title: Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins.
abstract: The marine bacterium Rhodopirellula baltica, a member of the phylum Planctomycetes, has distinct morphological properties and contributes to remineralization of biomass in the natural environment. On the basis of its recently determined complete genome we investigated its proteome by 2-DE and established a reference 2-DE gel for the soluble protein fraction. Approximately 1000 protein spots were excised from a colloidal Coomassie-stained gel (pH 4-7), analyzed by MALDI-MS and identified by PMF. The non-redundant data set contained 626 distinct protein spots, corresponding to 558 different genes. The identified proteins were classified into role categories according to their predicted functions. The experimentally determined and the theoretically predicted proteomes were compared. Proteins, which were most abundant in 2-DE gels and the coding genes of which were also predicted to be highly expressed, could be linked mainly to housekeeping functions in glycolysis, tricarboxic acid cycle, amino acid biosynthesis, protein quality control and translation. Absence of predictable signal peptides indicated a localization of these proteins in the intracellular compartment, the pirellulosome. Among the identified proteins, 146 contained a predicted signal peptide suggesting their translocation. Some proteins were detected in more than one spot on the gel, indicating post-translational modification. In addition to identifying proteins present in the published sequence database for R. baltica, an alternative approach was used, in which the mass spectrometric data was searched against a maximal ORF set, allowing the identification of four previously unpredicted ORFs. The 2-DE reference map presented here will serve as framework for further experiments to study differential gene expression of R. baltica in response to external stimuli or cellular development and compartmentalization.
authors.affiliation: Max Planck Institute for Marine Microbiology, Bremen, Germany.
authors.forename: Dörte
authors.initials: D
authors.lastname: Gade
authors.forename: Dorothea
authors.initials: D
authors.lastname: Theiss
authors.forename: Daniela
authors.initials: D
authors.lastname: Lange
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Mirgorodskaya
authors.forename: Thierry
authors.initials: T
authors.lastname: Lombardot
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Glöckner
authors.forename: Michael
authors.initials: M
authors.lastname: Kube
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Rudolf
authors.initials: R
authors.lastname: Amann
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Ralf
authors.initials: R
authors.lastname: Rabus
authors.forename: Johan
authors.initials: J
authors.lastname: Gobom
mesh_terms: D001419:Bacteria / Q000737:chemistry* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D015180:Electrophoresis, Gel, Two-Dimensional; D015870:Gene Expression; D008386:Marine Biology; D021382:Protein Sorting Signals; D020543:Proteome; D012995:Solubility; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D001426:Bacterial Proteins; D021382:Protein Sorting Signals; D020543:Proteome