State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, PR China.
J Proteome Res. 2010 Mar 5;9(3):1195-202. doi: 10.1021/pr900146t.
To gain a better understanding of the critical function of the endoplasmic reticulum (ER) in liver, we carried out a proteomic survey of mouse liver ER. The ER proteome was profiled with a new three-dimensional, gel-based strategy. From 6152 and 6935 MS spectra, 903 and 1042 proteins were identified with at least two peptides matches at 95% confidence in the rough (r) and smooth (s) ER, respectively. Comparison of the rER and sER proteomes showed that calcium-binding proteins are significantly enriched in the sER suggesting that the ion-binding function of the ER is compartmentalized. Comparison of the rat and mouse ER proteomes showed that 662 proteins were common to both, comprising 53.5% and 49.3% of those proteomes, respectively. We proposed that these proteins were stably expressed proteins that were essential for the maintenance of ER function. GO annotation with a hypergeometric model proved this hypothesis. Unexpectedly, 210 unknown proteins and some proteins previously reported to occur in the cytosol were highly enriched in the ER. This study provides a reference map for the ER proteome of liver. Identification of new ER proteins will enhance our current understanding of the ER and also suggest new functions for this organelle.
为了更好地理解内质网（ER）在肝脏中的关键功能，我们对小鼠肝脏 ER 进行了蛋白质组学调查。采用新的三维凝胶基策略对 ER 蛋白质组进行了分析。在粗面内质网（rER）和光面内质网（sER）中，分别从 6152 和 6935 个 MS 谱中鉴定出了 903 个和 1042 个至少有两个肽段匹配的蛋白质，置信度为 95%。rER 和 sER 蛋白质组的比较表明，钙结合蛋白在 sER 中显著富集，表明 ER 的离子结合功能是分区的。大鼠和小鼠 ER 蛋白质组的比较表明，有 662 个蛋白质是两者共有的，分别占这两个蛋白质组的 53.5%和 49.3%。我们提出这些蛋白质是稳定表达的蛋白质，对于维持 ER 功能是必需的。用超几何模型进行的 GO 注释证明了这一假设。出乎意料的是，210 种未知蛋白质和一些以前报道存在于细胞质中的蛋白质在内质网中高度富集。这项研究为肝脏 ER 蛋白质组提供了一个参考图谱。识别新的 ER 蛋白质将增强我们对 ER 的现有理解，并为这个细胞器提出新的功能。
