Evolution of protein phosphorylation across 18 fungal species

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Science  14 Oct 2016:
Vol. 354, Issue 6309, pp. 229-232
DOI: 10.1126/science.aaf2144
  • Fig. 1 Phylogenomics pipeline to estimate the age of phosphosites.

    (A) Estimated consensus species tree. Post–whole-genome duplication event species are highlighted in the blue box. Age estimates are from (B) Example of ancestral state inference combining experimentally determined sites (bold) with sequence-based phosphosite predictions. (C) Number of predicted origins at each point in the phylogeny. The bar plot represents species-specific phosphosites. (D) Distribution of origins of phosphosites from S. cerevisiae (Sc). (Left) Single-column age estimates. (Right) ±3 window age estimates. (E and F) Predicted phylogenetic history for SNF1 T210 (E) and CDC19 S22 (F). Phosphosites are in red in the 3D structures. Phylogenetic tree: Red boxes denote experimental phosphosites; the white-to-black color scheme represents the probability of phosphorylation (0 to 1). Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.

  • Fig. 2 Structural and functional characterization of sites.

    (A) Phosphosite distribution in interaction structures. The categories Old (>400 My), Middle (65 to 400 My), and Young (<65 My) correspond to Y0-Y1, Y2-Y6, and S1-Sc, respectively. (B) CDC33 (eIF4E) pulldown results color-coded on a model of a circular messenger ribonucleoprotein complex, with selected proteins involved in translation repression via P-body and/or stress-granule formation. (C) Age-group distributions for functional and polymorphic sites. (D) Fitness for WT and alanine-mutant strains, defined by the area under the curve (AUC). Error bars indicate SD. (E) Behavior of WT stress-responsive genes (defined by FDR < 0.05 and |log2FC| > 1) in an HTA1 S121A mutant upon stress.

  • Fig. 3 Phylogenetic analysis of functional groups and kinase motif recognition.

    (A) Enrichment of gene ontology terms for phosphosites of different age groups. (B) Per-species enrichment in kinase types and phosphomotifs (SP, proline-directed; DE, acidic; KR, basic). Proline-directed kinase specificity was predicted with Predikin. (C) Correlation between the relative usage of predicted proline (SP) kinases and the relative usage of proline motifs. Blue dots represent the Saccharomyces sensu stricto group. (D) Enrichment ratio in KAYAK kinase activities for proline, acidic, or basic motifs.

Supplementary Materials

  • Evolution of protein phosphorylation across 18 fungal species

    Romain A. Studer, Ricard A. Rodriguez-Mias, Kelsey M. Haas, Joanne I. Hsu, Cristina Viéitez, Carme Solé, Danielle L. Swaney, Lindsay B. Stanford, Ivan Liachko, René Böttcher, Maitreya J. Dunham, Eulàlia de Nadal, Francesc Posas, Pedro Beltrao, Judit Villén

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Supplementary Text
    • Figs. S1 to S12
    • Tables S1, S4, and S5
    • Captions for Tables S2 and S3
    • References
    Table S2
    Phosphosites identified by mass spectrometry. A total of 88,210 phosphosites were identified in 18 fungal species (1% FDR filtering at PSM level). Of these, 73,340 were localized at >95% confidence (Ascore >=13) and used in this study. Non-localized sites were assigned a sequence region where localization was ambiguous. When multiple non-localized sites were assigned to overlapping regions, only one site was listed For each site we show the peptide identification with the highest Ascore value, and the corresponding identification scores from Sequest, as well as the number of total PSMs for the site.
    Table S3
    Phosphosite age estimations.

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