Li2008 - Caulobacter Cell Cycle

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.
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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.
Submitter of this revision: Ashley Xavier
Modellers: Ashley Xavier
Metadata information
isDescribedBy (2 statements)
hasTaxon (1 statement)
hasProperty (2 statements)
Connected external resources
Name | Description | Size | Actions |
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Model files |
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Li2008.xml | SBML lvl2 file containing the model | 171.52 KB | Preview | Download |
Additional files |
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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
: Variable used inside SBML models
Species | Initial Concentration/Amount |
---|---|
DivK Cell division response regulator DivK |
0.66 mmol |
CcrM Modification methylase CcrMI |
0.5 mmol |
hcori | 1.0 mmol |
Ini DNA replication initiation |
0.0 mmol |
CtrA Cell cycle transcriptional regulator CtrA |
0.11 mmol |
DnaA Chromosomal replication initiator protein DnaA |
0.6 mmol |
Fts Cell division protein FtsQ ; Cell division protein FtsZ |
0.29 mmol |
GcrA Cell cycle regulatory protein GcrA |
0.78 mmol |
Zring organelle |
1.0 mmol |
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 |
(added: 07 Nov 2018, 13:19:12, updated: 10 Dec 2018, 13:50:43)