Modeling the Budding Yeast Cell Cycle

Cdc28/Cln3 (with the help of Bck2) initiates Start, when cell size reaches a critical value, by activating the transcription factors SBF and MBF (for Cln2 and Clb5 respectively).

• Cln3 mRNA and protein levels are relatively constant throughout the cell cycle (Wittenberg et al., 1990; Tyers et al., 1993).
• More careful studies showed that CLN3 promoter contains an ECB box (Early Cell cycle Box), and CLN3 transcript show a modest 3-5 fold oscillation, peaking during M/G1 interval (MacKay et al., 2001).
• Cln3 plays a major role in size control (Cross, 1988; Nash et al., 1988; Dirick et al., 1995).

Cdc28/Cln2 induces budding.

• Cln2 mRNA and protein levels fluctuate in a cell cycle, peaking in late G1 (Tyers et al., 1993; Spellman et al., 1998)
• Cln2 transcription is controlled by SBF (Nasmyth & Dirick, 1991), which is activated by Cln- and Clb5-kinases (Cross & Tinkelenberg, 1991; Schwob & Nasmyth, 1993; Dirick et al., 1995) and turned off by Clb2-kinase (Amon et al., 1993; Koch et al., 1996).
• Cln2 degradation is activated by SCF (Deshaies et al., 1995; Willems et al., 1996), with a half-life of 5-10min (Barral et al., 1995; Salama et al., 1994; Lanker et al., 1996)
• Cln2 inactivates the antagonist proteins of the B-type cyclins, CKIs (Verma et al., 1997b) and Cdh1 (Zachariae et al., 1998).
• CLN2 deletion mutant shows delay in budding but not in SBF activation (Dirick et al., 1995; Stuart & Wittenberg, 1995).

Cdc28/Clb5 is responsible for proper timing of DNA replication.

• Clb5 mRNA and protein levels fluctuate in a cell cycle, peaking in late G1 (Schwob & Nasmyth, 1993; Spellman et al., 1998)
• Clb5 transcription is controlled by MBF. In the model, MBF=SBF, but in reality, MBF is turned off by an unknown signal (likely to be Clb5-kinase itself) in addition to Clb2-kinase (Amon et al., 1993, Ayte et al., 2001).
• Clb5 degradation is activated by APC/Cdc20 (Visintin et al., 1997).
• Half-life is 5-10 min in alpha-factor arrrested cells; and 15-20 min in cells arrested at S or M phase (Seufert et al., 1995). There are two modes of Clb5 degradation, one is APC dependent with high rate from M to G1 transition, the other is APC independent, with low rate throughout the cell cycle (Irniger & Nasmyth 1997)
• Sic1 is a stoichiometric inhibitor of Cdc28/Clb5 dimers (Schwob, et al., 1994).
• Clb5 kinase is able to phosphorylate Cdh1, thereby preventing its binding with the APC (Zachariae et al., 1998). It also phosphorylates the Cdc6, rendering it susceptable to degradation by SCF (Elsasser et al., 1999).
• Clb5-kinase participates in the firing of DNA replication in S phase (Schwob & Nasmyth, 1993).
• Clb5-kinase prevents re-replication of DNA (Dahmann et al., 1995).
• Clb5-kinase regulates the loading of MCM (mini-chromosome maintenance) complexes onto origins of replicatioin (Tanaka et al., 1997) .
• cells with clb5∆ clb6∆ deletions show delay in DNA replication (Schwob & Nasmyth, 1993).

Cdc28/Clb2 is essential for entry into mitosis.

• Clb2-kinase activity is high about 10 min before anaphase (Surana et al., 1991); mRNA and protein peaks at M phase (Spellman et al., 1998; Shirayama et al., 1998).
• Clb2 transcription is controlled by Mcm1/SFF complex, which is activated by Clb2 itself through a positive feedback (Amon et al., 1993; Maher et al., 1995). SFF consists of Fhk2p and Ndd1p (Pic-Taylor et al., 2004).
• Clb2 degradation is activated by APC/Cdc20 (Yeong et al., 2000; Baumer et al., 2000; Wasch & Cross, 2002) and APC/Cdh1 (Schwab et al., 1997; Visintin et al., 1997).
• Clb2 half-life is short (<1 min) in G1 arrested cells, but long ( >2hrs) in cells arrested in S or M phases (Amon et al., 1994; Irniger et al., 1995)
• Cdc28/Clb2 forms inactive complexes with Sic1 (Mendenhall, 1993; Schwob, et al., 1994) and Cdc6 (Calzada et al., 2001; Elsasser et al., 1996).
• Clb2 stimulates Cdc20 synthesis (Prinz et al., 1998).
• Clb2-kinase phosphorylates components of the APC that favors its binding with Cdc20 (Rudner & Murray, 2000b).
• Clb2 kinase is able to phosphorylate Cdh1, thereby preventing its binding with the APC (Zachariae et al., 1998). It also phosphorylates the Sic1, rendering it susceptable to degradation by SCF (Verma et al., 1997b).
• Clb1,2 kinases are essential for entry into mitosis, mutants cells with clb1∆ clb2∆ deletions arrest in G2 (Surana et al., 1991).
• Clb1,2 kinase activity has to be suppressed for cells to exit from mitosis (Zachariae, 1999; Thornton & Toczyski, 2003).