Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Oct;11(10):1070-83.
doi: 10.1074/mcp.M111.012625. Epub 2012 Jul 13.

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

Affiliations
Free PMC article

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

Chunxia Song et al. Mol Cell Proteomics. .
Free PMC article

Abstract

In eukaryotes, hundreds of protein kinases (PKs) specifically and precisely modify thousands of substrates at specific amino acid residues to faithfully orchestrate numerous biological processes, and reversibly determine the cellular dynamics and plasticity. Although over 100,000 phosphorylation sites (p-sites) have been experimentally identified from phosphoproteomic studies, the regulatory PKs for most of these sites still remain to be characterized. Here, we present a novel software package of iGPS for the prediction of in vivo site-specific kinase-substrate relations mainly from the phosphoproteomic data. By critical evaluations and comparisons, the performance of iGPS is satisfying and better than other existed tools. Based on the prediction results, we modeled protein phosphorylation networks and observed that the eukaryotic phospho-regulation is poorly conserved at the site and substrate levels. With an integrative procedure, we conducted a large-scale phosphorylation analysis of human liver and experimentally identified 9719 p-sites in 2998 proteins. Using iGPS, we predicted a human liver protein phosphorylation networks containing 12,819 potential site-specific kinase-substrate relations among 350 PKs and 962 substrates for 2633 p-sites. Further statistical analysis and comparison revealed that 127 PKs significantly modify more or fewer p-sites in the liver protein phosphorylation networks against the whole human protein phosphorylation network. The largest data set of the human liver phosphoproteome together with computational analyses can be useful for further experimental consideration. This work contributes to the understanding of phosphorylation mechanisms at the systemic level, and provides a powerful methodology for the general analysis of in vivo post-translational modifications regulating sub-proteomes.

Conflict of interest statement

The authors have declared no conflict of interest.

Figures

Fig. 1.
Fig. 1.
The computational procedure for predicting ssKSRs from eukaryotic phosphoproteomic data and visualizing potential PPNs.
Fig. 2.
Fig. 2.
Eukaryotic PPNs were modeled and visualized based on predicted ssKSRs from the phosphoproteomic data. A, The PPN of S. cerevisiae contains 20,909 ssKSRs among 91 PKs and 1,598 substrates for the 7,041 p-sites; B, The PPN of H. sapiens contains 113,923 ssKSRs among the 380 PKs and 4,140 targets for the 22,817 p-sites.
Fig. 3.
Fig. 3.
Only one KSR of the kinase BUR1/CDK9, which phosphorylates the transcription elongation factor protein Spt5, is conserved in all five eukaryotic PPNs.
Fig. 4.
Fig. 4.
By sequence alignment, we observed that the two p-sites of T806 and T814 in human Spt5 are conserved in all five species. Both sites were predicted to be phosphorylated by BUR1/CDK9.
Fig. 5.
Fig. 5.
Overview of the strategy used for the large-scale phosphorylation analysis of the human liver. A, Scheme for sample preparation and data processing of the human liver. B, Distribution of identified unique phosphopeptides from 45 pooled fractions. C, Distribution of identified unique phosphopeptides in four groups based on the classification filtering strategy (26).
Fig. 6.
Fig. 6.
The data statistics of the human liver phosphoproteomic analysis. A, The distribution of singly, doubly, and triply phosphorylated peptides; B, The distribution of pS, pT and pY sites in the human liver phosphoproteome; (C) By comparing with known information (Whole), up to 5818 p-sites have been reported previously; D, The distribution of pS, pT and pY sites in the whole human phosphoproteome.

Similar articles

See all similar articles

Cited by 55 articles

See all "Cited by" articles

Publication types

MeSH terms

Feedback