Kleffmann Torsten, Russenberger Doris, von Zychlinski Anne, Christopher Wayne, Sjölander Kimmen, Gruissem Wilhelm, Baginsky Sacha
Institute of Plant Sciences and Functional Genomics Center Zurich, Swiss Federal Institute of Technology, ETH Zentrum, LFW E51.1, Universitätstrasse 2, CH-8092 Zurich, Switzerland.
Curr Biol. 2004 Mar 9;14(5):354-62. doi: 10.1016/j.cub.2004.02.039.
Chloroplasts are plant cell organelles of cyanobacterial origin. They perform essential metabolic and biosynthetic functions of global significance, including photosynthesis and amino acid biosynthesis. Most of the proteins that constitute the functional chloroplast are encoded in the nuclear genome and imported into the chloroplast after translation in the cytosol. Since protein targeting is difficult to predict, many nuclear-encoded plastid proteins are still to be discovered.
By tandem mass spectrometry, we identified 690 different proteins from purified Arabidopsis chloroplasts. Most proteins could be assigned to known protein complexes and metabolic pathways, but more than 30% of the proteins have unknown functions, and many are not predicted to localize to the chloroplast. Novel structure and function prediction methods provided more informative annotations for proteins of unknown functions. While near-complete protein coverage was accomplished for key chloroplast pathways such as carbon fixation and photosynthesis, fewer proteins were identified from pathways that are downregulated in the light. Parallel RNA profiling revealed a pathway-dependent correlation between transcript and relative protein abundance, suggesting gene regulation at different levels.
The chloroplast proteome contains many proteins that are of unknown function and not predicted to localize to the chloroplast. Expression of nuclear-encoded chloroplast genes is regulated at multiple levels in a pathway-dependent context. The combined shotgun proteomics and RNA profiling approach is of high potential value to predict metabolic pathway prevalence and to define regulatory levels of gene expression on a pathway scale.
叶绿体是起源于蓝细菌的植物细胞器。它们执行着具有全球意义的重要代谢和生物合成功能，包括光合作用和氨基酸生物合成。构成功能性叶绿体的大多数蛋白质由核基因组编码，并在胞质溶胶中翻译后导入叶绿体。由于蛋白质靶向难以预测，许多核编码的质体蛋白仍有待发现。
通过串联质谱分析，我们从纯化的拟南芥叶绿体中鉴定出690种不同的蛋白质。大多数蛋白质可归属于已知的蛋白质复合物和代谢途径，但超过30%的蛋白质功能未知，且许多蛋白质未被预测定位于叶绿体。新的结构和功能预测方法为功能未知的蛋白质提供了更丰富的注释信息。虽然在关键的叶绿体途径如碳固定和光合作用方面实现了近乎完整的蛋白质覆盖，但从在光照下下调的途径中鉴定出的蛋白质较少。平行的RNA分析揭示了转录本与相对蛋白质丰度之间的途径依赖性相关性，表明在不同水平上的基因调控。
叶绿体蛋白质组包含许多功能未知且未被预测定位于叶绿体的蛋白质。核编码的叶绿体基因的表达在依赖途径的背景下受到多个水平的调控。蛋白质组鸟枪法和RNA分析相结合的方法在预测代谢途径普遍性以及在途径规模上定义基因表达的调控水平方面具有很高的潜在价值。
