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Abstract

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-LCbased
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.