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is described by: http://identifiers.org/pubmed/17667951
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created:
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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. The original model submitted by the authors was slightly altered and now comprises the models originally submitted as MODEL2426780967, MODEL2427021978, MODEL2427095802. It reproduces figures 2A,3A and 3B from the publication. This model uses the glycolysis model from Pritchard and Kell (2002) with an additional parameter, WGD_E , to adjust for the differing enzyme conzentrations before the whole genome duplication (WGD) and parameters fV_xxx that adjust the Vmax of the different reactions (xxx eg. HXT or PYK). Figure 3A from the article can be re…
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type: SpeciesReference
stoichiometry: 2.0
species: 525591

894817
type: SpeciesReference
stoichiometry: 1.0
species: 525622

894781
type: SpeciesReference
stoichiometry: 3.0
species: 525564

525678
type: Reaction
name: PDC
is version of: http://identifiers.org/ec-code/4.1.1.1
product: 894420
reversible: false
kinetic law: 894444
is: R00636
product: 894432
fast: false
is version of: GO:0004737
reactant: 894408

894420
type: SpeciesReference
stoichiometry: 1.0
species: 525591

698840
type: LocalParameter
units: dimensionless
value: 1.9

698839
type: LocalParameter
units: metaid_0000058
value: 4.33

698837
type: LocalParameter
units: metaid_0000059
value: 857.8

894432
type: SpeciesReference
stoichiometry: 1.0
species: 525602

894408
type: SpeciesReference
stoichiometry: 1.0
species: 525588

bla0011
type: Parameter
constant: true
units: dimensionless
value: 1.0
name: WGD enzyme conc change

525635
type: Reaction
kinetic law: 893879
product: 893867
reactant: 893854
is version of: GO:0015758
fast: false
reversible: true
name: HXT

698753
type: LocalParameter
units: dimensionless
value: 0.91

698751
type: LocalParameter
units: metaid_0000058
value: 1.1918

698750
type: LocalParameter
units: metaid_0000071
value: 97.24

metaid_0000071
type: SBMLUnitsDef
unit: 893732
unit: 893720
name: mmolepermin

893732
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

893720
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

893867
type: SpeciesReference
stoichiometry: 1.0
species: 525530

893854
type: SpeciesReference
stoichiometry: 1.0
species: 525599

525599
type: Species
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

metaid_0000057
type: SBMLUnitsDef
unit: 893684
name: mmol

893684
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

525664
type: Reaction
reactant: 894228
reversible: true
is version of: GO:0004618
name: PGK
reactant: 894216
is version of: http://identifiers.org/ec-code/2.7.2.3
kinetic law: 894264
product: 894252
product: 894240
is: R01512
fast: false

894228
type: SpeciesReference
stoichiometry: 1.0
species: 525567

894216
type: SpeciesReference
stoichiometry: 1.0
species: 525539

698816
type: LocalParameter
units: metaid_0000058
value: 0.2

698815
type: LocalParameter
units: metaid_0000058
value: 0.003

698813
type: LocalParameter
units: metaid_0000058
value: 0.3

698812
type: LocalParameter
units: metaid_0000058
value: 0.53

698811
type: LocalParameter
units: dimensionless
value: 3200.0

698809
type: LocalParameter
units: metaid_0000059
value: 1288.0

894252
type: SpeciesReference
stoichiometry: 1.0
species: 525578

894240
type: SpeciesReference
stoichiometry: 1.0
species: 525533

bla0016
type: Parameter
constant: true
units: dimensionless
value: 1.0

bla0017
type: Parameter
constant: true
units: dimensionless
value: 1.0

525661
type: Reaction
is version of: http://identifiers.org/ec-code/1.2.1.12
fast: false
kinetic law: 894204
is: R01061
reactant: 894156
reactant: 894168
product: 894192
product: 894180
is version of: GO:0004365
name: TDH
reversible: true

698807
type: LocalParameter
units: metaid_0000058
value: 0.06

698805
type: LocalParameter
units: metaid_0000058
value: 0.0098

698804
type: LocalParameter
units: metaid_0000059
value: 6719.0

698803
type: LocalParameter
units: metaid_0000058
value: 0.09

698801
type: LocalParameter
units: metaid_0000058
value: 0.21

698800
type: LocalParameter
units: metaid_0000059
value: 1152.0

698799
type: LocalParameter
units: dimensionless
value: 1.0

894156
type: SpeciesReference
stoichiometry: 1.0
species: 525561

894168
type: SpeciesReference
stoichiometry: 1.0
species: 525564

894192
type: SpeciesReference
stoichiometry: 1.0
species: 525573

894180
type: SpeciesReference
stoichiometry: 1.0
species: 525567

ORG:
  orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College
n:
  given: Kenneth
  family: Wolfe

ORG:
  orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
n:
  given: Gavin
  family: Conant

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler