Modeling the Budding Yeast Cell Cycle

• Home
• Introduction
• Rationale
• Budding yeast biology
• Components & function
• Cell cycle progression
• Basic mechanism
• Major improvement
• Overview
• Wiring diagram
• Description
• Justification
• Cyclins
• Cdc20
• Cdh1
• Cdc14 activation
• Mitotic Exit Network
• Pds1/Esp1 interaction
• CKI
• Checkpoint proteins
• Formulation
• Simulation
• Conclusions
• Mathematical Model
• Equations
• Parameters
• Problems
• Predictions
• Robustness
• Mutants
• List of Mutants
• WT in glucose
• WT in galactose
• Cln
• Bck2
• cln1 cln2 cln3
• Clb5 Clb6
• Clb1 Clb2
• Sic1
• Cdc6
• Cdh1
• Cdc20
• APC
• MEN pathway
• Exit-of-mitosis
• Pds1 / Esp1
• Checkpoint
• PPX
• Model Downloads
• Previous model
• Current model
• Target model
• APC-del model
• Modeling Tools
• Get WinPP
• How to use WinPP
• JigCell
• Oscill8
• PET
• Simulate the Model
• Other Models
• The "target" model
• "APC-del" model
• Generic model
• Literature
• References
• Publications
• Who We Are
• Va Tech
• BUTE
• Rockefeller Univ.

Model for APC-deleted mutants of Thornton and Toczyski

The anaphase promoting complex/cyclosome (APC) is a highly conserved ubiquitin ligase that regulates cell cycle progression by targeting numerous proteins for proteolysis. It is essential for cell viability, as mutants lacking the APC arrest in metaphase. Thornton and Toczyski (Thornton & Toczyski, 2003), however, showed that the requirement for APC can be circumvented by simultaneously deleting the PDS1 and CLB5 genes and by inserting multiple copies of genomic SIC1 gene. In this mutant strain (apc2∆ apc1∆ cdh1∆ cdc20∆ pds1∆ clb5∆ SIC1-10X), denoted "apc-minus" for short, the obligatory oscillation of Clb2/Cdc28 activity is driven not by the synthesis and degradation of Clb2, but by the rise and fall of its inhibitor Sic1. We modified our basal parameter set slightly to account for this phenotype (Thornton et al., 2004) as well as 27 other related strains characterized by Thornton and Toczyski.

Changes made from the "no target" model:

Equation for growth

apc-del model	no-target model
logistic growth	exponential growth

Parameters	apc-del model	no-target model		Parameters	apc-del model	no-target model
	ln(2)/150	ln(2)/90			6.0	4.0
	0.00075	0.001			0.06	0.08
	0.05	0.04			2.2	2.0
	0.006	0.003			2.5	3.0
	0.38	0.4			0.8	0.2
	0.38	0.45			0.3	0.25
	0.5	0.1			0.06	0.05
	6.0	4.0			1.2	1.0

 

APC mutant phenotypes, experimental and simulated:

Results are published in Thornton et al., 2004.
To see the simulation jpg files, click on the number corresponding to the mutant.

