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. 2012 May 25;19(5):608-18.
doi: 10.1016/j.chembiol.2012.04.011.

Rapid determination of multiple linear kinase substrate motifs by mass spectrometry

Arminja N Kettenbach  1 , Tuobin Wang, Brendan K Faherty, Dean R Madden, Stefan Knapp, Chris Bailey-Kellogg, Scott A Gerber
Affiliations

Rapid determination of multiple linear kinase substrate motifs by mass spectrometry

Arminja N Kettenbach et al. Chem Biol. .

Abstract

Kinase-substrate recognition depends on the chemical properties of the phosphorylatable residue as well as the surrounding linear sequence motif. Detailed knowledge of these characteristics increases the confidence of linking identified phosphorylation sites to kinases, predicting phosphorylation sites, and designing optimal peptide substrates. Here, we present a mass spectrometry-based approach for determining linear kinase substrate motifs by elaborating the positional and chemical preference of the kinase for a phosphorylatable residue using libraries of naturally-occurring peptides that are amenable to peptide identification by commonly used proteomics platforms. We applied this approach to a structurally and functionally diverse set of purified kinases, which recapitulated their previously described substrate motifs and discovered additional ones, including preferences of certain kinases for phosphorylatable residues adjacent to peptide termini. Furthermore, we identify specific and distinguishable motif elements for the four members of the polo-like kinase (Plk) family and verify members of these motif elements for Plk1 in vivo.

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Figures

Figure 1
Figure 1. Workflow and results of kinase substrate motif assay
(A) Depiction of peptide kinase assay workflow. HeLa cells were lysed, digested, dephosphorylated, and separated into 12 fractions by strong cation exchange (SCX) chromatography. Select fractions were used in in vitro kinase reactions. Phosphopeptides were purified from non-phosphopeptides using titanium dioxide (TiO2) microspheres and analyzed by LC-MS/MS. Statistically significant motifs were extracted from the identified phosphopeptides by the in-house developed motif algorithm GrMPh. (B) Linear kinase motifs from Pim1 in vitro kinase reaction. (C) Averaged motif of all motif-containing peptides in (B). (D) Heat map representation of the log2 values of the ratio of foreground to background amino acid frequencies of motif-containing peptides in (A). See also Figures S1 – S9, S11 – S15, and Tables S1 and S2.
Figure 2
Figure 2. Chemical preference of phosphorylatable substrate residues
(A) Table depicting the preferences for phosphorylatable residues in motif-containing peptides (serine, threonine, or tyrosine) by the investigated kinases. (B) Validation of Haspin preference for phosphorylating threonine residues. Three different synthetic peptide substrates containing unique phosphorylatable residues were assayed for initial reaction kinetics. (C) Validation of Bmpr2 preference for phosphorylating serine and threonine residues, and capacity to phosphorylate tyrosines. Three different synthetic peptide substrates containing unique phosphorylatable residues were assayed for initial reaction kinetics as for Haspin. Note that unlike Haspin, Bmpr2 readily phosphorylated tyrosine residues, albeit at a reduced rate (~25%) relative to serine. See also Figures S7, S9 and S10.
Figure 3
Figure 3. Positional preference of the phosphorylated residue for Haspin, Bmpr2, and Camkk2b kinases
(A) Distribution of phosphorylation site location from the peptide N-terminus for Haspin (dashed-dotted line) and for all other kinases (solid grey line). For 61% of the motif-containing peptides phosphorylated by Haspin, the phosphorylation site was located at the second or third residue from the N-terminus of the peptide. In contrast, phosphorylation sites on motif-containing peptide from all other analyzed kinases were more evenly distributed across the peptide length. (B) Distribution of phosphorylation site location from the peptide C-terminus for Bmpr2 (solid black line), Camkk2b (dashed line), and all other kinases (solid grey line). For 53% of the motif-containing peptides phosphorylated by Bmpr2, the phosphorylation site was located at the second residue away from the C-terminus of the peptide. Similarly, 46% of the motif-containing peptides phosphorylated by Camkk2b exhibited phosphorylated residues two or three positions away from the C-terminus of the peptide. In contrast, phosphorylation sites on motif-containing peptides from all other kinases were more evenly distributed across the length of the peptides. (C) Validation of Haspin positional preference for phosphorylatable residues near the N-terminus of peptides. Three different peptide substrates were synthesized as positional isomers, with the preferred Haspin motif moved sequentially further away from the N-terminus, and were assayed for initial reaction kinetics. (D) Validation of Bmpr2 positional preference for phosphorylatable residues near the C-terminus of peptides. Three different peptide substrates were synthesized as positional isomers, with the preferred Bmpr2 motif moved sequentially further away from the C-terminus, and were assayed for initial reaction kinetics. See also Figures S7 – S9.
Figure 4
Figure 4. In vivo and in vitro identification of Polo-like kinase 1 (Plk1) linear substrate motifs
(A) SILAC-based workflow depicting in vivo identification of Plk1 substrates. HeLa cells were labeled with “heavy” and “light” amino acids in tissue culture, arrested in mitosis by nocodazole, differentially treated with a Plk1 inhibitor (BI-2536 dissolved in DMSO, heavy) or DMSO control (light), lysed, and trypsin-digested. Peptides were separated into 24 fractions by strong-cation exchange (SCX) chromatography and phosphopeptides were purified from non-phosphopeptides using titanium dioxide (TiO2) microspheres and analyzed by LC-MS/MS. Statistically significant motifs were extracted from phosphopeptides downregulated by 2.5-fold or more in the BI-2536-treated population by Motif-X. (B) Motif-X output for Plk substrates from nocodazole and Taxol-arrested HeLa cells. (C) Pie charts depicting the relative motif occurrence in HeLa cells arrested with nocodazole and Taxol, and in the in vitro kinase assay using purified Plk1 enzyme. Note that the relative distribution of primary Plk1 motifs observed in vivo with BI-2536 is similar to those with purified Plk1 in vitro. NS, no significant motifs. See also Figure S11 and Table S3.
Figure 5
Figure 5. Hierarchical clustering of in vitro Plk1, Plk2, Plk3, and Plk4 motifs
Hierarchical clustering of motifs identified in Plk1, Plk2, Plk3, and Plk4 in vitro kinase assays. Note the close relationship of acidic motifs for Plk2 and Plk3, and of hydrophobic motifs for Plk1 and Plk4. See also Figures S11 – S14.
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