Kersten Birgit, Agrawal Ganesh Kumar, Durek Pawel, Neigenfind Jost, Schulze Waltraud, Walther Dirk, Rakwal Randeep
Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
Proteomics. 2009 Feb;9(4):964-88. doi: 10.1002/pmic.200800548.
Phosphoproteomics involves identification of phosphoproteins, precise mapping, and quantification of phosphorylation sites, and eventually, revealing their biological function. In plants, several systematic phosphoproteomic analyses have recently been performed to optimize in vitro and in vivo technologies to reveal components of the phosphoproteome. The discovery of novel substrates for specific protein kinases is also an important issue. Development of a new tool has enabled rapid identification of potential kinase substrates such as kinase assays using plant protein microarrays. Progress has also been made in quantitative and dynamic analysis of mapped phosphorylation sites. Increased quantity of experimentally verified phosphorylation sites in plants has prompted the creation of dedicated web-resources for plant-specific phosphoproteomics data. This resulted in development of computational prediction methods yielding significantly improved sensitivity and specificity for the detection of phosphorylation sites in plants when compared to methods trained on less plant-specific data. In this review, we present an update on phosphoproteomic studies in plants and summarize the recent progress in the computational prediction of plant phosphorylation sites. The application of the experimental and computed results in understanding the phosphoproteomic networks of cellular and metabolic processes in plants is discussed. This is a continuation of our comprehensive review series on plant phosphoproteomics.
磷酸化蛋白质组学涉及磷酸化蛋白质的鉴定、磷酸化位点的精确图谱绘制和定量分析，最终揭示其生物学功能。在植物中，最近进行了多项系统性磷酸化蛋白质组学分析，以优化体外和体内技术，从而揭示磷酸化蛋白质组的组成成分。发现特定蛋白激酶的新底物也是一个重要问题。一种新工具的开发使得能够快速鉴定潜在的激酶底物，如使用植物蛋白质微阵列进行激酶分析。在已绘制的磷酸化位点的定量和动态分析方面也取得了进展。植物中经实验验证的磷酸化位点数量的增加促使创建了专门用于植物特异性磷酸化蛋白质组学数据的网络资源。这导致了计算预测方法的发展，与基于较少植物特异性数据训练的方法相比，该方法在检测植物磷酸化位点时具有显著提高的灵敏度和特异性。在本综述中，我们介绍了植物磷酸化蛋白质组学研究的最新情况，并总结了植物磷酸化位点计算预测的最新进展。还讨论了实验和计算结果在理解植物细胞和代谢过程的磷酸化蛋白质组网络中的应用。这是我们关于植物磷酸化蛋白质组学的全面综述系列的延续。
