Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs

Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry–based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass s...

蛋白质磷酸化与去磷酸化在植物生命活动中发挥关键作用。为构建亚细胞磷酸化信号网络分析及激酶-底物互作关系研究的坚实基础，我们针对拟南芥开展了荟萃分析，纳入27套已发表及未发表的实验室内部基于质谱（mass spectrometry）的磷酸化蛋白质组（phospho-proteome）数据集，这些数据集涵盖了多种生理过程、光合/非光合组织类型以及细胞培养体系。本次分析共整合得到60366条磷酸化肽段，对应8141个非冗余蛋白质。通过对数据进行质量与一致性筛选，我们获得了中等置信度和高置信度的磷酸化蛋白质集合及其对应的磷酸化位点。本文探讨了单磷酸化肽段与多磷酸化肽段之间的关联特征。研究明确了磷酸化蛋白质在各类细胞功能及亚细胞区室中的分布规律，发现蛋白质激酶存在显著富集现象。不同研究间磷酸化酪氨酸（pY，phosphotyrosine）的出现频率存在显著差异，该差异与蛋白质组学及质谱相关实验技术...