Ciliberto2003_Morphogenesis_Checkpoint
This a model from the article:
Mathematical model of the morphogenesis checkpoint in budding yeast.
Ciliberto A, Novak B, Tyson JJ J. Cell Biol.
[2003 Dec; Volume: 163 (Issue: 6 )] Page info: 1243-54 14691135
,
Abstract:
The morphogenesis checkpoint in budding yeast delays progression through the cell cycle in response to stimuli that prevent bud formation. Central to the checkpoint mechanism is Swe1 kinase: normally inactive, its activation halts cell cycle progression in G2. We propose a molecular network for Swe1 control, based on published observations of budding yeast and analogous control signals in fission yeast. The proposed Swe1 network is merged with a model of cyclin-dependent kinase regulation, converted into a set of differential equations and studied by numerical simulation. The simulations accurately reproduce the phenotypes of a dozen checkpoint mutants. Among other predictions, the model attributes a new role to Hsl1, a kinase known to play a role in Swe1 degradation: Hsl1 must also be indirectly responsible for potent inhibition of Swe1 activity. The model supports the idea that the morphogenesis checkpoint, like other checkpoints, raises the cell size threshold for progression from one phase of the cell cycle to the next.
The model reproduces Fig 3 of the paper.
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
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Mathematical model of the morphogenesis checkpoint in budding yeast.
- Ciliberto A, Novak B, Tyson JJ
- The Journal of cell biology , 12/ 2003 , Volume 163 , pages: 1243-1254 , PubMed ID: 14691135
- Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
- The morphogenesis checkpoint in budding yeast delays progression through the cell cycle in response to stimuli that prevent bud formation. Central to the checkpoint mechanism is Swe1 kinase: normally inactive, its activation halts cell cycle progression in G2. We propose a molecular network for Swe1 control, based on published observations of budding yeast and analogous control signals in fission yeast. The proposed Swe1 network is merged with a model of cyclin-dependent kinase regulation, converted into a set of differential equations and studied by numerical simulation. The simulations accurately reproduce the phenotypes of a dozen checkpoint mutants. Among other predictions, the model attributes a new role to Hsl1, a kinase known to play a role in Swe1 degradation: Hsl1 must also be indirectly responsible for potent inhibition of Swe1 activity. The model supports the idea that the morphogenesis checkpoint, like other checkpoints, raises the cell size threshold for progression from one phase of the cell cycle to the next.
Submitter of this revision: administrator
Modellers: administrator, Harish Dharuri
Metadata information
isDescribedBy (1 statement)
hasTaxon (1 statement)
isVersionOf (2 statements)
Gene Ontology obsolete cytokinesis after mitosis checkpoint
isPartOf (1 statement)
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000297_url.xml | SBML L2V4 representation of Ciliberto2003_Morphogenesis_Checkpoint | 94.38 KB | Preview | Download |
Additional files |
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| BIOMD0000000297-biopax2.owl | Auto-generated BioPAX (Level 2) | 53.12 KB | Preview | Download |
| BIOMD0000000297-biopax3.owl | Auto-generated BioPAX (Level 3) | 85.89 KB | Preview | Download |
