Multisite phosphorylation code of CDK

Abstract

The quantitative model of cyclin-dependent kinase (CDK) function states that cyclins temporally order cell cycle events at different CDK activity levels, or thresholds. The model lacks a mechanistic explanation, as it is not understood how different thresholds are encoded into substrates. We show that a multisite phosphorylation code governs the phosphorylation of CDK targets and that phosphorylation clusters act as timing tags that trigger specific events at different CDK thresholds. Using phospho-degradable CDK threshold sensors with rationally encoded phosphorylation patterns, we were able to predictably program thresholds over the entire range of the Saccharomyces cerevisiae cell cycle. We defined three levels of CDK multisite phosphorylation encoding: (i) Ser-Thr swapping in phosphorylation sites, (ii) patterning of phosphorylation sites, and (iii) cyclin-specific docking combined with modulation of CDK activity. Thus, CDK can signal via hundreds of differentially encoded targets at precise times to provide a temporally ordered phosphorylation pattern required for cell division.

The Hydrophobic Patch Directs Cyclin B to Centrosomes to Promote Global CDK Phosphorylation at Mitosis

“…This model is further supported by phosphoproteomic studies showing that the combination of a continuous increase of in vivo CDK activity through the cell cycle, together with differential substrate sensitivities to CDK activity, drives orderly cell cycle progression [5,12]. Differences in CDK activity toward different substrates could be generated by inherent properties of the substrate, cyclin-CDK localization, or by targeting of cyclin-CDK to specific substrates [13,14].…”

A new linear cyclin docking motif that mediates exclusively S‐phase CDK‐specific signaling

“…In addition to the differential docking mechanisms provided by cyclins, a key to the combinatorial complexity of CDK substrate phosphorylation is conferred by the phosphoadaptor subunit Cks1 (Kõivomägi et al , 2011b; McGrath et al , 2013), which provides a functional feature to the CDK complex that is unique among protein kinases. The majority of CDK targets contain multiple phosphorylation sites in intrinsically disordered regions (Holt et al , 2009), and the cyclin‐CDK‐Cks1 complex functions as a scaffold with three fixed points of substrate contact (Fig 1A), which allows the process of multisite phosphorylation to proceed in an ordered manner (Kõivomägi et al , 2013; Örd et al , 2019b). The phosphorylated TP motifs bind to the Cks1 phospho‐pocket and facilitate the phosphorylation of secondary sites located C‐terminally from the pTP priming sites (Kõivomägi et al , 2013; McGrath et al , 2013).…”

A processive phosphorylation circuit with multiple kinase inputs and mutually diversional routes controls G1/S decision

“…R ecent works on multisite phosphorylation networks of cyclin-dependent kinase (CDK) have revealed a new level of signal processing complexity that is based on signaling routes encoded into disordered proteins or disordered regions of proteins [1][2][3][4] . As the master regulators of the cell division cycle, CDKs use a combination of different docking interactions and activity thresholds to temporally order the phosphorylation of hundreds of their targets in the cell cycle [5][6][7][8][9][10][11][12][13] . Most of the CDK targets are phosphorylated at multiple sites distributed along disordered regions within these proteins 14 .…”