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.
Highlights
Phosphorylation is one of the most pervasive protein modification types in plants
The burgeoning amount of experimental phosphorylation site data has necessitated the development of databases to warehouse these data and provide an essential infrastructure for the research community
Since the initial release of P3DB, high-quality phosphorylation sites in this database have accumulated at a rapid pace due to improvements in enrichment techniques and mass spectrometry [Supplementary Figure S1a and b]
Summary
Phosphorylation is one of the most pervasive protein modification types in plants. Phosphorylation and dephosphorylation act as an important switch in signal transduction, chemical metabolism and other inter- or intra-cellular processes [1]. The burgeoning amount of experimental phosphorylation site data has necessitated the development of databases to warehouse these data and provide an essential infrastructure for the research community. As discovery plant phosphoproteomics extends beyond model organisms it is desirable to integrate and compare the diversity of phosphorylation events to fully interrogate the possibilities of regulation in Viridiplantae. In this regard P3DB aims to be a resource for the entire plant community. HPRD, the Human Protein Reference Database [5,6], covers a wide range of PTM data including phosphorylation. P3DB is a unique, complementary database to the current databases for its broad coverage of plant species, network-based data presentation and visualization, and community-based data services
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