metaid kineticLaw X12f
is version of: http://identifiers.org/ec-code/5.4.2.2
constant: false
units: dimensionless
value: NaN
name: phoshpoglucomutase
type: Parameter

416726
constant: false
value: NaN
name: flux_from_T6P
type: Parameter

metaid X4
initial concentration: 0.7
boundary condition: true
type: Species
initial amount: NaN
is: SBO:0000247
has only substance units: false
is: CHEBI:18066
name: UDPG
constant: false
in compartment: metaid cell

http://identifiers.org/biomodels.db/BIOMD0000000266#_456d3b1d_bf70_42d5_b559_1c51990fc6a2
name: mM
type: SBMLUnitsDef

416717
constant: false
value: NaN
name: flux_from_G1P
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#_476bb4c5_651d_46e3_9f25_1fd74c8fc9ab
name: milimole
type: SBMLUnitsDef

http://identifiers.org/biomodels.db/BIOMD0000000266#c67b843d_af04_4e0b_bcfb_ae3ed02de55a
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid X0
type: Species
in compartment: metaid external
boundary condition: true
is: SBO:0000247
initial concentration: 1.0
is: CHEBI:17925
name: glucose
constant: false
has only substance units: false
initial amount: NaN

http://identifiers.org/biomodels.db/BIOMD0000000266#f63ad72a_fe5d_4126_b50e_f0499541dfbe
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid kineticLaw X19
is: http://identifiers.org/ec-code/3.2.1.28
constant: false
units: dimensionless
value: NaN
name: trehalase
type: Parameter

416700
is version of: GO:0005980
constant: false
units: dimensionless
value: NaN
name: glycogen use
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#cdd59da2_8d9d_4974_9e0f_6ec1a48fb061
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid kineticLaw X11
is: http://identifiers.org/ec-code/1.1.1.49
constant: false
units: dimensionless
value: NaN
name: G6P dehydrogenase
type: Parameter

416714
constant: false
value: NaN
name: flux_from_G6P
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#f4d7007e_c0c2_4260_99ab_0530a28959d1
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid X7
is: SBO:0000247
in compartment: metaid cell
boundary condition: true
type: Species
name: trehalose
initial amount: NaN
initial concentration: 0.05
is: CHEBI:16551
has only substance units: false
constant: false

metaid cell
is: GO:0005622
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell
type: Compartment

metaid kineticLaw X12r
is version of: http://identifiers.org/ec-code/5.4.2.2
constant: false
units: dimensionless
value: NaN
name: phoshpoglucomutase
type: Parameter

metaid external
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: external
type: Compartment

416729
constant: false
value: NaN
name: flux_from_trehalose
type: Parameter

416721
constant: false
value: NaN
name: flux_to_glycogen
type: Parameter

416718
constant: false
value: NaN
name: flux_to_UDPG
type: Parameter

metaid X3
is: SBO:0000247
boundary condition: true
constant: false
in compartment: metaid cell
initial amount: NaN
initial concentration: 0.1
is: CHEBI:16077
type: Species
name: G1P
has only substance units: false

http://identifiers.org/biomodels.db/BIOMD0000000266#_5171caa6_bc0c_4042_a355_bb3a1bbdc46f
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

416671
is version of: GO:0009408
constant: true
units: dimensionless
value: 0.0
type: Parameter

metaid kineticLaw X10
constant: false
units: dimensionless
value: NaN
name: phosphofructokinase
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#d53a7ca2_fad0_470d_8239_8a4e9bf24d93
name: minutes
type: SBMLUnitsDef

metaid kineticLaw X14
is: http://identifiers.org/ec-code/2.4.1.11
constant: false
units: dimensionless
value: NaN
name: glycogen synthase
type: Parameter

416711
constant: false
value: NaN
name: flux_from_glucose
type: Parameter

416715
constant: false
value: NaN
name: flux_to_G1P
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#_5017c076_8bea_436d_bb19_7c5b7012339d
name: mM per minute
type: SBMLUnitsDef

metaid kineticLaw X18
is: http://identifiers.org/ec-code/3.1.3.12
constant: false
units: dimensionless
value: NaN
name: alpha,alpha--T6P phosphatase
type: Parameter

metaid X6
is: CHEBI:18283
name: T6P
type: Species
boundary condition: true
initial amount: NaN
is: SBO:0000247
initial concentration: 0.02
constant: false
has only substance units: false
in compartment: metaid cell

416720
constant: false
value: NaN
name: flux_from_UDPG
type: Parameter

416709
constant: false
value: NaN
name: flux_to_glucose
type: Parameter

metaid X2
has only substance units: false
type: Species
is: SBO:0000247
in compartment: metaid cell
is: CHEBI:17665
initial concentration: 1.0
boundary condition: true
name: G6P
constant: false
initial amount: NaN

metaid kineticLaw X15r
is version of: http://identifiers.org/ec-code/2.4.1.1
constant: false
units: dimensionless
value: NaN
name: glycogen phosphorylase
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#f95a9c20_cd49_4f8f_a59a_1b7b0cdf90d2
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

