Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER

Abstract

In budding yeast, synchronization of waves of mitotic cyclins that activate the Cdk1 kinase occur through Forkhead transcription factors. These molecules act as controllers of their sequential order and may account for the separation in time of incompatible processes. Here, a Forkhead-mediated design principle underlying the quantitative model of Cdk control is proposed for budding yeast. This design rationalizes timing of cell division, through progressive and coordinated cyclin/Cdk-mediated phosphorylation of Forkhead, and autonomous cyclin/Cdk oscillations. A "clock unit" incorporating this design that regulates timing of cell division is proposed for both yeast and mammals, and has a DRIVER operating the incompatible processes that is instructed by multiple CLOCKS. TIMERS determine whether the clocks are active, whereas CONTROLLERS determine how quickly the clocks shall function depending on external MODULATORS. This "clock unit" may coordinate temporal waves of cyclin/Cdk concentration/activity in the eukaryotic cell cycle making the driver operate the incompatible processes, at separate times.

Fig. 1. Waves of cyclins pattern for the mitotic (Clb) cyclins throughout cell cycle progression.

a Qualitative description of alternating waves of expression of mitotic cyclins throughout the cell cycle phases. In budding yeast, Clb indicates mitotic cyclins: Clb5,6 (red color) trigger DNA replication in S-phase; Clb3,4 (blue color) trigger completion of S-phase and early mitotic events in G2 phase; Clb1,2 (green color) trigger late mitotic events and cell division in M-phase. b Model for the transcriptional regulation of the mitotic Clb/Cdk1 complexes. A coherent type I feed-forward loop (FFL) may synchronize activation of mitotic Clb cyclins through the Fkh2 transcription factor: Clb5/Cdk1 promotes CLB3 transcription (arrow A), Clb3/Cdk1 promotes CLB2 transcription (arrow B) together with Clb5/Cdk1 (arrow C), and Clb2/Cdk1 promotes CLB2 transcription by a positive feedback loop (PFL, arrow D). For the sake of clarity, the Cdk1 subunit has been omitted. Arrows represent activating interactions among the Clb/Cdk1 complexes, whereas bar-headed black lines represent the mutual, inhibiting interactions between Clb/Cdk1 complexes and their stoichiometric inhibitor Sic1 (adapted from ref. ). c Systems biology-driven design that rationalizes the quantitative model or “threshold model” of Cdk1 control: a progressive activation of Fkh2 is realized through a processive, multi-step phosphorylation mediated by different thresholds of Clb/Cdk1 activities determined by the accumulation of Clb cyclins (adapted from).

Fig. 2. “Clock unit” of the budding yeast cell cycle.

a A “clock unit” of the cell cycle is formed by (i) a DRIVER (Cdk1 kinase) that, together with the CLOCK (cyclin: Clb cyclin; red color), drives cell cycle events through various phases; (ii) a TIMER (Cki, cyclin-dependent kinase inhibitor: Sic1; blue color) that inhibits the DRIVER; (iii) a CONTROLLER (TF, transcription factor: Fkh2) that activates the CLOCK (cyclin: CLB gene); and (iv) a MODULATOR (histone deacetylase: Sir2) that modulates the activity of the CONTROLLER. b “Clock unit” that integrates CLOCKS 1–3 (Clb cyclins; red color), CONTROLLER (Fkh2 transcription factor), MODULATOR (Sir2 histone deacetylase), CLOCK4 (TF TIMER, Ace2–Swi5 transcription factors; blue color), and TIMER (Cki, Clb/Cdk1 kinase inhibitor Sic1; blue color) together with the known regulations occurring among them.

Fig. 3. View of a dynamic cell cycle as “clock units”.

Interaction scheme of the “clock units” Clb5,6 (CLOCK1), Clb3,4 (CLOCK2), and Clb1,2 (CLOCK3), which interlock one other based on the regulation core in Fig. 2a. In addition, CLOCK4 (TF TIMER, Ace2–Swi5 transcription factors) (i) is activated by the CONTROLLER, (ii) activates the TIMER (Cki), and (iii) is inhibited by the DRIVER. Red arrows and bar-headed red lines indicate CLOCKS 1–3-mediated reactions, whereas blue arrows and bar-headed blue lines indicate CLOCK4-mediated reactions. Blue crosses indicate inhibition of CLOCKS 1–3 by CLOCK4.

Fig. 4. Molecular regulation that controls timing of eukaryotic cell division.

a, b Comparison between the integrated “clock units” in budding yeast (a) and in mammalian cells (b). Homologous molecules and regulations are indicated in black color; regulations that are currently known in one organism but not in the other, and vice versa, are indicated in red color; additional regulations that occur in mammalian cells are indicated in dotted gray color (see text for details). For simplicity, the DRIVER (Cdk) has been omitted.