解析叶绿体被膜蛋白组的隐藏组分:提高 MS 灵敏度的机遇与局限。

Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity.

机构信息

From the ‡University Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France.

§University Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France.

出版信息

Mol Cell Proteomics. 2019 Jul;18(7):1285-1306. doi: 10.1074/mcp.RA118.000988. Epub 2019 Apr 8.

Abstract

The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides etc.) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins ( 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast subcompartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared with the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.

摘要

叶绿体是一种主要的植物细胞细胞器,履行着重要的代谢和生物合成功能。位于叶绿体与其他细胞区室的界面处,叶绿体包膜系统是一个战略性的屏障,控制着离子、代谢物和蛋白质的交换,从而调节植物细胞的基本代谢功能(激素前体、氨基酸、色素、糖、维生素、脂质、核苷酸等的合成)。然而,揭示叶绿体包膜蛋白组的内容仍然是一个具有挑战性的难题;构成这个功能双层膜系统的许多蛋白质仍然有待鉴定。事实上,包膜只含有叶绿体蛋白质的 1%(整个细胞蛋白质组的 0.4%)。换句话说,包膜中的大多数蛋白质在细胞、叶绿体甚至包膜水平上都非常稀少,以至于使用靶向 MS 研究仍然无法检测到它们。在细胞分级过程中,叶绿体亚区室之间以及与其他细胞区室之间的交叉污染,阻碍了许多包膜蛋白的准确定位。本研究的目的是利用技术上改进的 MS 灵敏度,更好地定义叶绿体包膜的蛋白质组(将真正的包膜蛋白与污染物区分开来)。这种基于 MS 的分析依赖于一个富集因子,该因子是为在纯化的包膜级分中鉴定的每种蛋白质相对于在粗细胞提取物中获得的相同蛋白质的值计算得出的。使用这种方法,在纯化的包膜级分中总共检测到 1269 种蛋白质,其中 462 种可以通过结合基于 MS 的谱计数分析和使用文献和预测工具的数据进行手动注释来分配包膜定位。其中许多蛋白质是以前未知的包膜成分,这些数据构成了一个新的有价值的资源,为更广泛的植物科学界提供了定义控制质体生物发生和功能基本方面的原则和分子机制的资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dae9/6601204/864b6596b930/zjw0061959430010.jpg

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