AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins
AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins
复制标题
DOI：
10.1074/mcp.m900325-mcp200
复制
发表时间：
2010-06-01
影响因子：
7
通讯作者：
Rolland, Norbert
中科院分区：
文献类型：
--
作者：
Ferro, Myriam;Brugiere, Sabine;Rolland, Norbert
蛋白质组学领域的最新进展使一系列高通量实验得以在叶绿体样本上进行，这些数据可以在几个公共数据库中找到。然而，许多叶绿体蛋白的准确定位往往仍然是假设的。对于包膜蛋白来说尤其如此。在同一组实验中，我们通过聚焦于基质、类囊体膜和被膜中蛋白质的定位，进一步了解了叶绿体蛋白质组的知识。基于LC-MS/MS的分析首次允许建立AT_Clo数据库(http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/)，，该数据库由10,654个独特的肽序列鉴定，这些蛋白质存在于高纯度的拟南芥叶片叶绿体及其亚组分中。该数据库还提供丰富的蛋白质组学信息(肽序列和分子量、色谱保留时间、MS/MS光谱和光谱计数)，用于收集独特的叶绿体蛋白质准确的质量和时间标签数据库，收集已识别的多肽及其各自精确的分析坐标、相对分子质量和保留时间。我们使用半定量蛋白质组学方法(光谱计数)评估了每种蛋白质在三个叶绿体隔室中的分配。这些数据与对文献的深入研究一起汇编，以提供先前已知和新鉴定的蛋白质的准确亚质内定位。因此，获得了一个独特的知识库，其中包含了关于包膜组份中识别的蛋白质的广泛信息，从而使人们能够对这一膜系统有新的见解。总之，我们获得的数据提供了一些与该膜系统无关的蛋白质的胞质或亚胞质定位的意想不到的信息。基于光谱计数的策略被进一步验证，因为可以解剖叶绿体内众所周知的途径(例如，光合作用和氨基酸、脂肪酸或甘油脂生物合成)的区隔。它还允许重新研究叶绿体新陈代谢和功能的区隔。分子与细胞蛋白质组学9：1063-1084,2010。
Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further validated as the compartmentation of well known pathways (for instance, photosynthesis and amino acid, fatty acid, or glycerolipid biosynthesis) within chloroplasts could be dissected. It also allowed revisiting the compartmentation of the chloroplast metabolism and functions. Molecular & Cellular Proteomics 9:1063-1084, 2010.