P3DB: An Integrated Database for Plant Protein Phosphorylation

Protein phosphorylation is widely recognized as the most widespread, enzyme-catalyzed post-translational modification in eukaryotes. In particular, plants have appropriated this signaling mechanism as evidenced by the twofold higher frequency of protein kinases within the genome compared to other eukaryotes. While all aspects of plant protein phosphorylation research have grown in the past 10 years; phosphorylation site mapping using high-resolution mass spectrometry has grown exponentially. In Arabidopsis alone there are thousands of experimentally determined phosphorylation sites. To archive these events in a user-intuitive format we have developed P3DB, the Plant Protein Phosphorylation Database (p3db.org). This database is a repository for plant protein phosphorylation site data, currently hosting information on 32,963 non-redundant sites collated from 23 experimental studies from six plant species. These data can be queried for a protein-of-interest using an integrated BLAST module to query similar sequences with known phosphorylation sites among the multiple plants currently investigated. The paper demonstrates how this resource can help identify functionally conserved phosphorylation sites in plants using a multi-system approach.

[1]  M. Mann,et al.  Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S , 2005, Molecular & Cellular Proteomics.

[2]  Ruedi Aebersold,et al.  PhosphoPep—a database of protein phosphorylation sites in model organisms , 2008, Nature Biotechnology.

[3]  L. Iakoucheva,et al.  The importance of intrinsic disorder for protein phosphorylation. , 2004, Nucleic acids research.

[4]  Wolfram Weckwerth,et al.  Comparative analysis of phytohormone-responsive phosphoproteins in Arabidopsis thaliana using TiO2-phosphopeptide enrichment and mass accuracy precursor alignment. , 2010, The Plant journal : for cell and molecular biology.

[5]  Joachim Selbig,et al.  PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor , 2007, Nucleic Acids Res..

[6]  Alexandra ME Jones,et al.  Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses , 2007, The Plant journal : for cell and molecular biology.

[7]  Wolfram Weckwerth,et al.  A survey of the Arabidopsis thaliana mitochondrial phosphoproteome , 2009, Proteomics.

[8]  Jianjiong Gao,et al.  Phosphoproteomic Analysis of Seed Maturation in Arabidopsis, Rapeseed, and Soybean1[C][W][OA] , 2012, Plant Physiology.

[9]  W. Gruissem,et al.  Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks1[W] , 2009, Plant Physiology.

[10]  M. Tomita,et al.  Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants1[W][OA] , 2010, Plant Physiology.

[11]  M. Tomita,et al.  Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis , 2008, Molecular systems biology.

[12]  Hao Li,et al.  Phosphoproteomic analysis of ethylene‐regulated protein phosphorylation in etiolated seedlings of Arabidopsis mutant ein2 using two‐dimensional separations coupled with a hybrid quadrupole time‐of‐flight mass spectrometer , 2009, Proteomics.

[13]  Robert Schmidt,et al.  PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update , 2009, Nucleic Acids Res..

[14]  M. Mann,et al.  Mapping of phosphorylation sites of gel-isolated proteins by nanoelectrospray tandem mass spectrometry: potentials and limitations. , 1999, Analytical chemistry.

[15]  Zhuo Shen,et al.  Large-scale analysis of phosphorylated proteins in maize leaf , 2011, Planta.

[16]  Florian Gnad,et al.  PHOSIDA 2011: the posttranslational modification database , 2010, Nucleic Acids Res..

[17]  Allegra Via,et al.  Phospho.ELM: a database of phosphorylation sites—update 2008 , 2007, Nucleic Acids Res..

[18]  Ching-Huang Lin,et al.  Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana , 2009, Proteome Science.

[19]  A. Stensballe,et al.  Phosphoproteomics of the Arabidopsis Plasma Membrane and a New Phosphorylation Site Databasew⃞ , 2004, The Plant Cell Online.

[20]  Heribert Hirt,et al.  Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis. , 2008, Journal of proteome research.

[21]  M. Sussman,et al.  Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes1[W] , 2009, Plant Physiology.

[22]  Hanno Steen,et al.  A simple and effective method for detecting phosphopeptides for phosphoproteomic analysis. , 2009, Journal of proteomics.

[23]  Amos Bairoch,et al.  Annotation of post‐translational modifications in the Swiss‐Prot knowledge base , 2004, Proteomics.

[24]  M. Sussman,et al.  In planta changes in protein phosphorylation induced by the plant hormone abscisic acid , 2010, Proceedings of the National Academy of Sciences.

[25]  D. Chevalier,et al.  The Protein Phosphatases and Protein Kinases of Arabidopsis thaliana , 2007, The arabidopsis book.

[26]  Dong Xu,et al.  Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites* , 2010, Molecular & Cellular Proteomics.

[27]  Wolfram Weckwerth,et al.  Combining metal oxide affinity chromatography (MOAC) and selective mass spectrometry for robust identification of in vivo protein phosphorylation sites , 2005, Plant Methods.

[28]  David J Studholme,et al.  Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. , 2009, Journal of proteomics.

[29]  M. Tchórzewski.  The acidic ribosomal P proteins. , 2002, The international journal of biochemistry & cell biology.

[30]  Dong Xu,et al.  P3DB: a plant protein phosphorylation database , 2008, Nucleic Acids Res..

[31]  Akhilesh Pandey,et al.  Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. , 2009, Methods in molecular biology.

[32]  W. Schulze,et al.  Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings , 2012, The Plant journal : for cell and molecular biology.

[33]  Albert J R Heck,et al.  Quantitative Phosphoproteomics of Early Elicitor Signaling in Arabidopsis*S , 2007, Molecular & Cellular Proteomics.

[34]  Bin Zhang,et al.  PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse , 2011, Nucleic Acids Res..

[35]  Alexandra M. E. Jones,et al.  Identification of novel proteins and phosphorylation sites in a tonoplast enriched membrane fraction of Arabidopsis thaliana , 2008, Proteomics.

[36]  P. Radivojac,et al.  PROTEINS: Structure, Function, and Bioinformatics Suppl 7:176–182 (2005) Exploiting Heterogeneous Sequence Properties Improves Prediction of Protein Disorder , 2022 .

[37]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.