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Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395
Author(s) -
Koßmehl Sebastian,
Wöhlbrand Lars,
Drüppel Katharina,
Feenders Christoph,
Blasius Bernd,
Rabus Ralf
Publication year - 2013
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201300112
Subject(s) - periplasmic space , subcellular localization , biology , protein subcellular localization prediction , biogenesis , membrane protein , microbiology and biotechnology , proteome , proteomics , cytoplasm , secretion , cell fractionation , transport protein , secretory protein , biochemistry , bacterial outer membrane , cell envelope , effector , gene , membrane , escherichia coli
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.