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Prevalence and significance of the commonest phosphorylated motifs in the human proteome: a global analysis

Abstract

Protein phosphorylation is the most frequent post-translational modification by which the properties of eukaryotic proteins can be reversibly modified. In humans, over 500 protein kinases generate a huge phosphoproteome including more than 200,000 individual phosphosites, a figure which is still continuously increasing. The in vivo selectivity of protein kinases is the outcome of a multifaceted and finely tuned process where numerous factors play an integrated role. To gain information about the actual contribution to this process of local features that reflect the interaction of the protein targets with the catalytic site of the kinases, the prevalence of the commonest motifs determining the consensus sequence of Ser/Thr-specific kinases has been examined in the whole human phosphoproteome and in the phosphoproteomes generated by a panel of the 47 most pleiotropic protein kinases. Our analysis shows that: (1) most phosphosites do conform to at least one of the motifs considered, with a substantial proportion conforming to two or more of them; (2) some motifs, with special reference to the one recognized by protein kinase CK2 (pS/pT-x-x-E/D) are very promiscuous, being abundantly represented also at the phosphosites of all the other protein kinases considered; (3) by contrast, other phosphorylated motifs, notably pS/pT-P, pS/pT-Q and pS-x-E, are more discriminatory and selective, being nearly absent in the phosphosites that are not attributable to certain categories of kinases. The information provided will prove helpful to make reliable inferences based on the manual inspection of individual phosphosites.

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Funding

This work was supported by a grant from AIRC (Italian Association for Cancer Research), Project IG 18756.

Author information

Correspondence to Lorenzo A. Pinna.

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Electronic supplementary material

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Supplementary file1 Table S1. Summary of the number of phospho-sites notoriously generated by individual protein kinases (drawn from PhosphoSitePlus) denoting how many of these conform to each of the commonest phosphomotifs. (XLS 235 kb)

Supplementary file2 Table S2. Phosphosites generated by GSK3 conforming only to the motifs pS/pT-P and pS/pT-x-x-x-pS/pT, or to both or to neither of these are separately listed. Constructed with data from PhosphoSitePlus. Phosphosites generated by both isoforms of GSK3 have been collectively considered. Lower case letters denote phosphorylated residues. (XLS 38 kb)

Supplementary file3 Table S3. Classification of the 47 most pleiotropic protein kinases according to the presence in their phosphosites of basic, acidic, phosphorylated, pS/pT-P and pS/pT-Q signatures. (DOCX 13 kb)

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Cesaro, L., Pinna, L.A. Prevalence and significance of the commonest phosphorylated motifs in the human proteome: a global analysis. Cell. Mol. Life Sci. (2020). https://doi.org/10.1007/s00018-020-03474-2

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Keywords

  • Consensus sequences
  • Specificity determinants
  • Protein kinase specificity
  • Phosphosites
  • CK2
  • GSK3