Li2009- Assymetric Caulobacter cell cycle

  public model
Model Identifier
BIOMD0000000727
Short description 
The asymmetric cell division cycle of Caulobacter crescentus is orchestrated by an elaborate gene-protein regulatory network, centered on three major control proteins, DnaA, GcrA and CtrA. The regulatory network is cast into a quantitative computational model to investigate in a systematic fashion how these three proteins control the relevant genetic, biochemical and physiological properties of proliferating bacteria. Different controls for both swarmer and stalked cell cycles are represented in the mathematical scheme. The model is validated against observed phenotypes of wild-type cells and relevant mutants, and it predicts the phenotypes of novel mutants and of known mutants under novel experimental conditions. Because the cell cycle control proteins of Caulobacter are conserved across many species of alpha-proteobacteria, the model we are proposing here may be applicable to other genera of importance to agriculture and medicine
Format
SBML (L2V4)
Related Publication
  • Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus.
  • Li S, Brazhnik P, Sobral B, Tyson JJ
  • PLoS computational biology , 8/ 2009 , Volume 5 , Issue 8 , pages: e1000463 , PubMed ID: 19680425
  • Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
  • The asymmetric cell division cycle of Caulobacter crescentus is orchestrated by an elaborate gene-protein regulatory network, centered on three major control proteins, DnaA, GcrA and CtrA. The regulatory network is cast into a quantitative computational model to investigate in a systematic fashion how these three proteins control the relevant genetic, biochemical and physiological properties of proliferating bacteria. Different controls for both swarmer and stalked cell cycles are represented in the mathematical scheme. The model is validated against observed phenotypes of wild-type cells and relevant mutants, and it predicts the phenotypes of novel mutants and of known mutants under novel experimental conditions. Because the cell cycle control proteins of Caulobacter are conserved across many species of alpha-proteobacteria, the model we are proposing here may be applicable to other genera of importance to agriculture and medicine (e.g., Rhizobium, Brucella).
Contributors
Submitter of the first revision: Ashley Xavier
Submitter of this revision: Krishna Kumar Tiwari
Modellers: Ashley Xavier, Krishna Kumar Tiwari

Metadata information

is (2 statements)
BioModels Database MODEL1812110002
BioModels Database BIOMD0000000727

isDescribedBy (3 statements)
PubMed 19680425
BioModels Database BIOMD0000000718
DOI 10.1371/journal.pcbi.1000463

hasTaxon (1 statement)
isDerivedFrom (5 statements)
Gene Ontology cell cycle
BioModels Database BIOMD0000000718
Taxonomy Caulobacter vibrioides
Gene Ontology regulation of cell cycle
Mathematical Modelling Ontology Ordinary differential equation model

hasProperty (3 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Gene Ontology cell cycle
Gene Ontology regulation of cell cycle

Curation status
Curated
Modelling approach(es)
ordinary differential equation model
Tags

Connected external resources

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Name Description Size Actions

Model files
Li2009.xml SBML file for Li2009 model 316.41 KB Preview | Download

Additional files
Li2009_final.cps copasi file 348.73 KB Preview | Download

  • Model originally submitted by : Ashley Xavier
  • Submitted: Dec 11, 2018 4:02:16 PM
  • Last Modified: Jul 12, 2019 4:58:12 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Jul 12, 2019 4:58:12 PM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: updated xml file for bqbiol error
  • Version: 2 public model Download this version
    • Submitted on: Dec 11, 2018 4:02:16 PM
    • Submitted by: Ashley Xavier
    • With comment: Automatically added model identifier BIOMD0000000727

(*) 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
Species Initial Concentration/Amount
GcrA

Cell cycle regulatory protein GcrA 		0.65 mmol
CtrA

Cell cycle transcriptional regulator CtrA 		0.04 mmol
PerP

Aspartyl protease perP 		0.55 mmol
FtsZ

Cell division protein FtsZ 		0.53 mmol
Z 1.0 mmol
CtrA P

Cell cycle transcriptional regulator CtrA 		0.08 mmol
DivK

Cell division response regulator DivK 		0.66 mmol
DNA

DNA 		1.05 mmol
Reactions
Reactions Rate Parameters
GcrA => Caulobacter*kd_GcrA*GcrA kd_GcrA = 0.022
=> CtrA; CtrA_P, hctrA Caulobacter*ks_CtrA_P2*CtrA_P^2/(Ja_CtrA_CtrA_P^2+CtrA_P^2)*hctrA ks_CtrA_P2 = 0.14; Ja_CtrA_CtrA_P = 0.45
CtrA => CtrA_P; CtrA, CckA_P Caulobacter*ktrans_CtrA*CtrA*CckA_P ktrans_CtrA = 0.095
=> PerP; CtrA_P, PodJL Caulobacter*ks_PerP*CtrA_P*PodJL ks_PerP = 0.04
PerP => ; Z Caulobacter*ksep_PerP*PerP*H*(1-Z)/((Jsep_PerP+1)-Z) H = 0.0; ksep_PerP = 0.011; Jsep_PerP = 0.3
FtsZ => ; Zring, FtsZ Caulobacter*kd_FtsZ2*(1-Zring)*FtsZ kd_FtsZ2 = 0.02
Z => ; FtsQ, Zring, ParAADP Caulobacter*(kZ_closed1+kZ_closed2*FtsQ^4/(JZ_FtsQ^4+FtsQ^4)*(Zring/thethaZring)^4/(1+(Zring/thethaZring)^4+(ParAADP/thethaParAADP)^4))*Z/(Ja_closed+Z) kZ_closed1 = 1.0E-4; thethaParAADP = 0.3; thethaZring = 0.3; kZ_closed2 = 1.6; JZ_FtsQ = 0.8; Ja_closed = 0.05
CtrA_P => ; DivK_P, CpdR, RcdA, CtrA_P Caulobacter*kd_CtrA2*DivK_P^2/(Jd_CtrA_DivK_P^2+DivK_P^2)*CpdR^4/(jd_CtrA_CpdR^4+CpdR^4)*RcdA^4/(jd_CtrA_RcdA^4+RcdA^4)*CtrA_P Jd_CtrA_DivK_P = 0.55; jd_CtrA_RcdA = 0.5; kd_CtrA2 = 0.25; jd_CtrA_CpdR = 0.6
DivK => Caulobacter*kd_DivK*DivK kd_DivK = 0.002
=> DNA; Elong, Count Caulobacter*kelong*Elong^4/(Pelong^4+Elong^4)*Count Pelong = 0.05; kelong = 0.0065
Curator's comment:
(added: 11 Dec 2018, 16:01:30, updated: 11 Dec 2018, 16:01:30)
Fig 4 of the publication. The time period of this reproduction is shorter than the published version. The event for Z == 0 was modified as z <= 0.1 for the model to work.Additional events were added according to the matlab supplementary code.