Ciliberto2003 - CyclinE / Cdk2 timer in the cell cycle of Xenopus laevis embryo

  public model
Model Identifier
BIOMD0000000697
Short description
Ciliberto2003 - CyclinE / Cdk2 timer in the cell cycle of Xenopus laevis embryo

This model is described in the article:

Ciliberto A, Petrus MJ, Tyson JJ, Sible JC.
Biophys. Chem. 2003 Jul; 104(3): 573-589

Abstract:

Early cell cycles of Xenopus laevis embryos are characterized by rapid oscillations in the activity of two cyclin-dependent kinases. Cdk1 activity peaks at mitosis, driven by periodic degradation of cyclins A and B. In contrast, Cdk2 activity oscillates twice per cell cycle, despite a constant level of its partner, cyclin E. Cyclin E degrades at a fixed time after fertilization, normally corresponding to the midblastula transition. Based on published data and new experiments, we constructed a mathematical model in which: (1) oscillations in Cdk2 activity depend upon changes in phosphorylation, (2) Cdk2 participates in a negative feedback loop with the inhibitory kinase Wee1; (3) cyclin E is cooperatively removed from the oscillatory system; and (4) removed cyclin E is degraded by a pathway activated by cyclin E/Cdk2 itself. The model's predictions about embryos injected with Xic1, a stoichiometric inhibitor of cyclin E/Cdk2, were experimentally validated.

This model is hosted on BioModels Database and identified by: BIOMD0000000697.

To cite BioModels Database, please use: Chelliah V et al. BioModels: ten-year anniversary. Nucl. Acids Res. 2015, 43(Database issue):D542-8.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Format
SBML (L2V4)
Related Publication
  • A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos.
  • Ciliberto A, Petrus MJ, Tyson JJ, Sible JC
  • Biophysical chemistry , 7/ 2003 , Volume 104 , Issue 3 , pages: 573-589 , PubMed ID: 12914904
  • Biology Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0406, USA. ancilibe@vt.edu
  • Early cell cycles of Xenopus laevis embryos are characterized by rapid oscillations in the activity of two cyclin-dependent kinases. Cdk1 activity peaks at mitosis, driven by periodic degradation of cyclins A and B. In contrast, Cdk2 activity oscillates twice per cell cycle, despite a constant level of its partner, cyclin E. Cyclin E degrades at a fixed time after fertilization, normally corresponding to the midblastula transition. Based on published data and new experiments, we constructed a mathematical model in which: (1) oscillations in Cdk2 activity depend upon changes in phosphorylation, (2) Cdk2 participates in a negative feedback loop with the inhibitory kinase Wee1; (3) cyclin E is cooperatively removed from the oscillatory system; and (4) removed cyclin E is degraded by a pathway activated by cyclin E/Cdk2 itself. The model's predictions about embryos injected with Xic1, a stoichiometric inhibitor of cyclin E/Cdk2, were experimentally validated.
Contributors
Submitter of the first revision: Vijayalakshmi Chelliah
Submitter of this revision: Rahuman Sheriff
Modellers: Vijayalakshmi Chelliah, Rahuman Sheriff

Metadata information

is (2 statements)
BioModels Database MODEL0913242281
BioModels Database BIOMD0000000697

isDescribedBy (1 statement)
PubMed 12914904

hasPart (1 statement)
Gene Ontology regulation of cell cycle

hasProperty (1 statement)
Mathematical Modelling Ontology Ordinary differential equation model

occursIn (1 statement)
Brenda Tissue Ontology embryo

hasTaxon (1 statement)

Curation status
Curated


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Connected external resources

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Model files

BIOMD0000000697_url.xml SBML L2V4 representation of Ciliberto2003 - CyclinE / Cdk2 timer in the cell cycle of Xenopus laevis embryo 136.91 KB Preview | Download

