Huang Shaobai, Taylor Nicolas L, Narsai Reena, Eubel Holger, Whelan James, Millar A Harvey
Australian Research Council Centre of Excellence in Plant Energy Biology, M316, University of Western Australia, Crawley, 6009 Western Australia, Australia.
Plant Physiol. 2009 Feb;149(2):719-34. doi: 10.1104/pp.108.131300. Epub 2008 Nov 14.
Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comparisons of mitochondria purified by density gradients and after further surface charge purification have been used to ensure that the proteins identified copurify with mitochondria and to remove contaminants from the analysis. This rigorous approach to defining a subcellular proteome has yielded 322 nonredundant rice proteins and highlighted contaminants in previously reported rice mitochondrial proteomes. Comparative analysis with the Arabidopsis (Arabidopsis thaliana) mitochondrial proteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria, with only approximately 20% not having a clear homolog in the Arabidopsis mitochondrial proteome. As in Arabidopsis, only approximately 60% of the rice mitochondrial proteome is predictable using current organelle-targeting prediction tools. Use of the rice protein data set to explore rice transcript data provided insights into rice mitochondrial biogenesis during seed germination, leaf development, and heterogeneity in the expression of nucleus-encoded mitochondrial components in different rice tissues. Highlights include the identification of components involved in thiamine synthesis, evidence for coexpressed and unregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylating segment of the tricarboxylic acid cycle, the differential expression of DNA and RNA replication components, and enhanced expression of specific metabolic components in photosynthetic tissues.
水稻（Oryza sativa）中的线粒体对于拓展我们对以下方面的理解至关重要：组织在厌氧后复氧的细胞反应、碳氮代谢的交叉点以及呼吸能量产生在细胞质雄性不育中的作用。我们将密度梯度和表面电荷纯化技术与蛋白质组学相结合，以提供涵盖可溶性和整合膜蛋白的水稻幼苗线粒体深度蛋白质组。通过密度梯度纯化以及进一步表面电荷纯化后对线粒体进行定量比较，以确保鉴定出的蛋白质与线粒体共纯化，并从分析中去除污染物。这种严格定义亚细胞蛋白质组的方法已产生322种非冗余水稻蛋白质，并突出了先前报道的水稻线粒体蛋白质组中的污染物。与拟南芥（Arabidopsis thaliana）线粒体蛋白质组的比较分析揭示了植物线粒体中广泛的已知和未知功能蛋白质的保守性，只有约20%在拟南芥线粒体蛋白质组中没有明确的同源物。与拟南芥一样，使用当前的细胞器靶向预测工具只能预测约60%的水稻线粒体蛋白质组。利用水稻蛋白质数据集探索水稻转录数据，为种子萌发、叶片发育过程中的水稻线粒体生物发生以及不同水稻组织中核编码线粒体成分表达的异质性提供了见解。亮点包括鉴定出参与硫胺素合成的成分、蛋白质复合物特定成分共表达和非调节表达的证据、三羧酸循环脱羧段的选择性花药增强亚类、DNA和RNA复制成分的差异表达以及光合组织中特定代谢成分的增强表达。
