JWS Online
Info! This is a derivative of the model jones1
Info! This is a derivative of the model smallbone14

moriya1

moriya1

 Detail
 Download

Reactions

re12

Cdc13_Synthesis

s57 > s56

re14

Trim_Dissociation_Rum1degradation

s137 > s60 + s61

re15

s161 > s166 + s46

re16

Trim_Dissociation_Rum1degradation

s161 > s56 + s61

re17

s137 > s166 + s46

re18

Cdc13_Dephosphorylation

s137 > s161

re19

Cdc13_Synthesis

s55 > s67

re20

Cdc13_Phosphorylation

s67 > s63

re21

Cdc13_Dephosphorylation

s63 > s67

re22

Rum1+Cdc13_association

s166 + s67 = s149

re23

s149 > s166 + s94

re24

Rum1+Cdc13_association

s166 + s63 = s153

re25

s153 > s166 + s94

re27

Cdc13_Dephosphorylation

s153 > s149

re28

s67 > s94

re29

s153 > s63

re3

s65 > s47

re30

s149 > s67 + s61

re31

s63 > s94

re32

s71 > s70

re33

s70 > s71

re34

s73 > s72

re35

s72 > s74

re36

s76 > s75

re37

s75 > s77

re38

s78 > s81

re39

s79 > s80

re4

s47 > s65

re40

s80 > s79

re41

s60 > s46

re42

s56 > s46

re43

s161 > s137

re44

s149 > s153

re45

s82 > s83

re46

s83 > s82

re47

s85 > s84

re48

s84 > s88

re5

s51 > s50

re53

s81 > s93

re54

s56 + s166 = s161

re56

s60 > s56

re57

s56 > s60

re58

s166 + s60 = s137

re6

s50 > s51

re60

s166 > s61

re62

s52 > s166

re66

s89 > s90

re67

s91 > s92

re68

s90 > s91

re7

s66 > s48

re8

s48 > s66

Parameters

Global parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

Vdcyc = kdcyc + kdcycsrw * s47 + kdcycsrw_dash * Srw1T + kdcycslp * s48 + kdcycslp_dash * Slp1T

Vdrum = kdrum + kdrumpuc * Puc1 + kdrumci1 * s75 + kdrumcig * s67 + kdrumcig_dash * s63 + kdrumc13 * s56 + kdrumc13_dash * s60

kwee = kwee_dash * Wee1T + (kwee_dash2 - kwee_dash) * s80

BB = oriT + s84 + (ko18r + Vdc18) / ko18

UDNA = Rad3 * (k * s84 + k_dash * s90 * Cdc18 / ((ko18r + Vdc18) / ko18 + Cdc18))

Cdc18 = s84 - chrom

preRC = (oriT - s90 - s91) * Cdc18 / ((ko18r + Vdc18) / ko18 + Cdc18)

chrom = 2.0 * oriT * s84 / (BB + sqrt(pow(BB, 2.0) - 4.0 * oriT * s84))

k25 = k25_dash * Cdc25T + (k25_dash2 - k25_dash) * s83

Vdc18 = kdc18 + kdc18c13 * s56 + kdc18cig * s67 + kdc18cig_dash * s63

Function definitions

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


Species:

Reactions:

Middle-click: pin/unpin nodes
Shift-click: pool/unpool species
Right-click: context menu
Apply alternate model layout to overlapping elements in current model:

log scales

y-axis min/max

x-axis min/max

Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico.

  • Hisao Moriya
  • Ayako Chino
  • Orsolya Kapuy
  • Attila Csikász-Nagy
  • Bela Novák
Mol. Syst. Biol. 2011; 7 : 556
Abstract
Cellular systems are generally robust against fluctuations of intracellular parameters such as gene expression level. However, little is known about expression limits of genes required to halt cellular systems. In this study, using the fission yeast Schizosaccharomyces pombe, we developed a genetic 'tug-of-war' (gTOW) method to assess the overexpression limit of certain genes. Using gTOW, we determined copy number limits for 31 cell-cycle regulators; the limits varied from 1 to >100. Comparison with orthologs of the budding yeast Saccharomyces cerevisiae suggested the presence of a conserved fragile core in the eukaryotic cell cycle. Robustness profiles of networks regulating cytokinesis in both yeasts (septation-initiation network (SIN) and mitotic exit network (MEN)) were quite different, probably reflecting differences in their physiologic functions. Fragility in the regulation of GTPase spg1 was due to dosage imbalance against GTPase-activating protein (GAP) byr4. Using the gTOW data, we modified a mathematical model and successfully reproduced the robustness of the S. pombe cell cycle with the model.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000406) Biomodels notes: This model correspond to the gTOW (genetic tug-of-war) Model described in the paper. Figure 7c of the reference publication has been reproduced here, using Copasi v4.7 (Build 34). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.