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creator:
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    orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
  n:
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    family: Conant
created:
  W3 CDTF: Wed Sep 12 09:25:26 BST 2007
is: MODEL2427135959
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name: Conant2007_glycolysis_2C
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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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creator:
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    orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College
  n:
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    family: Wolfe
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  n:
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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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757742
type: LocalParameter
units: metaid_0000069
value: 1.0

757741
type: LocalParameter
units: metaid_0000069
value: 1.0

912979
type: SpeciesReference
stoichiometry: 1.0
species: 525594

912967
type: SpeciesReference
stoichiometry: 1.0
species: 525588

525612
type: Species
is: C00116
is: CHEBI:17754
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.15
initial amount: NaN
in compartment: 525523

525704
type: Reaction
reactant: 912858
product: 912882
reactant: 912846
product: 912870
reversible: false
name: trehalose_synthesis
kinetic law: 912894
fast: false
is version of: GO:0005992

912858
type: SpeciesReference
stoichiometry: 2.0
species: 525536

912882
type: SpeciesReference
stoichiometry: 1.0
species: 525619

912846
type: SpeciesReference
stoichiometry: 1.0
species: 525533

912870
type: SpeciesReference
stoichiometry: 1.0
species: 525539

757739
type: LocalParameter
units: metaid_0000059
value: 2.4

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

912377
type: SpeciesReference
stoichiometry: 1.0
species: 525578

912353
type: SpeciesReference
stoichiometry: 1.0
species: 525567

912340
type: SpeciesReference
stoichiometry: 1.0
species: 525539

912365
type: SpeciesReference
stoichiometry: 1.0
species: 525533

757689
type: LocalParameter
units: metaid_0000058
value: 0.2

757687
type: LocalParameter
units: metaid_0000058
value: 0.003

757686
type: LocalParameter
units: metaid_0000058
value: 0.3

757685
type: LocalParameter
units: metaid_0000058
value: 0.53

757684
type: LocalParameter
units: dimensionless
value: 3200.0

757682
type: LocalParameter
units: metaid_0000059
value: 1288.0

525638
type: Reaction
reactant: 912015
product: 912051
is version of: GO:0004396
fast: false
reactant: 912027
reversible: true
is: R02848
name: HXK
is version of: http://identifiers.org/ec-code/2.7.1.1
product: 912039
kinetic law: 912063

912015
type: SpeciesReference
stoichiometry: 1.0
species: 525530

525530
type: Species
is: C00031
is: CHEBI:4167
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.097652231064563
initial amount: NaN
in compartment: 525523

912051
type: SpeciesReference
stoichiometry: 1.0
species: 525539

912027
type: SpeciesReference
stoichiometry: 1.0
species: 525533

912039
type: SpeciesReference
stoichiometry: 1.0
species: 525536

757640
type: LocalParameter
units: metaid_0000058
value: 0.23

757639
type: LocalParameter
units: metaid_0000058
value: 30.0

757637
type: LocalParameter
units: dimensionless
value: 2000.0

757636
type: LocalParameter
units: metaid_0000058
value: 0.15

757635
type: LocalParameter
units: metaid_0000058
value: 0.08

757633
type: LocalParameter
units: metaid_0000059
value: 236.7

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

525711
type: Reaction
fast: false
product: 912943
is version of: GO:0006105
reactant: 912906
product: 912930
kinetic law: 912955
reversible: false
name: succinate_synthesis
reactant: 912918

912943
type: SpeciesReference
stoichiometry: 1.0
species: 525622

912906
type: SpeciesReference
stoichiometry: 3.0
species: 525564

912930
type: SpeciesReference
stoichiometry: 3.0
species: 525573

757740
type: LocalParameter
units: metaid_0000065
value: 21.4

912918
type: SpeciesReference
stoichiometry: 2.0
species: 525591

525696
type: Reaction
has part: R00842
has version: http://identifiers.org/ec-code/3.1.3.21
reactant: 912738
kinetic law: 912774
has version: http://identifiers.org/ec-code/1.1.1.8
is version of: GO:0006114
reversible: true
has part: R07298
product: 912762
name: glycerol-3-phosphate_dehydrogenase
product: 912750
reactant: 912726
fast: false

912738
type: SpeciesReference
stoichiometry: 1.0
species: 525573

757736
type: LocalParameter
units: metaid_0000058
value: 0.93

757735
type: LocalParameter
units: metaid_0000058
value: 1.0

757734
type: LocalParameter
units: dimensionless
value: 4300.0

757732
type: LocalParameter
units: metaid_0000058
value: 0.023

757731
type: LocalParameter
units: metaid_0000058
value: 0.4

757730
type: LocalParameter
units: metaid_0000059
value: 47.11

912762
type: SpeciesReference
stoichiometry: 1.0
species: 525612

912750
type: SpeciesReference
stoichiometry: 1.0
species: 525564

912726
type: SpeciesReference
stoichiometry: 1.0
species: 525558

525672
type: Reaction
fast: false
reactant: 912437
name: ENO
is: R00658
reversible: true
is version of: http://identifiers.org/ec-code/4.2.1.11
product: 912449
is version of: GO:0004634
kinetic law: 912461

912437
type: SpeciesReference
stoichiometry: 1.0
species: 525582

912449
type: SpeciesReference
stoichiometry: 1.0
species: 525585

757700
type: LocalParameter
units: metaid_0000058
value: 0.5

757698
type: LocalParameter
units: dimensionless
value: 6.7

757697
type: LocalParameter
units: metaid_0000058
value: 0.04

757696
type: LocalParameter
units: metaid_0000059
value: 201.6

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

757631
type: LocalParameter
units: dimensionless
value: 0.91

757629
type: LocalParameter
units: metaid_0000058
value: 1.1918

757628
type: LocalParameter
units: metaid_0000071
value: 97.24

911991
type: SpeciesReference
stoichiometry: 1.0
species: 525530

911979
type: SpeciesReference
stoichiometry: 1.0
species: 525599