BIOMD0000000461
type: SBMLModel
reaction: v2 meta
parameter: kxs meta
parameter: kzs meta
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
creator:
  ORG:
    orgname: The University of Rostock
  n:
    given: Ulf
    family: Liebal
species: x meta
parameter: kxd meta
reaction: v3 meta
occurs in: http://identifiers.org/taxonomy/1423
species: sigb meta
species: IPTG meta
is described by: http://identifiers.org/pubmed/22511268
area units: area
parameter: kbd meta
compartment: compartment meta
is: MODEL1212180000
notes: Liebal2012 - B.subtilis transcription inhibition 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 are 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 Transcription inhibition model (MODEL1212180000). 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 concentrations after t…
length unit: length
species: lacz meta
modified:
  W3 CDTF: Mon Jun 10 14:47:44 BST 2013
created:
  W3 CDTF: Thu Jun 06 20:36:21 BST 2013
parameter: kbs meta
parameter: kzd meta
curated: true
is: GO:0030162
reaction: v1 meta
name: Liebal2012 - B.subtilis transcription inhibition model

v2 meta
type: Reaction
reactant: 565162
name: v2
reversible: true
fast: false
is: GO:0009058
is: GO:0006508
modifier: 565188
product: 565175
kinetic law: 565201

565162
type: SpeciesReference
stoichiometry: 1.0
species: sigb meta

sigb meta
type: Species
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

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

x meta
type: Species
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

lacz meta
type: Species
initial concentration: 0.0
initial amount: NaN
has only substance units: false
is: GO:0004565
constant: false
is: http://identifiers.org/ec-code/3.2.1.23
boundary condition: false
name: lacz
in compartment: compartment meta

565175
type: SpeciesReference
stoichiometry: 1.0
species: lacz meta

kxs meta
type: Parameter
is: GO:0009058
constant: true
value: 0.76
name: kxs

kzs meta
type: Parameter
is: GO:0009058
constant: true
value: 4.0E-4
name: kzs

kxd meta
type: Parameter
is: GO:0006508
constant: true
value: 9.0
name: kxd

v3 meta
type: Reaction
reactant: 565214
name: v3
product: 565227
kinetic law: 565240
reversible: true
is: GO:0009058
fast: false
is: GO:0006508

565214
type: SpeciesReference
stoichiometry: 1.0
species: sigb meta

565227
type: SpeciesReference
stoichiometry: 1.0
species: x meta

IPTG meta
type: Species
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

kbd meta
type: Parameter
is: GO:0006508
constant: true
value: 0.044
name: kbd

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

kzd meta
type: Parameter
is: GO:0006508
constant: true
value: 0.041
name: kzd

v1 meta
type: Reaction
fast: false
kinetic law: 565149
is: GO:0009058
reversible: true
is: GO:0006508
reactant: 565123
product: 565136
name: v1

565123
type: SpeciesReference
stoichiometry: 1.0
species: IPTG meta

565136
type: SpeciesReference
stoichiometry: 1.0
species: sigb meta