Abstract
The order and timing of cell-cycle events is controlled by changing substrate specificity and different activity thresholds of cyclin-dependent kinases (CDKs). However, it is not understood how a single protein kinase can trigger hundreds of switches in a sufficiently time-resolved fashion. We show that cyclin–Cdk1–Cks1–dependent phosphorylation of multisite targets in Saccharomyces cerevisiae is controlled by key substrate parameters including distances between phosphorylation sites, distribution of serines and threonines as phosphoacceptors and positioning of cyclin-docking motifs. The component mediating the key interactions in this process is Cks1, the phosphoadaptor subunit of the cyclin–Cdk1–Cks1 complex. We propose that variation of these parameters within networks of phosphorylation sites in different targets provides a wide range of possibilities for differential amplification of Cdk1 signals, thus providing a mechanism to generate a wide range of thresholds in the cell cycle.
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Acknowledgements
We would like to thank L. Holt and D. Morgan for valuable comments on the manuscript. We thank D. Kellogg (University of California, Santa Cruz) for kindly providing the strains and J. Mihhejev for excellent technical assistance and S. Kasvandik for assistance with MS. This work was supported by an International Senior Research Fellowship from the Wellcome Trust (no. 079014/Z/06/Z , to M.L.), an installation grant from the European Molecular Biology Organization and Howard Hughes Medical Institute (no. 1253, to M.L.), a targeted financing scheme and an institutional grant from the Estonian government (IUT2-21, to M.L.) and funding to S.M.R. from the American Cancer Society (RSG-12-131-01-CCG).
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M.K., M.Ö., A.I., E.V., R.V., I.F. and R.K. designed and performed the experiments. The ITC experiments were performed by E.R.M.B., and the structural model was constructed by S.M.R.; M.L. coordinated the project and wrote the manuscript with assistance from S.M.R., M.K. and M.Ö.
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Integrated supplementary information
Supplementary Figure 1 Analysis of the Cdk1-dependent phosphorylation of Sic1ΔC version with the threonines at the CDK phosphorylation sites mutated to serines, and additional control experiments supplementing the analysis of Cks1-dependent phosphorylation steps using the two-site Sic1ΔC-based substrate constructs.
(a,b) The comparison of the phosphorylation time courses of the wild type Sic1ΔC and all-Ser-Sic1ΔC using Cln2-Cdk1-Cks1 (a) and Clb5-Cdk1-Cks1 (b); (c) The turnover of primary substrates (S0) for the experiment presented in Fig. 2b; (d) Multisite phosphorylation patterns of wild type Sic1ΔC and all-Ser-Sic1ΔC in reaction with Cks1wt and Cks1mut using Clb2-Cdk1-Cks1 complex; (e) Phosphorylation of two-site Sic1ΔC-based substrate constructs containing the indicated sites confirms that phosphorylation of secondary site T48 requires a threonine-based N-terminal priming site; (f) A control experiment to supplement Fig. 3b shows that the suboptimal secondary sites at positions +12 and +14 are not likely to be phosphorylated independently of the priming site; (g) A control experiment to supplement Fig. 6b-e confirms that the two-site construct T5-T33-Sic1ΔC can be used for the processivity experiments as the serine version (S5-S33) of the construct did not accumulate the two-phosphate form comparably to T5-T33-Sic1ΔC in the assay conditions and the reaction time-window used.
Supplementary Figure 2 The in vivo demonstration of the requirement of threonine as the N-terminal priming site for Cks1-dependent phosphorylation steps.
(a,b) The intermediate phosphorylated forms of the all-serine version of Sic1 accumulate in vivo. The overexpression of the all-Ser-Sic1 caused inviability of cells as shown in Fig. 2d. In order to demonstrate that the protein levels and the phosphorylation shifts are different in case of wild type Sic1 and all-ser-Sic1 mutant, the phosphorylation patterns were followed after the induction of the Sic1 versions by galactose in hydroxyurea (a) or nocodazole (b) arrested cells; (c) Cells constitutively expressing the Sic1ΔC-based constructs containing either threonine or serine in position 5 were released from a pheromone arrest and the phosphorylation shifts were analyzed using Phos-Tag SDS-PAGE and western blotting. The two lower panels present similar experiments with the exception that the cyclin-specific docking motifs were mutated in the Sic1ΔC constructs (rxl-vllpp mutation14).
