631321
stoichiometry: 1.0
species: sigb meta
type: SpeciesReference

v1 meta
fast: false
reversible: true
name: v1
product: 631243
reactant: 631230
is: GO:0009058
type: Reaction
is: GO:0006508
kinetic law: 631256

kxs meta
is: GO:0009058
constant: true
value: 9.32517E-8
name: kxs
type: Parameter

631269
stoichiometry: 1.0
species: sigb meta
type: SpeciesReference

v2 meta
reactant: 631269
reversible: true
type: Reaction
product: 631282
modifier: 631295
fast: false
name: v2
is: GO:0009058
kinetic law: 631308
is: GO:0006508

kzs meta
is: GO:0009058
constant: true
value: 9.03538E-7
name: kzs
type: Parameter

IPTG meta
is: CHEBI:61448
constant: true
boundary condition: true
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: compartment meta
name: IPTG
type: Species

BIOMD0000000459
created:
  W3 CDTF: Thu Jun 06 20:26:06 BST 2013
reaction: v3 meta
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
notes: Liebal2012 - B.subtilis post-transcription instability model An important transcription factor of B.subsilis is sigma B . Liebal et al. (2012) have performed experiments in B.subtilis wild type and mutant straits to test and validate a mathematical model of the dynamics of sigma B activity. The following three models were constructed and their ability to fit the experimental data were tested. 1) Transcription inhibition model (MODEL1212180000), 2) sigma B proteolysis model (MODEL1302080000) and 3) Post-transcriptional instability model (MODEL1302080001). This model corresponds to the post-transcription instability model (MODEL1302080001). This model is described in the article: Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis. Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O. 2012 Jun;8(6):1806-14. Abstract: In Bacillus subtilis the σ(B) mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, we need to explore the mechanism by which the components interact. Here, we performed experiments in B. subtilis wild type and mutant strains to test and validate a mathematical model of the dynamics of σ(B) activity. In the mutant strain BSA115, σ(B) transcription is inducible by the addition of IPTG and negative control of σ(B) activity by the anti-sigma factor RsbW is absent. In contrast to our expectations of a continuous β-galactosidase activity from a ctc::lacZ fusion, we observed a transient activity in the mutant. To explain this experimental finding, we constructed mathematical models reflecting different hypotheses regarding the regulation of σ(B) and β-galactosidase dynamics. Only the model assuming instability of either ctc::lacZ mRNA or β-galactosidase protein is able to reproduce the experiments in silico. Subsequent Northern blot experiments revealed stable high-level ctc::lacZ mRNA concentra…
is: MODEL1302080001
modified:
  W3 CDTF: Mon Jun 10 14:51:33 BST 2013
length unit: length
compartment: compartment meta
parameter: kxd meta
type: SBMLModel
reaction: v2 meta
parameter: kxs meta
species: sigb meta
has property: GO:0030162
parameter: kbs meta
species: IPTG meta
species: x meta
parameter: kzd meta
reaction: v1 meta
parameter: kzx meta
is described by: http://identifiers.org/pubmed/22511268
creator:
  ORG:
    orgname: The University of Rostock
  n:
    given: Ulf
    family: Liebal
name: Liebal2012 - B.subtilis post-transcriptional instability model
parameter: kzs meta
occurs in: http://identifiers.org/taxonomy/1423
species: lacz meta
curated: true
area units: area
parameter: kbd meta

631230
stoichiometry: 1.0
species: IPTG meta
type: SpeciesReference

sigb meta
is: IPR006288
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: compartment meta
name: sigb
type: Species

kzd meta
is: GO:0006508
constant: true
value: 1.34615E-7
name: kzd
type: Parameter

631334
stoichiometry: 1.0
species: x meta
type: SpeciesReference

kbs meta
is: GO:0009058
constant: true
value: 100.0
name: kbs
type: Parameter

x meta
is: CHEBI:35222
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: compartment meta
name: x
type: Species

kxd meta
is: GO:0006508
constant: true
value: 1.08559E-9
name: kxd
type: Parameter

631282
stoichiometry: 1.0
species: lacz meta
type: SpeciesReference

v3 meta
fast: false
product: 631334
is: GO:0009058
kinetic law: 631347
reactant: 631321
reversible: true
name: v3
type: Reaction
is: GO:0006508

kzx meta
is: CHEBI:35222
constant: true
value: 0.00317772
name: kzx
type: Parameter

compartment meta
is: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

631243
stoichiometry: 1.0
species: sigb meta
type: SpeciesReference

lacz meta
is: GO:0015925
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: compartment meta
name: lacz
type: Species

kbd meta
is: GO:0006508
constant: true
value: 0.0164812
name: kbd
type: Parameter