PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor

Abstract

The PhosPhAt database provides a resource consolidating our current knowledge of mass spectrometry-based identified phosphorylation sites in Arabidopsis and combines it with phosphorylation site prediction specifically trained on experimentally identified Arabidopsis phosphorylation motifs. The database currently contains 1187 unique tryptic peptide sequences encompassing 1053 Arabidopsis proteins. Among the characterized phosphorylation sites, there are over 1000 with unambiguous site assignments, and nearly 500 for which the precise phosphorylation site could not be determined. The database is searchable by protein accession number, physical peptide characteristics, as well as by experimental conditions (tissue sampled, phosphopeptide enrichment method). For each protein, a phosphorylation site overview is presented in tabular form with detailed information on each identified phosphopeptide. We have utilized a set of 802 experimentally validated serine phosphorylation sites to develop a method for prediction of serine phosphorylation (pSer) in Arabidopsis. An analysis of the current annotated Arabidopsis proteome yielded in 27 782 predicted phosphoserine sites distributed across 17 035 proteins. These prediction results are summarized graphically in the database together with the experimental phosphorylation sites in a whole sequence context. The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt) provides a valuable resource to the plant science community and can be accessed through the following link http://phosphat.mpimp-golm.mpg.de

Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis

“…Four of the respective phosphorylation sites have not been described previously (Heazlewood et al, 2008). All SnRK2 kinases identified in our study were differentially phosphorylated at multiple Ser/Thr residues in their kinase domains after stress treatments (Fig.…”

Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants

“…Conversely, there is no evidence for redox regulation of BAM3, and the enzyme has optimum activity at less alkaline pH (Santelia et al, 2015;Monroe et al, 2014). Furthermore, large-scale site-specific phosphorylation profiling of Arabidopsis proteins revealed the presence of one or more phosphorylation sites on both BAM1 and AMY3 proteins (de la Fuente van Bentem et al, 2008;Reiland et al, 2009;Xue et al, 2013;Heazlewood et al, 2008). Given the rapid activation of leaf starch degradation in response to the osmotic stress, it is likely that posttranslational modifications such as protein phosphorylation or redox regulation played a major role in activating BAM1 and AMY3 in the light.…”

Overexpression of the Trehalase Gene AtTRE1 Leads to Increased Drought Stress Tolerance in Arabidopsis and Is Involved in Abscisic Acid-Induced Stomatal Closure

“…To reach its apoplastic location, the AtTRE1 protein is likely to be transported via the endomembrane system and then secreted by vesicular exocytosis; therefore, it may be subject to glycosylation at one or more sites (Frison et al, 2007). Within the AtTRE1 protein, four residues and one hotspot (residues 191-213) are predicted with high confidence to be phosphorylated, and a further 38 residues have potential to be phosphorylated (Heazlewood et al, 2008). Moreover, Ser-195, which is part of the phosphorylation hotspot, falls within the RXXS/T motif, which is a characteristic target site for the SNF1-related protein kinases SnRK2.2, SnRK2.6/Ost1, and SnRK2.3 (Furihata et al, 2006).…”