Additional files

BIOMD0000000697-biopax2.owl Auto-generated BioPAX (Level 2) 44.32 KB Preview | Download
BIOMD0000000697-biopax3.owl Auto-generated BioPAX (Level 3) 75.55 KB Preview | Download
BIOMD0000000697.m Auto-generated Octave file 15.83 KB Preview | Download
BIOMD0000000697.pdf Auto-generated PDF file 234.33 KB Preview | Download
BIOMD0000000697.png Auto-generated Reaction graph (PNG) 310.13 KB Preview | Download
BIOMD0000000697.sci Auto-generated Scilab file 170.00 Bytes Preview | Download
BIOMD0000000697.svg Auto-generated Reaction graph (SVG) 74.38 KB Preview | Download
BIOMD0000000697.vcml Auto-generated VCML file 953.00 Bytes Preview | Download
BIOMD0000000697.xpp Auto-generated XPP file 12.12 KB Preview | Download
BIOMD0000000697_urn.xml Auto-generated SBML file with URNs 136.55 KB Preview | Download
MODEL0913242281_fig5.sedml SEDML file to generate Figure 5a and 5b 5.11 KB Preview | Download
MODEL0913242281_fig6.sedml SEDML file to generate Figure 6a, 6b and 6c 6.27 KB Preview | Download
MODEL0913242281_final.cps Model is implemented in the attached COPASI file. The parameters are set to generate Figure 5. 149.33 KB Preview | Download

  • Model originally submitted by : Vijayalakshmi Chelliah
  • Submitted: Apr 30, 2009 1:00:15 PM
  • Last Modified: May 1, 2018 1:26:48 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: May 1, 2018 1:26:48 PM
    • Submitted by: Rahuman Sheriff
    • With comment: Notes updated using online editor.
  • Version: 2 public model Download this version
    • Submitted on: Apr 30, 2009 1:00:15 PM
    • Submitted by: Vijayalakshmi Chelliah
    • With comment: Current version of Ciliberto2003_CyclinECdk2Timer
  • Version: 1 public model Download this version
    • Submitted on: Apr 30, 2009 1:00:15 PM
    • Submitted by: Vijayalakshmi Chelliah
    • With comment: Original import of Ciliberto2003_CyclinECdk2Timer

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Reactions
Reactions Rate Parameters
Xic + Cdk2_CycE => Xic_Cdk2_CycE compartment*kassoc*Xic*Cdk2_CycE kassoc = 0.1 1/s
Xic_PCdk2_CycE => Xic_Cdk2_CycE compartment*k25A*Xic_PCdk2_CycE k25A = 0.1 1/s
Xic_Cdk2_CycE => Xic_Cdk2_CycErem compartment*kon*phi*Xic_Cdk2_CycE kon = 0.02 1/s; phi = 0.0390625 1
Xic + PCdk2_CycErem => Xic_PCdk2_CycErem compartment*kassoc*Xic*PCdk2_CycErem kassoc = 0.1 1/s
Cyc_total = Xic_PCdk2_CycE+Xic_Cdk2_CycE+Xic_PCdk2_CycErem+Xic_Cdk2_CycErem+PCdk2_CycErem+Cdk2_CycErem+Cdk2_CycE+PCdk2_CycE [] []
Cdk2_CycErem => Cdk2_CycE compartment*koff*Cdk2_CycErem koff = 1.0E-4 1/s
Cdk2_CycE => Cdk2_CycErem compartment*kon*phi*Cdk2_CycE kon = 0.02 1/s; phi = 0.0390625 1
PCdk2_CycE => Cdk2_CycE compartment*k25A*PCdk2_CycE k25A = 0.1 1/s
Xic + Cdk2_CycErem => Xic_Cdk2_CycErem compartment*kassoc*Xic*Cdk2_CycErem kassoc = 0.1 1/s
PCdk2_CycE => PCdk2_CycErem compartment*kon*phi*PCdk2_CycE kon = 0.02 1/s; phi = 0.0390625 1
Curator's comment:
(added: 01 May 2018, 12:51:55, updated: 01 May 2018, 12:51:55)
Figure 5a of the reference publication has been reproduced using Copasi 4.23. Use attached SED-ML file (MODEL0913242281_fig5.sedml) to reproduce the simulation.