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

Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX - Nucleic Acids Res. (2007)

Bottom Line: For each protein, a phosphorylation site overview is presented in tabular form with detailed information on each identified phosphopeptide.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.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia.

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.

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Venn diagram of experimental phosphorylation sites retrieved from the PhosPhAt database for different nutrient stress experiments. The overlap between different experiments comprises mainly plasma membrane proton ATPases and aquaporins, the proteins unique for each condition include transporters and kinases among others. Nitrate: nitrate starvation and resupply; Phosphate: phosphate starvation and resupply; Carbon: carbon starvation and sucrose re-supply.
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Figure 2: Venn diagram of experimental phosphorylation sites retrieved from the PhosPhAt database for different nutrient stress experiments. The overlap between different experiments comprises mainly plasma membrane proton ATPases and aquaporins, the proteins unique for each condition include transporters and kinases among others. Nitrate: nitrate starvation and resupply; Phosphate: phosphate starvation and resupply; Carbon: carbon starvation and sucrose re-supply.

Mentions: A more powerful and useful analysis of the data can be undertaken through the use of the experimental form selectors. The redundancy in phosphorylation site entries in the phosphat table allows the user to address information about phosphorylation sites experimentally identified under different biological conditions or in different tissues. For example, phosphopeptides sets for nitrate starvation and re-supply, phosphate starvation and re-supply, as well as carbon starvation and sucrose re-supply be obtained through the query form and compared (Figure 2). Such comparative analyses may help to assign biological functions to specific phosphorylation sites.Figure 2.


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

Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX - Nucleic Acids Res. (2007)

Venn diagram of experimental phosphorylation sites retrieved from the PhosPhAt database for different nutrient stress experiments. The overlap between different experiments comprises mainly plasma membrane proton ATPases and aquaporins, the proteins unique for each condition include transporters and kinases among others. Nitrate: nitrate starvation and resupply; Phosphate: phosphate starvation and resupply; Carbon: carbon starvation and sucrose re-supply.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238998&req=5

Figure 2: Venn diagram of experimental phosphorylation sites retrieved from the PhosPhAt database for different nutrient stress experiments. The overlap between different experiments comprises mainly plasma membrane proton ATPases and aquaporins, the proteins unique for each condition include transporters and kinases among others. Nitrate: nitrate starvation and resupply; Phosphate: phosphate starvation and resupply; Carbon: carbon starvation and sucrose re-supply.
Mentions: A more powerful and useful analysis of the data can be undertaken through the use of the experimental form selectors. The redundancy in phosphorylation site entries in the phosphat table allows the user to address information about phosphorylation sites experimentally identified under different biological conditions or in different tissues. For example, phosphopeptides sets for nitrate starvation and re-supply, phosphate starvation and re-supply, as well as carbon starvation and sucrose re-supply be obtained through the query form and compared (Figure 2). Such comparative analyses may help to assign biological functions to specific phosphorylation sites.Figure 2.

Bottom Line: For each protein, a phosphorylation site overview is presented in tabular form with detailed information on each identified phosphopeptide.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.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia.

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.

Show MeSH
Related in: MedlinePlus