Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395
Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395
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DOI：
10.1002/pmic.201300112
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发表时间：
2013-10-01
期刊：
影响因子：
3.4
通讯作者：
Rabus, Ralf
中科院分区：
文献类型：
--
作者：
Kossmehl, Sebastian;Woehlbrand, Lars;Rabus, Ralf
Phaeoproteobacterium DSM 17395是α变形菌Roseoproteobacterium进化枝的代谢多功能、次级代谢产物产生和表面定殖成员。预期跨革兰氏阴性细胞包膜区室化的蛋白质与P.lubens DSM 17395的栖息地成功相关。亚细胞分级分离之后分别进行基于凝胶或纳米LC的蛋白质和肽的分离。随后对总共1187种蛋白质的基于MS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）。使用多维标度来可视化在五个不同隔室中分配的蛋白质的扩散。实验推断的亚细胞蛋白定位进行了比较PSORTb预测蛋白分泌和膜定位。确定的亚细胞定位的确定的蛋白质被解释为重建不同的细胞包膜隔室的功能性状，特别是蛋白质分泌和分选，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，74个基因（包括17个编码迄今未知功能的蛋白质）的功能预测可以细化。
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.