| BIOMD0000000297.m | Auto-generated Octave file | 18.87 KB | Preview | Download |
| BIOMD0000000297.pdf | Auto-generated PDF file | 338.89 KB | Preview | Download |
| BIOMD0000000297.png | Auto-generated Reaction graph (PNG) | 666.86 KB | Preview | Download |
| BIOMD0000000297.sci | Auto-generated Scilab file | 67.00 Bytes | Preview | Download |
| BIOMD0000000297.svg | Auto-generated Reaction graph (SVG) | 108.67 KB | Preview | Download |
| BIOMD0000000297.vcml | Auto-generated VCML file | 116.60 KB | Preview | Download |
| BIOMD0000000297.xpp | Auto-generated XPP file | 14.67 KB | Preview | Download |
| BIOMD0000000297_urn.xml | Auto-generated SBML file with URNs | 99.10 KB | Preview | Download |
| f3.sedml | Reproduces Figure3 a - d | 9.16 KB | Preview | Download |
- Model originally submitted by : Harish Dharuri
- Submitted: Mar 17, 2008 10:26:57 AM
- Last Modified: Dec 21, 2018 5:07:14 PM
Revisions
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Version: 3
- Submitted on: Dec 21, 2018 5:07:14 PM
- Submitted by: administrator
- With comment: Include the additional files provided by the submitter in the original submission: f3.sedml
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Version: 2
- Submitted on: Jan 31, 2012 1:52:48 PM
- Submitted by: Harish Dharuri
- With comment: Current version of Ciliberto2003_Morphogenesis_Checkpoint
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Version: 1
- Submitted on: Mar 17, 2008 10:26:57 AM
- Submitted by: Harish Dharuri
- With comment: Original import of Ciliberto2003_Morphogenesis_Checkpoint
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: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| Trim Protein SIC1 ; G2/mitotic-specific cyclin-2 ; Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein cdc28 |
0.084410675 item |
| SBF G1-specific transcription factors activator MSA1 |
0.12405464 item |
| PTrim G2/mitotic-specific cyclin-2 ; Protein SIC1 ; Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein cdc28 |
1.402314E-5 item |
| Cdc20a APC/C activator protein CDC20 |
1.4384692 item |
| Swe1M Mitosis inhibitor protein kinase SWE1 |
0.018360127 item |
| Cln G1/S-specific cyclin CLN2 ; G1/S-specific cyclin CLN1 |
0.053600963 item |
| Sic Protein SIC1 |
0.0035491784 item |
| PSwe1 Mitosis inhibitor protein kinase SWE1 |
2.0500785E-4 item |
| Clb G2/mitotic-specific cyclin-2 |
0.18453673 item |
| Reactions | Rate | Parameters |
|---|---|---|
| PTrim => Trim | PTrim*kmih | kmih = 0.0 |
| SBF => ; Clb | SBF*(kisbf_prime+kisbf_doubleprime*Clb)/(jisbf+SBF) | kisbf_doubleprime = 2.0; kisbf_prime = 1.0; jisbf = 0.01 |
| PTrim => PClb; Cln, Clb | PTrim*(kdsic_prime*Cln+kdsic_doubleprime*Clb+kdsic) | kdsic = 0.01; kdsic_prime = 1.0; kdsic_doubleprime = 3.0 |
| Cdc20 => Cdc20a; IE | kacdc20*Cdc20*IE/(jacdc20+Cdc20) | jacdc20 = 0.001; kacdc20 = 1.0 |
| Swe1M => PSwe1M; Clb | Viwee*Swe1M*Clb/(Jiwee+Swe1M) | Viwee = 1.0; Jiwee = 0.05 |
| Cln => | kdcln*Cln | kdcln = 0.1 |
| Sic => ; Cln, Clb | Sic*(kdsic_prime*Cln+kdsic_doubleprime*Clb+kdsic) | kdsic = 0.01; kdsic_prime = 1.0; kdsic_doubleprime = 3.0 |
| PSwe1 => PSwe1M | khsl1*BUD*PSwe1 | BUD = 0.0; khsl1 = 1.0 |
| Clb => ; Cdh1, Cdc20a | Clb*(kdclb_doubleprime*Cdh1+kdclb_tripleprime*Cdc20a+kdclb_prime) | kdclb_tripleprime = 0.1; kdclb_prime = 0.015; kdclb_doubleprime = 1.0 |
| Cdc20a => Cdc20 | Cdc20a*kicdc20/(jicdc20+Cdc20a) | jicdc20 = 0.001; kicdc20 = 0.25 |
(added: 13 Jan 2011, 13:22:22, updated: 13 Jan 2011, 13:22:22)