Modeling the START transition in the budding yeast cell cycle
Fig 2
(A) The core model of SBF activation and inactivation by Clns and Clbs. Presented in the figure are the most important interactions considered in START-BYCC for SBF activation and inactivation. The core components are Swi4 (orange icon), Swi6 (turquoise icon), Whi5 (red icon), the promoter (purple bar), kinases (Cln3, Cln1,2, Clb5,6, Clb1,2) and export protein (Msn5) (white box). The nucleus is represented with a blue-gray background, while the white space corresponds to the cytoplasm. Promoter-bound complexes enclosed in boxes with borders in dark green, light green, and red represent complexes with maximal, residual, and no activity, respectively. White-filled circles represent activatory phosphorylations done by Cln3, Cln1,2, and Clb5,6; whereas the black-filled circles represent the inactivating phosphorylations by Clbs (Clb5,6 & Clb1,2 for Swi6 phosphorylation and Clb1,2 for Swi4 phosphorylation). The Cln (white) phosphorylation on Whi5 and Clb (black) phosphorylation on Swi6 (S160) are needed for export to the cytoplasm. To avoid overcrowding, remaining complexes corresponding to modifications on other free forms are not included in the figure. All the concerned equations are listed in S2 Text. Key facts about the abundance, regulation, and localization of all the components are described in S2 Table. (B) Ratios of the promoter to Swi4/Mbp1, Swi6, and Whi5 (Roughly based on Ghaemmaghami et al. [84]; e.g., when rescaled, we would have four promoters, 11 each of Swi4/Mbp1, 20 Whi5, and 60 Swi6 molecules).