Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395

Phaeobacter inhibens DSM 17395 is a metabolically versatile, secondary metabolite producing and surface colonizing member of the alphaproteobacterial Roseobacter clade. Proteins compartmentalized across the Gram‐negative cell envelope are expected to be relevant for the habitat success of P. inhiben...

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Published in:Proteomics (Weinheim) 2013-10, Vol.13 (18-19), p.2743-2760
Main Authors: Koßmehl, Sebastian, Wöhlbrand, Lars, Drüppel, Katharina, Feenders, Christoph, Blasius, Bernd, Rabus, Ralf
Format: Article
Language:English
Subjects:
Bacterial Proteins - metabolism
Bacteriology
Cell envelope
Cell Wall - metabolism
Databases, Protein
Electrophoresis, Polyacrylamide Gel
Membrane proteomics
Microbiology
Multidimensional scaling
Protein Transport
Proteins
Proteome - metabolism
Proteomics
PSORTb
Roseobacter
Roseobacter - metabolism
Subcellular fractionation
Subcellular Fractions - metabolism
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Summary:Phaeobacter inhibens DSM 17395 is a metabolically versatile, secondary metabolite producing and surface colonizing member of the alphaproteobacterial Roseobacter clade. Proteins compartmentalized across the Gram‐negative cell envelope are expected to be relevant for the habitat success of P. inhibens DSM 17395. Subcellular fractionation was followed by gel‐ or nano‐LC‐based separation of proteins and peptides, respectively. Subsequent MS‐based identification of in total 1187 proteins allowed allocation to cytoplasm (303 proteins), cytoplasmic membrane (346), periplasm (325), outer membrane (76), and extracellular milieu (22). Multidimensional scaling was used to visualize the spreading of heuristically allocated proteins across the five different compartments. Experimentally inferred subcellular protein localization was compared with PSORTb prediction of protein secretion and membrane localization. Determined subcellular localizations of identified proteins were interpreted to reconstruct the functional traits of the different cell envelope compartments, in particular protein secretion and sorting, direct effector molecule transit, and cell envelope biogenesis. From a proteogenomic perspective, functional prediction of 74 genes (including 17 coding for proteins of hitherto unknown function) could be refined.
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.201300112