#	Mutant	Experiment	Simulation*
1.	wild type	viable	viable**
2.	cdc20∆	metaphase arrest (Shirayama et al., 1998)	metaphase arrest
3.	cdh1∆	viable (Schwab et al., 1997; Visintin et al., 1997)	viable
4.	clb5∆	viable (Epstein & Cross, 1992)	viable
5.	pds1∆	viable (Yamamoto et al., 1996)	viable
6.	10XSIC1	viable (Thornton & Toczyski, 2003)	viable
7.	cdc20∆   cdh1∆	metaphase arrest (Irniger et al., 1995)	metaphase arrest
8.	cdc20∆   clb5∆	metaphase arrest (Shirayama et al., 1999)	metaphase arrest
9.	cdc20∆   pds1∆	telophase arrest (Shirayama et al., 1999)	telophase arrest
10.	cdc20∆   10XSIC1	inviable (Thornton & Toczyski, 2003)	metaphase arrest
11.	cdh1∆   clb5∆	viable (Thornton & Toczyski, 2003)	viable
12.	cdh1∆   pds1∆	viable (Ross & Cohen-Fix, 2003)	viable
13.	cdh1∆   10XSIC1	Unknown	viable
14.	clb5∆   pds1∆	viable (Thornton & Toczyski, 2003)	viable
15.	clb5∆   10XSIC1	viable (Thornton & Toczyski, 2003)	viable
16.	pds1∆   10XSIC1	viable (Thornton & Toczyski, 2003)	viable
17.	cdc20∆   cdh1∆   clb5∆	inviable (Shirayama et al., 1999)	metaphase arrest
18.	cdc20∆   cdh1∆   pds1∆	inviable (Shirayama et al., 1999)	telophase arrest
19.	cdc20∆   cdh1∆   10XSIC1	inviable (Thornton & Toczyski, 2003)	mitotic catastrophe
20.	cdc20∆   clb5∆   pds1∆	viable (Shirayama et al., 1999)	viable
21.	cdc20∆   clb5∆   10XSIC1	inviable (Thornton & Toczyski, 2003)	mitotic catastrophe
22.	cdc20∆   pds1∆   10XSIC1	viable (Thornton & Toczyski, 2003)	viable
23.	cdh1∆   clb5∆   pds1∆	Unknown	viable
24.	cdh1∆   clb5∆   10XSIC1	Unknown	mitotic catastrophe
25.	cdh1∆   pds1∆   10XSIC1	Unknown	viable
26.	clb5∆   pds1∆   10XSIC1 = control "APC-plus"	viable (Thornton & Toczyski, 2003)	viable
27.	cdc20∆   cdh1∆   clb5∆   pds1∆	inviable (Shirayama et al., 1999)	telophase arrest
28.	cdc20∆   cdh1∆   clb5∆   10XSIC1	inviable (Thornton & Toczyski, 2003)	mitotic catastrophe
29.	cdc20∆   cdh1∆   pds1∆   10XSIC1	inviable (Thornton & Toczyski, 2003)	dies at 6 th cycle
30.	cdc20∆   clb5∆   pds1∆   10XSIC1	viable (Thornton & Toczyski, 2003)	viable
31.	cdh1∆   clb5∆   pds1∆   10XSIC1	viable (Thornton & Toczyski, 2003)	viable
32.	cdc20∆   cdh1∆   clb5∆   pds1∆   10XSIC1= "apc-minus"	viable (Thornton & Toczyski, 2003)	viable

*The deletion of essential APC subunits was simulated by eliminating both Cdc20 and Cdh1 activity, which account for all APC activity in this model. We modeled clb5∆ by reducing Clb5 expression 10-fold, to take into account the related but more weakly expressed Clb6 protein, which is not included as a separate quantity in the model. Although 10 extra copies of SIC1 were used to suppress APC mutants, Sic1 over-expression was modeled by increasing the expression of Sic1 only 6-fold, as our attempts at modeling 10-fold over-expression of Sic1 resulted in a permanent G1 block. Whether or not 10 extra copies of SIC1 yield a 10-fold increase in Sic1 expression in vivo, however, still requires confirmation. Deletion of PDS1 was modeled by reducing Pds1 expression to zero.

**For simulation results, "viable" indicates that the simulated cell cycle satisfies our criterion for cell viability, and "mitotic catastrophe" indicates that nuclear division occurs prior to activation of Esp1.

Simulations:
(a) the wild type

(b) "APC-plus" control (=clb5∆ pds1∆ 10XSIC1), viable.

(c) "apc-minus" (=cdc20∆ cdh1∆ clb5∆ pds1∆ 10XSIC1), viable.

Problems of the "apc-del" model:

Despite its ability to predict correctly the viability of various mutants in Thronton's experiment and the relative timing of budding in the "apc-minus" and the "APC-plus" strain (the former buds later), the model is at odds with several experimental observations.

• Total Clb2 level in the "apc-minus" cells: The model predicts that the level should be high and show a two-fold fluctuation dring the cell cycle, because Clb2 synthesis is controlled by the transcription factor MCM1/SFF complex in a cell-cycle regulated manner, whereas the degradation occurs at a constitutively low background rate. In experiments, Clb2 level appeared to be high, but remained constant throughout the cycle. It is possible that a two-fold fluctuation in high levels of Clb2 may have escaped notice.


• Sic1 level in "apc-minus" cells: The model predicts that the level of Sic1 should be three-fold higher in the "apc-minus" strain than in the "APC-plus" control strain. This is because Clb2 activates the transcription factor (Swi5) for Sic1 synthesis. In experiments, the level of Sic1 in the two strains are nearly identical.


• Timing of budding and initiation of DNA replication in "APC-plus" and "apc-minus" cells: The model predicts that budding and DNA synthesis should be uncoupled in both strains due to the genetic modifications they contain (clb5∆ and SIC1-10X). The time of bud emergence should be the same as in wild type since Cln/CDK activity is not affected by these mutations. S-phase is predicted to occur 2-2.5 hrs after bud emergence. In synchrony experiments, however, both "APC-plus" and "apc-minus" cells took an unexpectedly log tme to bud, such that budding and S-phase occurred almost simultaneously. This result could be accounted for if Sic1 has some minor ability to inhibit the Cln/CDK activity that only becomes apparent when Sic1 is grossly overexpressed.

Download the "apc-del" model:

To download, right click and choose "Save Target As" for Internet Explorer, or "Save Link Target As" for Netscape.
apc-del.ode
apc-del.set