P³DB 3.0: From plant phosphorylation sites to protein networks

Abstract

In the past few years, the Plant Protein Phosphorylation Database (P3DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P3DB with respect to format, new datasets and analytic tools. In the P3DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein–protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data—all of which provides context for the phosphorylation event. In addition, P3DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P3DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P3DB a comprehensive, systematic and interactive platform for phosphoproteomics research.

Proteomic and phosphoproteomic analyses reveal extensive phosphorylation of regulatory proteins in developing rice anthers

“…Thus, combining two datasets, we totally identified 6831 proteins presented in RAMs. A comparison with the Plant Protein Phosphorylation DataBase (P 3 DB) (Yao et al ., ) revealed that 1544 phosphoproteins in our RAMs dataset were absent from the current P 3 DB (Figure a). Thus, our data not only greatly enlarged the Plant Protein Phosphorylation DataBase, but also paved a way for functionally investigating proteins with phosphorylation modification during rice anther development.…”

The Kinase Activity of Calcineurin B-like Interacting Protein Kinase 26 (CIPK26) Influences Its Own Stability and that of the ABA-regulated Ubiquitin Ligase, Keep on Going (KEG)

“…Searches of the Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 4.0) and Plant Protein Phosphorylation Database (P3DB) identified five (S195, S438, S436, S440, and S974) experimentally determined phosphorylation sites within KEG (Gao et al, 2009; Durek et al, 2010; Yao et al, 2012, 2014; Supplementary Figure S1A ). To determine if these amino acids may represent relevant and conserved phosphorylation sites we compared KEG amino acid sequence to those from nine other plant species ( Supplementary File S1 and Figures S1B , 2 ).…”

AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana

“…To date, several structure-related PPI databases have been established (Higurashi et al 2009;Mosca et al 2013;Yao et al 2014). However, there is still room for improvement.…”