Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome
Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome
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DOI：
10.1074/mcp.m116.064527
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发表时间：
2017-02-01
影响因子：
7
通讯作者：
Lobel, Peter
中科院分区：
文献类型：
--
作者：
Jadot, Michel;Boonen, Marielle;Lobel, Peter
准确了解蛋白质在细胞内的位置对于生物医学研究的众多领域非常重要，包括评估假定的蛋白质-蛋白质相互作用的保真度，在整个系统水平上模拟细胞过程，以及调查代谢和疾病途径。许多蛋白质还没有定位，或者还没有完全定位，部分原因是大多数研究没有考虑到整个亚细胞的分布。因此，蛋白质经常被分配给一个细胞器，而相当大的一部分可能驻留在其他地方。作为建立全面细胞图谱的一步，我们使用亚细胞分级结合经典的资产负债表分析和等压标记/定量质谱学来确定>；6000大鼠肝脏蛋白质的位置。我们提供了描述每种蛋白质在八个主要细胞间隔中的分布的定量数据和误差估计：核、线粒体、溶酶体、过氧化体、内质网、高尔基体、质膜和胞浆。考虑细胞内的总分布改善了细胞器分配的质量，并分配了具有多个位置的蛋白质。蛋白质分配和支持数据可通过ProLocate网站(http://prolocate.cabm.rutgers.edu).)在线获取作为这个数据集的一个有用的例子，我们使用细胞器分配来帮助分析一个6个月大的婴儿的整个外显子组测序数据，该婴儿死于一种不明原因的疑似神经退行性溶酶体储存障碍。测序数据使用溶酶体蛋白的列表进行优先排序，这些溶酶体蛋白包括该细胞器中稳定的居民以及在这项研究中确定的新的候选蛋白。后者包括由SLC31A1编码的铜转运蛋白1，我们将其定位于质膜和溶酶体。患者在SLC31A1中有两个预测的功能丧失突变，这表明这可能代表了一种迄今未描述的隐性溶酶体储存病基因。
Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle whereas a significant fraction may reside elsewhere. As a step toward a comprehensive cellular map, we used subcellular fractionation with classic balance sheet analysis and isobaric labeling/quantitative mass spectrometry to assign locations to > 6000 rat liver proteins. We provide quantitative data and error estimates describing the distribution of each protein among the eight major cellular compartments: nucleus, mitochondria, lysosomes, peroxisomes, endoplasmic reticulum, Golgi, plasma membrane and cytosol. Accounting for total intracellular distribution improves quality of organelle assignments and assigns proteins with multiple locations. Protein assignments and supporting data are available online through the Prolocate website (http://prolocate.cabm.rutgers.edu). As an example of the utility of this data set, we have used organelle assignments to help analyze whole exome sequencing data from an infant dying at 6 months of age from a suspected neurodegenerative lysosomal storage disorder of unknown etiology. Sequencing data was prioritized using lists of lysosomal proteins comprising wellestablished residents of this organelle as well as novel candidates identified in this study. The latter included copper transporter 1, encoded by SLC31A1, which we localized to both the plasma membrane and lysosome. The patient harbors two predicted loss of function mutations in SLC31A1, suggesting that this may represent a heretofore undescribed recessive lysosomal storage disease gene.