione (DMTA(V)-GSH). The collision induced dissociation behavior of these compounds was investigated in detail to identify optimum SRM transitions for each complex. Both methods were based on reversed-phase chromatography using gradient elution with methanol, formic acid, and water as solvents. The amount of methanol that was used with this HPLC method (up to 12% vol/vol) was compatible with ICP-MS, without the need of a specially adapted interface. Subsequently, these analytical methods were applied to carry out a preliminary investigation about the role of As-GSH complexes in the methylation of arsenite by methylcobalamin (CH(3)B(12)) in the presence of glutathione (GSH). For the first time, the complexes ATG, MADG, and trace amounts of DMAG were detected as products of this reaction.