Modeling the Budding Yeast Cell Cycle

Budding Yeast Model

Biochemical model and description of the wiring diagram

Click here for the wiring diagram of the budding yeast model. The diagram should be read from bottom-left toward top-right. Solid arrows represent biochemical reactions, and dashed lines represent how components may influence one another.

The kinase partner of the cyclins, Cdc28, is not shown explicitly. There is an excess of Cdc28 and it combines rapidly with cyclins as soon as they are synthesized.

Newborn daughter cells must grow to a critical size to have enough Cln3 and Bck2 to activate the transcription factors, MBF and SBF, which drive synthesis of two classes of cyclins, Cln2 and Clb5. Cln2 is primarily responsible for bud emergence and Clb5 for initiating DNA synthesis. Clb5-dependent kinase activity is not immediately evident because the G1-phase cell is full of cyclin-dependent kinase inhibitors (CKI; namely, Sic1 and Cdc6). After the CKIs are phosphorylated by Cln2/Cdc28, they are rapidly degraded by SCF, releasing Clb5/Cdc28 to do its job.

A fourth class of "mitotic cyclins", denoted Clb2, are out of the picture in G1 because their transcription factor, Mcm1, is inactive, their degradation pathway, Cdh1/APC, is active, and their stoichiometric inhibitors, CKI, are abundant. Cln2- and Clb5-dependent kinases remove CKI and inactivate Cdh1, allowing Clb2 to appear, after some delay, as it activates its own transcription factor, Mcm1.

Clb2/Cdc28 turns off SBF. MBF turns off at the same time, but by an unknown process that does not require Clb2 (in the model we let MBF=SBF). As Clb2/Cdc28 drives the cell into mitosis, it also sets the stage for exit from mitosis by stimulating the synthesis of Cdc20 and by activating an intermediary enzyme IE (which has been identified as the phosphorylated form of APC in the active Cdc20/APC complex). Meanwhile, Cdc20 is kept inactive by the Mad2-dependent checkpoint signal responsive to unattached chromosomes. When the replicated chromosomes are attached to the metaphase spindle, Cdc20/APC becomes active.

Cdc20/APC plays several roles in mitotic exit. First, it degrades Pds1, releasing Esp1, a protease involved in sister chromatid separation. It also degrades Clb5 and partially Clb2, lowering their potency on Cdh1 inactivation. Cdc20/APC also promotes degradation of an unknown phosphatase (PPX) after the removal of Pds1. The role of PPX is to keep Net1 in its active unphosphorylated form which is able to sequester Cdc14, a phosphatase, in the nucleolus. When PPX is degraded, Net1 gets phosphorylated by Cdc15 (the endpoint of the "MEN" pathway in the model), it releases its hold on Cdc14. (PPX is functionally equivalent to the 'opposite of the FEAR pathway' in Cdc14 release.)

Cdc14 then does battle against the cyclin-dependent kinases: activating Cdh1, stabilizing CKIs, and activating Swi5 (the transcription factor for CKIs). As Clb2-kinase activity is quenched by Cdh1/APC degradation and by CKI inhibition to below a threshold value, a signal for exit from mitosis is triggered, the cell divides and returns to G1 phase.