Li2008 - Caulobacter Cell Cycle

  public model
Model Identifier
BIOMD0000000718
Short description

This a model from the article:
A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells.
Shenghua Li, Paul Brazhnik, Bruno Sobral, John J. Tyson PLoS Comput Biol 2008 Jan 25:4(1): e9 18225942 ,
Abstract:
Progression of a cell through the division cycle is tightly controlled at different steps to ensure the integrity of genome replication and partitioning to daughter cells. From published experimental evidence, we propose a molecular mechanism for control of the cell division cycle in Caulobacter crescentus. The mechanism, which is based on the synthesis and degradation of three ‘‘master regulator’’ proteins (CtrA, GcrA, and DnaA), is converted into a quantitative model, in order to study the temporal dynamics of these and other cell cycle proteins. The model accounts for important details of the physiology, biochemistry, and genetics of cell cycle control in stalked C. crescentus cell. It reproduces protein time courses in wild-type cells, mimics correctly the phenotypes of many mutant strains, and predicts the phenotypes of currently uncharacterized mutants. Since many of the proteins involved in regulating the cell cycle of C. crescentus are conserved among many genera of a-proteobacteria, the proposed mechanism may be applicable to other species of importance in agriculture and medicine.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..

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.

Format
SBML (L2V4)
Related Publication
  • A quantitative study of the division cycle of Caulobacter crescentus stalked cells.
  • Li S, Brazhnik P, Sobral B, Tyson JJ
  • PLoS computational biology , 1/ 2008 , Volume 4 , Issue 1 , pages: e9 , PubMed ID: 18225942
  • Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
  • Progression of a cell through the division cycle is tightly controlled at different steps to ensure the integrity of genome replication and partitioning to daughter cells. From published experimental evidence, we propose a molecular mechanism for control of the cell division cycle in Caulobacter crescentus. The mechanism, which is based on the synthesis and degradation of three "master regulator" proteins (CtrA, GcrA, and DnaA), is converted into a quantitative model, in order to study the temporal dynamics of these and other cell cycle proteins. The model accounts for important details of the physiology, biochemistry, and genetics of cell cycle control in stalked C. crescentus cell. It reproduces protein time courses in wild-type cells, mimics correctly the phenotypes of many mutant strains, and predicts the phenotypes of currently uncharacterized mutants. Since many of the proteins involved in regulating the cell cycle of C. crescentus are conserved among many genera of alpha-proteobacteria, the proposed mechanism may be applicable to other species of importance in agriculture and medicine.
Contributors
Submitter of the first revision: Ashley Xavier
Submitter of this revision: Ashley Xavier
Modellers: Ashley Xavier

Metadata information

is (2 statements)
BioModels Database MODEL1811070001
BioModels Database BIOMD0000000718

isDescribedBy (2 statements)
hasTaxon (1 statement)
hasProperty (2 statements)
Gene Ontology regulation of cell cycle
Gene Ontology cell cycle


Curation status
Curated

Tags

Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

Li2008.xml SBML lvl2 file containing the model 171.52 KB Preview | Download

Additional files

Li2008_reactions.cps copasi file to generate figure 4 206.61 KB Preview | Download

  • Model originally submitted by : Ashley Xavier
  • Submitted: Nov 7, 2018 1:23:02 PM
  • Last Modified: Nov 7, 2018 1:23:02 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Nov 7, 2018 1:23:02 PM
    • Submitted by: Ashley Xavier
    • With comment: Automatically added model identifier BIOMD0000000718
Legends
: Variable used inside SBML models


Species
Reactions
Reactions Rate Parameters
DivK => Caulobacter*kd_DivK*DivK kd_DivK = 0.002 1/min
=> CcrM; I Caulobacter*ks_CcrM*I ks_CcrM = 0.072 1/min
hcori => ; CcrM Caulobacter*km_cori*CcrM^4/(Jm_cori^4+CcrM^4)*hcori km_cori = 0.4 1/min; Jm_cori = 0.95 1
=> Ini; DnaA, GcrA, CtrA, hcori Caulobacter*ka_Ini*(DnaA/thetaDnaA)^4*(GcrA/thetaGcrA)^4/(1+(DnaA/thetaDnaA)^4+(GcrA/thetaGcrA)^4+(CtrA/thetaCtrA)^4+hcori/thetacori) thetacori = 2.0E-4 1; ka_Ini = 0.01 1/min; thetaGcrA = 0.45 1; thetaCtrA = 0.2 1; thetaDnaA = 0.6 1
=> CtrA; CtrA, hctrA Caulobacter*ks_CtrA_P2*CtrA^2/(Ja_CtrA_CtrA^2+CtrA^2)*hctrA ks_CtrA_P2 = 0.073 1/min; Ja_CtrA_CtrA = 0.45 1
=> DnaA; GcrA, CtrA, hcori Caulobacter*ks_DnaA*Ji_DnaA_GcrA^2/(Ji_DnaA_GcrA^2+GcrA^2)*CtrA^2/(Ja_DnaA_CtrA^2+CtrA^2)*(2-hcori) Ja_DnaA_CtrA = 0.3 1; ks_DnaA = 0.0165 1/min; Ji_DnaA_GcrA = 0.5 1
DnaA => Caulobacter*kd_DnaA*DnaA kd_DnaA = 0.007 1/min
=> Fts; CtrA, hfts Caulobacter*ks_Fts*CtrA*hfts ks_Fts = 0.063 1/min
GcrA => ; CtrA, DnaA Caulobacter*kd_GcrA*GcrA kd_GcrA = 0.022 1/min
=> Zring Caulobacter*kzring_open*(1-Zring)/((Ja_open+1)-Zring) Ja_open = 0.01 1; kzring_open = 0.8 1/min
Curator's comment:
(added: 07 Nov 2018, 13:19:12, updated: 10 Dec 2018, 13:50:43)
Unlike the publication description Zring = 0 is never achieved in the simulations, a reset condition of Zring < 0.11 was used and it reproduced the publication figure 4 accurately. The simulations were done using COPASI 4.24 and plotted in R 3.5.1.