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creator:
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    orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College
  n:
    given: Kenneth
    family: Wolfe
creator:
  ORG:
    orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
  n:
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    family: Conant
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  n:
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    family: Endler
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created:
  W3 CDTF: Wed Sep 12 09:25:26 BST 2007
is: MODEL2427135959
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name: Conant2007_glycolysis_2C
species: 525632
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occurs in: http://identifiers.org/taxonomy/4932
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is described by: http://identifiers.org/pubmed/17667951
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modified:
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notes: This a model from the article: Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Conant GC, Wolfe KH Mol. Syst. Biol. [2007 ; Volume: 3 (Issue: )]: 129 17667951 , Abstract: After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic genes could have conferred an almost immediate selective advantage to an ancestor of Saccharomyces cerevisiae, providing a rationale for the success of the WGD. We propose that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes. This increase gave post-WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose-rich environments. Our hypothesis is supported by data from enzyme kinetics and comparative genomics. Because changes in gene dosage follow directly from post-WGD deletions, dosage selection can confer an almost instantaneous benefit after WGD, unlike neofunctionalization or subfunctionalization, which require specific mutations. We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD. This model reproduces fig. 2C from the corrigendum to the publication The parameter Vmax_PDH was corrected by a factor 60 from 6.32 mM/min in the publication to 379.2 mM/min in accordance with the authors. see the corrigendum at msb or its pubmed entry (pmid:18594520) This model comprises the glycolysis model from Pritchard and Kell (2002) with an extension for the metabolisation of pyruvate in the mitochondria by pyruvate dehydrogenase and an additional parameter, WGD_E , to adjust for the differing enzyme concentrations before the whole genome …

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initial amount: NaN
in compartment: 525523
type: Species

525664
is version of: http://identifiers.org/ec-code/2.7.2.3
product: 912377
reversible: true
is: R01512
fast: false
reactant: 912353
type: Reaction
reactant: 912340
product: 912365
kinetic law: 912389
name: PGK
is version of: GO:0004618

912654
stoichiometry: 1.0
species: 525539
type: SpeciesReference

912315
stoichiometry: 1.0
species: 525573
type: SpeciesReference

bla0010
constant: true
units: dimensionless
value: 1.0
name: toggle_transport
type: Parameter

525675
is version of: http://identifiers.org/ec-code/2.7.1.40
kinetic law: 912522
is version of: GO:0004743
name: PYK
reversible: true
reactant: 912485
fast: false
product: 912510
product: 912498
is: R00200
reactant: 912473
type: Reaction

912135
stoichiometry: 1.0
species: 525539
type: SpeciesReference

525685
kinetic law: 912666
product: 912654
reactant: 912642
is version of: GO:0016887
fast: false
reversible: false
type: Reaction

757749
units: metaid_0000058
value: 20.0
type: LocalParameter

912498
stoichiometry: 1.0
species: 525533
type: SpeciesReference

911809
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

912918
stoichiometry: 2.0
species: 525591
type: SpeciesReference

912930
stoichiometry: 3.0
species: 525573
type: SpeciesReference

911918
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

525635
kinetic law: 912003
product: 911991
reactant: 911979
is version of: GO:0015758
fast: false
reversible: true
name: HXT
type: Reaction

525585
is: C00074
is: CHEBI:18021
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0632352144936527
initial amount: NaN
in compartment: 525523
type: Species

525523
is: GO:0005829
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

525533
is: C00002
is: CHEBI:15422
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.52512746499271
initial amount: NaN
in compartment: 525523
type: Species

912786
stoichiometry: 1.0
species: 525533
type: SpeciesReference

525599
is: C00031
is: CHEBI:4167
constant: false
boundary condition: true
has only substance units: false
initial concentration: 50.0
initial amount: NaN
in compartment: 525523
type: Species

757680
units: metaid_0000058
value: 0.06
type: LocalParameter

bla0011
constant: true
units: dimensionless
value: 0.65
name: WGD enzyme conc change
type: Parameter

911930
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

525578
is: C00197
is: CHEBI:17794
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.885688538360659
initial amount: NaN
in compartment: 525523
type: Species

757729
units: metaid_0000066
value: 100.0
type: LocalParameter

912846
stoichiometry: 1.0
species: 525533
type: SpeciesReference

912870
stoichiometry: 1.0
species: 525539
type: SpeciesReference

525564
is: C00003
is: CHEBI:15846
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.50329030201531
initial amount: NaN
in compartment: 525523
type: Species

757739
units: metaid_0000059
value: 2.4
type: LocalParameter

911894
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

912798
stoichiometry: 1.0
species: 525536
type: SpeciesReference

757719
units: metaid_0000058
value: 0.11
type: LocalParameter

757660
units: dimensionless
value: 0.397
type: LocalParameter

757709
units: metaid_0000058
value: 1.5
type: LocalParameter

912147
stoichiometry: 1.0
species: 525545
type: SpeciesReference

757728
units: metaid_0000066
value: 45.0
type: LocalParameter

757641
units: metaid_0000059
value: 1056.0
type: LocalParameter

525567
is: C00236
is: CHEBI:16001
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.36873499865602E-4
initial amount: NaN
in compartment: 525523
type: Species

757747
units: metaid_0000058
value: 160.0
type: LocalParameter

912906
stoichiometry: 3.0
species: 525564
type: SpeciesReference

912485
stoichiometry: 1.0
species: 525585
type: SpeciesReference

757708
units: metaid_0000058
value: 21.0
type: LocalParameter

911906
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

912413
stoichiometry: 1.0
species: 525582
type: SpeciesReference

913027
stoichiometry: 1.0
species: 525632
type: SpeciesReference

912291
stoichiometry: 1.0
species: 525564
type: SpeciesReference

525609
is: C00469
is: CHEBI:16236
constant: false
boundary condition: true
has only substance units: false
initial concentration: 50.0
initial amount: NaN
in compartment: 525523
type: Species

757727
units: metaid_0000065
value: 39.5
type: LocalParameter

525548
is: C00020
is: CHEBI:16027
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.292884853320091
initial amount: NaN
in compartment: 525523
type: Species

912678
stoichiometry: 2.0
species: 525539
type: SpeciesReference

912606
stoichiometry: 1.0
species: 525573
type: SpeciesReference

757748
units: metaid_0000058
value: 50.0
type: LocalParameter

757640
units: metaid_0000058
value: 0.23
type: LocalParameter

912582
stoichiometry: 1.0
species: 525564
type: SpeciesReference

525720
type: Reaction
fast: false
modifier: 913039
reactant: 913003
kinetic law: 913063
has part: http://identifiers.org/ec-code/2.3.1.12
has part: http://identifiers.org/ec-code/1.2.4.1
product: 913015
is version of: GO:0034604
is version of: R00209
has part: http://identifiers.org/ec-code/1.8.1.4
name: pyruvate dehydrogenase
product: 913027
modifier: 913051
reversible: false