Fig. 1: Schematic views of the minimal cell cycle model for budding yeast and full interaction diagram for designs 1A, 1B, 1C, 2, and 3.
a The molecular players driving phase-specific cell cycle events. b Linear cascade of the three Clb/Cdk1 complexes, and mutual inhibition between these and the Clb/Cdk1 inhibitor Sic1. c Interactions among the Clb/Cdk1 complexes. Solid lines indicate (7) proven interactions, whereas dotted lines indicate (3) hypothetical interactions (see Supplementary Table 2). d Full interaction diagram for designs 1A, 1B, 1C, 2, and 3 of the minimal cell cycle network. The scheme illustrates the core interactions in all model designs presented in this work, i.e. black and red arrows for the basal and activatory regulations, respectively, and highlights the progressive changes to the core structure introduced in designs 1A–3 (blue, red cross, orange, and green, respectively). Dotted arrows indicate the Cln(/Cdk1)- and Clb(/Cdk1)-mediated phosphorylation of Sic1 in Clb/Cdk1/Sic1 ternary complexes, resulting in its degradation. The complex formation between Clb/Cdk1 complexes and Sic1 is indicated with the KA parameter, referring to the quasi-steady-state assumption introduced in Design 3 (see Supplementary Information, Section 1.6.2), which should be taken to be the regular complex formation (k+ for formation, k− for dissociation) for designs 1A–2. Model derivations are reported in Supplementary Information, Section 1, and details of the reactions and their experimental evidence are reported in Supplementary Table 2.
