Novak1997 - Cell Cycle

  public model
Model Identifier
BIOMD0000000007
Short description
Novak1997 - Cell Cycle

Modeling the control of DNA replication in fission yeast.

This model is described in the article:

Novak B., Tyson JJ.
Proc. Natl. Acad. Sci. U.S.A. 1997:94(17):9147-52

Abstract:

A central event in the eukaryotic cell cycle is the decision to commence DNA replication (S phase). Strict controls normally operate to prevent repeated rounds of DNA replication without intervening mitoses ("endoreplication") or initiation of mitosis before DNA is fully replicated ("mitotic catastrophe"). Some of the genetic interactions involved in these controls have recently been identified in yeast. From this evidence we propose a molecular mechanism of "Start" control in Schizosaccharomyces pombe. Using established principles of biochemical kinetics, we compare the properties of this model in detail with the observed behavior of various mutant strains of fission yeast: wee1(-) (size control at Start), cdc13Delta and rum1(OP) (endoreplication), and wee1(-) rum1Delta (rapid division cycles of diminishing cell size). We discuss essential features of the mechanism that are responsible for characteristic properties of Start control in fission yeast, to expose our proposal to crucial experimental tests.

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 (L2V3)
Related Publication
  • Modeling the control of DNA replication in fission yeast.
  • Novak B, Tyson JJ
  • Proceedings of the National Academy of Sciences of the United States of America , 8/ 1997 , Volume 94 , pages: 9147-9152 , PubMed ID: 9256450
  • Department of Agricultural Chemical Technology, Technical University of Budapest, 1521 Budapest, St. Gellert ter 4, Hungary.
  • A central event in the eukaryotic cell cycle is the decision to commence DNA replication (S phase). Strict controls normally operate to prevent repeated rounds of DNA replication without intervening mitoses ("endoreplication") or initiation of mitosis before DNA is fully replicated ("mitotic catastrophe"). Some of the genetic interactions involved in these controls have recently been identified in yeast. From this evidence we propose a molecular mechanism of "Start" control in Schizosaccharomyces pombe. Using established principles of biochemical kinetics, we compare the properties of this model in detail with the observed behavior of various mutant strains of fission yeast: wee1(-) (size control at Start), cdc13Delta and rum1(OP) (endoreplication), and wee1(-) rum1Delta (rapid division cycles of diminishing cell size). We discuss essential features of the mechanism that are responsible for characteristic properties of Start control in fission yeast, to expose our proposal to crucial experimental tests.
Contributors
Submitter of the first revision: Nicolas Le Novère
Submitter of this revision: Nicolas Le Novère
Modellers: Nicolas Le Novère

Metadata information

is
BioModels Database MODEL6614787694
BioModels Database BIOMD0000000007
isDescribedBy
PubMed 9256450
isDerivedFrom
PubMed 10395816
hasTaxon
isVersionOf
Gene Ontology mitotic cell cycle
KEGG Pathway Cell cycle
isHomologTo

Curation status
Curated

Tags

Connected external resources

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Model files

BIOMD0000000007_url.xml SBML L2V3 representation of Novak1997 - Cell Cycle 62.21 KB Preview | Download

Additional files

BIOMD0000000007-biopax2.owl Auto-generated BioPAX (Level 2) 36.91 KB Preview | Download
BIOMD0000000007-biopax3.owl Auto-generated BioPAX (Level 3) 58.81 KB Preview | Download
BIOMD0000000007.m Auto-generated Octave file 13.04 KB Preview | Download
BIOMD0000000007.pdf Auto-generated PDF file 257.27 KB Preview | Download
BIOMD0000000007.png Auto-generated Reaction graph (PNG) 138.19 KB Preview | Download
BIOMD0000000007.sci Auto-generated Scilab file 67.00 Bytes Preview | Download
BIOMD0000000007.svg Auto-generated Reaction graph (SVG) 87.50 KB Preview | Download
BIOMD0000000007.vcml Auto-generated VCML file 900.00 Bytes Preview | Download
BIOMD0000000007.xpp Auto-generated XPP file 9.81 KB Preview | Download
BIOMD0000000007_manual.png Manually generated Reaction graph (PNG) 138.19 KB Preview | Download
BIOMD0000000007_manual.svg Manually generated Reaction graph (SVG) 87.50 KB Preview | Download
BIOMD0000000007_urn.xml Auto-generated SBML file with URNs 60.94 KB Preview | Download

  • Model originally submitted by : Nicolas Le Novère
  • Submitted: Sep 13, 2005 1:33:30 PM
  • Last Modified: Mar 26, 2014 2:20:21 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Mar 26, 2014 2:20:21 PM
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Novak1997 - Cell Cycle
  • Version: 1 public model Download this version
    • Submitted on: Sep 13, 2005 1:33:30 PM
    • Submitted by: Nicolas Le Novère
    • With comment: Original import of Novak1997_CellCycle

(*) 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
G1K + R => G1R G1K*k8*R-G1R*k8r k8 = 10.0; k8r = 0.1
=> G1K k5 k5 = 0.00175
G1R => R G1R*k6prime k6prime = 0.0
G2K + R => G2R G2K*k7*R-G2R*k7r k7r = 0.1; k7 = 100.0
IEB => IE; MPF IEB*ki*MPF/(IEB+Kmi)-IE*kir/(IE+Kmir) Kmi = 0.01; Kmir = 0.01; ki = 0.4; kir = 0.1
Wee1B = 1-Wee1 [] []
IEB = 1-IE [] []
Rum1Total = G1R+G2R+PG2R+R [] []
=> R k3 k3 = 0.09375
G1R => G1K G1R*k4 k4 = 0.1875
Curator's comment:
(added: 15 Oct 2009, 16:25:07, updated: 15 Oct 2009, 16:25:07)
The figure corresponds to figure 2A of the original puplication. The plots in the paper were not reproduced by the model as such, but this is the best we were able to get from the parameters used in the paper without initial conditions. The model was simulated using Mathematica 6.0 - MathSBML 2.7.1.