Geisler-Lee Jane, O'Toole Nicholas, Ammar Ron, Provart Nicholas J, Millar A Harvey, Geisler Matt
Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901, USA.
Plant Physiol. 2007 Oct;145(2):317-29. doi: 10.1104/pp.107.103465. Epub 2007 Aug 3.
The complex cellular functions of an organism frequently rely on physical interactions between proteins. A map of all protein-protein interactions, an interactome, is thus an invaluable tool. We present an interactome for Arabidopsis (Arabidopsis thaliana) predicted from interacting orthologs in yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), and human (Homo sapiens). As an internal quality control, a confidence value was generated based on the amount of supporting evidence for each interaction. A total of 1,159 high confidence, 5,913 medium confidence, and 12,907 low confidence interactions were identified for 3,617 conserved Arabidopsis proteins. There was significant coexpression of genes whose proteins were predicted to interact, even among low confidence interactions. Interacting proteins were also significantly more likely to be found within the same subcellular location, and significantly less likely to be found in conflicting localizations than randomly paired proteins. A notable exception was that proteins located in the Golgi were more likely to interact with Golgi, vacuolar, or endoplasmic reticulum sorted proteins, indicating possible docking or trafficking interactions. These predictions can aid researchers by extending known complexes and pathways with candidate proteins. In addition we have predicted interactions for many previously unknown proteins in known pathways and complexes. We present this interactome, and an online Web interface the Arabidopsis Interactions Viewer, as a first step toward understanding global signaling in Arabidopsis, and to whet the appetite for those who are awaiting results from high-throughput experimental approaches.
生物体复杂的细胞功能常常依赖于蛋白质之间的物理相互作用。因此，所有蛋白质-蛋白质相互作用的图谱，即相互作用组，是一种非常有价值的工具。我们展示了一个基于酵母（酿酒酵母）、线虫（秀丽隐杆线虫）、果蝇（黑腹果蝇）和人类（智人）中相互作用的直系同源物预测得到的拟南芥（阿拉伯芥）相互作用组。作为内部质量控制，根据每个相互作用的支持证据数量生成了一个置信值。对于3617个保守的拟南芥蛋白，共鉴定出1159个高置信度、5913个中等置信度和12907个低置信度的相互作用。即使在低置信度的相互作用中，其蛋白质被预测会相互作用的基因也存在显著的共表达。与随机配对的蛋白质相比，相互作用的蛋白质也更有可能在相同的亚细胞位置被发现，并且在相互冲突的定位中被发现的可能性显著更低。一个显著的例外是，位于高尔基体中的蛋白质更有可能与高尔基体、液泡或内质网分选的蛋白质相互作用，这表明可能存在对接或运输相互作用。这些预测可以通过用候选蛋白质扩展已知的复合物和途径来帮助研究人员。此外，我们还预测了已知途径和复合物中许多先前未知蛋白质的相互作用。我们展示了这个相互作用组以及一个在线网络界面——拟南芥相互作用查看器，作为理解拟南芥全局信号传导的第一步，并激发那些等待高通量实验方法结果的人的兴趣。
