Physiologia Plantarum 160: 458–475. 2017 © 2017 Scandinavian Plant Physiology Society, ISSN 0031-9317 A phosphoproteomic landscape of rice (Oryza sativa) tissues Yifeng Wang, Xiaohong Tong, Jiehua Qiu, Zhiyong Li, Juan Zhao, Yuxuan Hou, Liqun Tang and Jian Zhang * State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China Correspondence *Corresponding author, e-mail: zhangjian@caas.cn Received 7 November 2016 doi:10.1111/ppl.12574 Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a compre- hensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nip- ponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4613 peptides were differ- entially phosphorylated (DP) among the tissues. Motif-X analysis revealed eight significantly enriched motifs, such as [sP], [Rxxs] and [tP] from the rice phosphosites. Hierarchical clustering analysis divided the DP peptides into 63 subgroups, which showed divergent spatial-phosphorylation patterns among tissues. These clustered proteins are functionally related to nutrition uptake in roots, photosynthesis in leaves and tissue differentiation in panicles. Phos- phorylations were specific in the tissues where the target proteins execute their functions, suggesting that phosphorylation might be a key mechanism to regu- late the protein activity in different tissues. This study greatly expands the rice phosphoproteomic dataset, and also offers insight into the regulatory roles of phosphorylation in tissue development and functions. Introduction Posttranslational modification (PTM) is a key step for functional protein maturation. Till now, over 300 types of experimentally verified or putative PTMs have been reported and deposited in PTM databases (Chen and Harmon 2006, Lee et al. 2006, Zhao and Jensen 2009, Khoury et al. 2011, Huang et al. 2016). Together with alternative splicing, PTMs greatly increase the proteome complexity, by precisely and efficiently regulating the individual biological behaviors in response to compli- cated growth signals and environmental cues. Among Abbreviations – ABA, abscisic acid; BR, brassinosteroid; 2D-DIGE, two-dimensional difference gel electrophoresis; DP, differentially phosphorylated; GDC, glycine decarboxylase complex; GO, gene ontology; iTRAQ, isobaric tags for relative and absolute quantitation; LC-MS/MS, liquid chromatography and tandem mass spectrometry; LEA, late embryogenesis abundant; MP, mature panicles; PLA2, plastochron2; PPI, protein–protein interaction; PTM, posttranslational modification; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SM, shoot meristem; YP, young panicles. the numerous reported PTMs, phosphorylation is a major type that has been extensively studied since its first report in 1926 (Lipmann and Levene 1932). Protein phospho- rylation refers to the covalent addition of a phosphate group to a hydroxyl group of hydroxyl amino acids like serine, threonine and tyrosine, but occasionally on hydroxyl-proline (Reinders and Sickmann 2005). On the contrary, the reversible removal of a phosphate group on proteins is called dephosphorylation. In general, phosphorylation and dephosphorylation are catalyzed by kinases and phosphatases, respectively. Phosphory- lation/dephosphorylation on specific sites of a protein 458 Physiol. Plant. 160, 2017