Supplementary Figure 3 The proline in position –2 is an additional specificity determinant for phosphoepitope interaction with Cks1.
(a) The effect of -2Pro on the rate of secondary phosphorylation was studied using the substrate constructs T33-T48-Sic1ΔC and -2P-T33-T48-Sic1ΔC; (b) Full-length version of Sic1 containing the Pro in position -2 from the site T33 was overexpressed under the galactose promoter to assay the ability of cells to degrade the construct T33-T45-T48-S76-S80-Sic1; (c) Representative ITC data for Cks1/phospho-Sic1 binding experiments. The values of the obtained binding constants for the indicated Sic1ΔC-based constructs are given in Supplementary Table 1.
Supplementary Figure 4 Relative effects of cyclin-docking sites and Cdk consensus sites on the Cks1-dependent phosphorylation steps and analysis of the distance requirements for a Cks1-dependent docking step.
(a-c) The effect of the hpm mutation and the mutation of lysine in position +3 on the rate of the secondary phosphorylation at position T33 was studied using the constructs T5-T33-Sic1ΔC and T5-T33+3A-Sic1ΔC; (d) Diagram showing the distance requirement for Cks1-dependent docking steps studied using Sic1ΔC-based substrate constructs containing T5 as the primary phosphorylation site and suboptimal TP sites as secondary sites using Clb5- and Cln2-Cdk1; (e-g) A scheme and examples of MS spectra of the analysis of distance requirements for Cks1-dependnet phosphorylation step in case of Far1; (h,i) The effect of the replacement of optimal CDK consensus motif with a suboptimal motif on the phosphorylation of the indicated Sic1ΔC-based substrate constructs; (j) The suboptimal Cdk1 sites (SP and TP consensus sites) do not get phosphorylated in vivo without the help of Cks1- or cyclin-dependent docking interactions.
Supplementary Figure 5 A general kinetic scheme of a sequential multiphosphorylation process.
For the sake of clarity, each form of substrate containing a certain number of phosphates is considered as kinetically equal.
Supplementary Figure 6 Modeling of processivity in the phosphorylation of a two-site kinase substrate.
(a) The kinetic scheme outlining the phosphorylation events. (b) The ODE model used for simulation of the time courses. (c-h) The time course simulations of the ODE model.
Supplementary Figure 7 Processivity analysis of the phosphorylation of Sic1ΔC-based constructs Whi5 and Fin1.
(a) Schemes showing the positions of phosphorylation sites in substrate constructs used in the experiments presented in panels 'b-d' (b) Experiment with low enzyme concentrations, similar to the ones presented in Fig. 6d,e, performed for T33+12TP-Sic1ΔC; (c) Full time courses of phosphorylation of T5-T33-Sic1ΔC with Clb5-Cdk1 in complex with Cks1wt and Cks1mut; (d) Graph showing the XMP values obtained by the quantification of data from panel 'c'. (e-j) The analysis of the processivity of Whi5 and Fin1 phosphorylation. A series of low concentrations of cyclin-Cdk1 complexes were used in a similar assay as presented for the Sic1ΔC-based constructs in Figure 6.
Supplementary Figure 8 Uncropped lanes from the autoradiography scans and western blots.
The horizontal panels 'a' and 'b' belong to Fig.1, panels 'd-f' to Fig.2, panels 'g-i' to Fig. 3, panels 'j' and 'k' to Fig. 6. The coomassie stained Phos-Tag gels in panel 'c' show the estimated migration of unphosphorylated or phosphorylated Sic1ΔC containing single Cdk1 site (Sic1ΔC-T33, Sic1ΔC-T33S) or all physiological phosphorylation sites (Sic1ΔC-wt). The arrows indicate the approximate estimated migration of nonradioactive unphosphorylated protein. For the rest of the details see the Online Methods and the Supplementary Results section.
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Kõivomägi, M., Örd, M., Iofik, A. et al. Multisite phosphorylation networks as signal processors for Cdk1. Nat Struct Mol Biol 20, 1415–1424 (2013). https://doi.org/10.1038/nsmb.2706
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DOI: https://doi.org/10.1038/nsmb.2706
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