Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
Proteomics. 2013 Oct;13(18-19):2743-60. doi: 10.1002/pmic.201300112.
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.
抑食金球藻（Phaeobacter inhibens）DSM 17395 是一种代谢多功能、产生次生代谢产物和定殖于表面的 α 变形菌玫瑰杆菌群成员。预计定殖于革兰氏阴性细胞包膜的蛋白对于抑食金球藻（P. inhibens）DSM 17395 的生境成功至关重要。采用亚细胞分级分离，随后分别进行凝胶或纳升液相色谱法分离蛋白质和肽。基于 MS 的总共 1187 种蛋白质的鉴定允许分配到细胞质（303 种蛋白质）、细胞质膜（346 种）、周质（325 种）、外膜（76 种）和细胞外环境（22 种）。多维缩放用于可视化启发式分配的蛋白质在五个不同隔室中的分布。实验推断的亚细胞蛋白定位与 PSORTb 预测的蛋白分泌和膜定位进行了比较。确定的鉴定蛋白的亚细胞定位用于解释不同细胞包膜隔室的功能特征，特别是蛋白分泌和分类、直接效应分子转运和细胞包膜生物发生。从蛋白质基因组学的角度来看，可以对 74 个基因（包括 17 个编码迄今未知功能的蛋白质）的功能预测进行细化。