416724
constant: false
value: NaN
name: flux_to_T6P
type: Parameter

416672
is version of: GO:0046323
constant: false
units: dimensionless
value: NaN
name: glucose transport into cell
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000266#_2a2fa805_8037_4b34_ad0f_f719f10e8d37
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid kineticLaw X15f
is version of: http://identifiers.org/ec-code/2.4.1.1
constant: false
units: dimensionless
value: NaN
name: glycogen phosphorylase
type: Parameter

metaid kineticLaw X9
constant: false
units: dimensionless
value: NaN
name: hexokinase/glucokinase
type: Parameter

416712
constant: false
value: NaN
name: flux_to_G6P
type: Parameter

metaid kineticLaw X13
is: http://identifiers.org/ec-code/2.7.7.9
constant: false
units: dimensionless
value: NaN
name: UDPG pyrophosphorylase
type: Parameter

metaid kineticLaw X17
is: http://identifiers.org/ec-code/2.4.1.15
constant: false
units: dimensionless
value: NaN
name: alpha,alpha-T6P synthase
type: Parameter

416723
constant: false
value: NaN
name: flux_from_glucogen
type: Parameter

metaid X5
boundary condition: true
in compartment: metaid cell
type: Species
is: CHEBI:28087
initial amount: NaN
is: SBO:0000247
has only substance units: false
constant: false
name: glycogen
initial concentration: 1.0

416727
constant: false
value: NaN
name: flux_to_trehalose
type: Parameter

BIOMD0000000266
species: metaid X3
rule: 416655
is: MODEL1007210000
parameter: 416715
rule: 416642
rule: 416643
parameter: metaid kineticLaw X19
parameter: 416671
rule: 416666
has part: GO:0005992
parameter: 416720
curated: true
parameter: 416718
area units: metaid_0000005
parameter: metaid kineticLaw X15r
rule: 416667
rule: 416639
species: metaid X7
name: Voit2003_Trehalose_Cycle
parameter: 416709
parameter: metaid kineticLaw X15f
rule: 416630
parameter: metaid kineticLaw X10
rule: 416646
has version: GO:0033638
parameter: metaid kineticLaw X17
rule: 416658
rule: 416654
species: metaid X2
rule: 416640
parameter: metaid kineticLaw X13
species: metaid X1
rule: 416669
rule: 416651
length unit: length
type: SBMLModel
parameter: 416723
rule: 416633
rule: 416634
rule: 416664
rule: 416637
parameter: metaid kineticLaw X12r
has part: GO:0005978
parameter: metaid kineticLaw X9
notes: This is the S systems model described in the article: Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis Eberhard O Voit, J Theor Biol 2003 223:55-78 PubmedID: 12782117 ; DOI: 10.1016/S0022-5193(03)00072-9 Abstract: The physiological hallmark of heat-shock response in yeast is a rapid, enormous increase in the concentration of trehalose. Normally found in growing yeast cells and other organisms only as traces, trehalose becomes a crucial protector of proteins and membranes against a variety of stresses, including heat, cold, starvation, desiccation, osmotic or oxidative stress, and exposure to toxicants. Trehalose is produced from glucose 6-phosphate and uridine diphosphate glucose in a two-step process, and recycled to glucose by trehalases. Even though the trehalose cycle consists of only a few metabolites and enzymatic steps, its regulatory structure and operation are surprisingly complex. The article begins with a review of experimental observations on the regulation of the trehalose cycle in yeast and proposes a canonical model for its analysis. The first part of this analysis demonstrates the benefits of the various regulatory features by means of controlled comparisons with models of otherwise equivalent pathways lacking these features. The second part elucidates the significance of the expression pattern of the trehalose cycle genes in response to heat shock. Interestingly, the genes contributing to trehalose formation are up-regulated to very different degrees, and even the trehalose degrading trehalases show drastically increased activity during heat-shock response. Again using the method of controlled comparisons, the model provides rationale for the observed pattern of gene expression and reveals benefits of the counterintuitive trehalase up-regulation. To induce a heat shock, set the parameter heat_shock from 0 to 1. This changess the parameter values of X8 to X19 from 1 to the values …
rule: 416657
parameter: 416726
is part of: sce00500
rule: 416663
species: metaid X6
rule: 416645
is described by: http://identifiers.org/pubmed/12782117
parameter: metaid kineticLaw X18
rule: 416660
species: metaid X5
rule: 416652
is version of: GO:0005991
parameter: 416711
parameter: 416729
parameter: metaid kineticLaw X14
compartment: metaid cell
rule: 416648
parameter: metaid kineticLaw X12f
rule: 416649
parameter: 416724
volume units: 623578
parameter: 416714
species: metaid X0
parameter: metaid kineticLaw X11
rule: 416636
parameter: 416721
rule: 416628
occurs in: http://identifiers.org/taxonomy/4932
parameter: 416727
parameter: 416717
rule: 416661
parameter: 416700
rule: 416631
parameter: 416672
parameter: 416712

metaid X1
name: glucose
type: Species
is: SBO:0000247
boundary condition: true
initial concentration: 0.03
in compartment: metaid cell
is: CHEBI:17925
constant: false
initial amount: NaN
has only substance units: false

W3 CDTF: Wed Jun 05 16:47:45 BST 2013

orgname: EMBL-EBI

W3 CDTF: Tue Jul 20 01:00:00 BST 2010

ORG:
  orgname: University of Manchester
n:
  given: Kieran
  family: Smallbone

n:
  given: Lukas
  family: Endler