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BIOMD0000000176
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curated: true
creator:
  ORG:
    orgname: Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
  n:
    given: Gavin
    family: Conant
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is described by: http://identifiers.org/pubmed/17667951
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  W3 CDTF: Wed May 16 15:25:08 BST 2012
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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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stoichiometry: 1.0
species: 525561
type: SpeciesReference

698849
units: metaid_0000058
value: 0.031
type: LocalParameter

525711
name: succinate_synthesis
reversible: false
product: 894805
kinetic law: 894829
is version of: GO:0006105
reactant: 894793
product: 894817
reactant: 894781
type: Reaction
fast: false

698869
units: metaid_0000065
value: 21.4
type: LocalParameter

893867
stoichiometry: 1.0
species: 525530
type: SpeciesReference

698855
units: metaid_0000065
value: 39.5
type: LocalParameter

698809
units: metaid_0000059
value: 1288.0
type: LocalParameter

894624
stoichiometry: 1.0
species: 525564
type: SpeciesReference

894793
stoichiometry: 2.0
species: 525591
type: SpeciesReference

698815
units: metaid_0000058
value: 0.003
type: LocalParameter

894240
stoichiometry: 1.0
species: 525533
type: SpeciesReference

893952
stoichiometry: 1.0
species: 525536
type: SpeciesReference

698829
units: metaid_0000058
value: 0.14
type: LocalParameter

698856
units: metaid_0000066
value: 45.0
type: LocalParameter

894180
stoichiometry: 1.0
species: 525567
type: SpeciesReference

bla0013
constant: true
units: dimensionless
value: 1.0
type: Parameter

698828
units: metaid_0000059
value: 1000.0
type: LocalParameter

894096
stoichiometry: 1.0
species: 525561
type: SpeciesReference

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

metaid_0000066
unit: 893841
unit: 893829
unit: 893816
name: permMpermin
type: SBMLUnitsDef

698837
units: metaid_0000059
value: 857.8
type: LocalParameter

894132
stoichiometry: 1.0
species: 525561
type: SpeciesReference

698780
units: metaid_0000058
value: 0.0995
type: LocalParameter

894168
stoichiometry: 1.0
species: 525564
type: SpeciesReference

698847
units: metaid_0000058
value: 0.11
type: LocalParameter

698818
units: metaid_0000058
value: 1.2
type: LocalParameter

525641
is version of: GO:0004347
is version of: http://identifiers.org/ec-code/5.3.1.9
is: R00771
kinetic law: 893976
fast: false
type: Reaction
product: 893964
reversible: true
name: PGI
reactant: 893952

698867
units: metaid_0000059
value: 6.0
type: LocalParameter

698857
units: metaid_0000066
value: 100.0
type: LocalParameter

893829
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

bla0012
constant: true
units: dimensionless
value: 1.0
type: Parameter

894456
stoichiometry: 1.0
species: 525564
type: SpeciesReference

698827
units: metaid_0000058
value: 0.5
type: LocalParameter

698781
units: dimensionless
value: 0.0174
type: LocalParameter

698807
units: metaid_0000058
value: 0.06
type: LocalParameter

894612
stoichiometry: 1.0
species: 525573
type: SpeciesReference

metaid_0000065
unit: 893780
name: permin
type: SBMLUnitsDef

894817
stoichiometry: 1.0
species: 525622
type: SpeciesReference

698817
units: metaid_0000059
value: 2585.0
type: LocalParameter

525530
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
type: Species

bla0021
constant: true
units: dimensionless
value: 1.0
type: Parameter

894084
stoichiometry: 1.0
species: 525558
type: SpeciesReference

698868
units: metaid_0000059
value: 2.4
type: LocalParameter

525591
is: C00084
is: CHEBI:15343
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.178140579850657
initial amount: NaN
in compartment: 525523
type: Species

893816
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

525700
fast: false
product: 894684
name: glycogenbranch
type: Reaction
product: 894696
kinetic law: 894708
reactant: 894660
reversible: false
is version of: GO:0005978
reactant: 894672

894252
stoichiometry: 1.0
species: 525578
type: SpeciesReference

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

698761
units: metaid_0000058
value: 30.0
type: LocalParameter

698858
units: metaid_0000059
value: 47.11
type: LocalParameter

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

orgname: EMBL-EBI

given: Lukas
family: Endler

W3 CDTF: Wed Aug 06 11:23:52 BST 2008