Phosphoproteome profiling of rice tissues provides new insights into responsive mechanisms and kinase activity upon salt stress

Rice is a model monocot plant and a major food crop worldwide that is known as the most salt-sensitive cereal. Phosphorylation of proteins regulates the stimulus perception and triggers responses; however, remains largely unknown in crops, particularly in rice under salinity. Here, we report in-depth physiological, proteomic, and phosphoproteomic kinetics of rice shoot and root tissues in response to short-term salt stress. We identified 8160 proteins, 5684 phosphopeptides that assigned to 3142 ‎phosphoproteins. In the root, hypophosphorylation of KAT1, BORs, HAKs, NHX2, and NHX8 transporters, RBOHs and nitrate reductase implied less efficiency in ion, minerals, and ROS haemostasis, thus likely resulting in membrane damages and sensitivity of rice to salinity. Predominantly, the PKA, CDK, MAPK, and PP2A families modulated plant response through interaction with densely interconnected protein modules. We identified 17 phosphomotifs reflecting the identities of the upstream kinases. Furthermore, phylogenetic mapping of 245 identified kinases together with the kinase of known target motifs and function, expanded the biological characters of kinases in rice. We also assigned target motifs for rice kinase families, including PDK1, PKA, CAMKL, CK1, CDK, GSK, and MAPK. This study expands the set of kinase substrates and their signaling networks. Our data also assigns new stress-responsive functions to a large number of novel phosphoproteins, thus will serve as a resource for further studies of salt stress signaling in plants. [Display omitted] •We represent the largest profiling of 5422 phosphopeptides in rice upon salinity.•Critical transporters hypophosphorylated like KAT1, BORs, HAKs, NHX2/8, NCX1, CAX1.•CAMTA1/3/4, CDPK12/17/20/24, CBL23, RLKs, and PP2C likely caused salt sensitivity.•Phospho-regulation by PKA, CDK, MAPK, and PP2A families modulated plant response.•This study assigns stress-responsive functions to numerous novel phosphoproteins.