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BIOMD0000000177 - Conant2007_glycolysis_2C

 

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Reference Publication
Publication ID: 17667951
Conant GC, Wolfe KH.
Increased glycolytic flux as an outcome of whole-genome duplication in yeast.
Mol. Syst. Biol. 2007; 3: 129
Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland. conantg@tcd.ie  [more]
Model
Original Model: BIOMD0000000177.xml.origin
Submitter: Gavin Conant
Submission ID: MODEL2427135959
Submission Date: 06 Aug 2008 09:22:59 UTC
Last Modification Date: 16 May 2012 14:27:52 UTC
Creation Date: 12 Sep 2007 08:25:26 UTC
Encoders:  Gavin Conant
   Lukas Endler
   Kenneth Wolfe
set #1
bqbiol:hasPart KEGG Pathway sce00010
Gene Ontology glycolytic process
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
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 duplication (WGD).
To switch off transport of pyruvate to the mitochondria, set the parameter t_m = 0.
Figure 2C from the article can be reproduced by manually changing the value of parameter WGD_E in the range between 0.65 and 1.0 and calculating the ratios of ratio of PDC/PDH fluxes in the altered model to the one of the model with WGD_E = 1.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 17667951 Submission Date: 06 Aug 2008 09:22:59 UTC Last Modification Date: 16 May 2012 14:27:52 UTC Creation Date: 12 Sep 2007 08:25:26 UTC
Mathematical expressions
Reactions
HXT HXK PGI PFK
FBA TPI TDH PGK
PGM ENO PYK PDC
ADH ATPase adenylate_kinase glycerol-3-phosphate_dehydrogenase
glycogenbranch trehalose_synthesis succinate_synthesis pyruvate_shuttling
pyruvate dehydrogenase      
Physical entities
Compartments Species
cytoplasm GLCi ATP G6P
ADP F6P F16bP
Fru2,6-P2 AMP DHAP
GAP NAD BPG
NADH P3G P2G
PEP PYR AcAld
GLCo CO2 EtOH
Glycerol Glycogen Trehalose
Succinate    
mitochondrion PYRmito AcCoA CO2mito
Global parameters
toggle_transport WGD enzyme conc change    
Reactions (21)
 
 HXT [GLCo] ↔ [GLCi];  
 
 HXK [GLCi] + [ATP] ↔ [G6P] + [ADP];  
 
 PGI [G6P] ↔ [F6P];  
 
 PFK [ATP] + [F6P] → [ADP] + [F16bP];   {AMP} , {Fru2,6-P2}
 
 FBA [F16bP] ↔ [DHAP] + [GAP];  
 
 TPI [DHAP] ↔ [GAP];  
 
 TDH [GAP] + [NAD] ↔ [BPG] + [NADH];  
 
 PGK [ADP] + [BPG] ↔ [ATP] + [P3G];  
 
 PGM [P3G] ↔ [P2G];  
 
 ENO [P2G] ↔ [PEP];  
 
 PYK [ADP] + [PEP] ↔ [ATP] + [PYR];  
 
 PDC [PYR] → [AcAld] + [CO2];  
 
 ADH [NAD] + [EtOH] ↔ [NADH] + [AcAld];  
 
 ATPase [ATP] → [ADP];  
 
 adenylate_kinase 2.0 × [ADP] ↔ [ATP] + [AMP];  
 
 glycerol-3-phosphate_dehydrogenase [DHAP] + [NADH] ↔ [NAD] + [Glycerol];  
 
 glycogenbranch [ATP] + [G6P] → [ADP] + [Glycogen];  
 
 trehalose_synthesis [ATP] + 2.0 × [G6P] → [ADP] + [Trehalose];  
 
 succinate_synthesis 3.0 × [NAD] + 2.0 × [AcAld] → 3.0 × [NADH] + [Succinate];  
 
 pyruvate_shuttling [PYR] ↔ [PYRmito];  
 
 pyruvate dehydrogenase [PYRmito] → [AcCoA] + [CO2mito];   {NAD} , {NADH}
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 GLCi
Compartment: cytoplasm
Initial concentration: 0.097652231064563
 
 ATP
Compartment: cytoplasm
Initial concentration: 2.52512746499271
 
 G6P
Compartment: cytoplasm
Initial concentration: 2.67504014044787
 
 ADP
Compartment: cytoplasm
Initial concentration: 1.28198768168719
 
 F6P
Compartment: cytoplasm
Initial concentration: 0.624976405532373
 
 F16bP
Compartment: cytoplasm
Initial concentration: 6.22132076069411
 
 Fru2,6-P2
Compartment: cytoplasm
Initial concentration: 0.02
 
 AMP
Compartment: cytoplasm
Initial concentration: 0.292884853320091
 
 DHAP
Compartment: cytoplasm
Initial concentration: 1.00415254899644
 
 GAP
Compartment: cytoplasm
Initial concentration: 0.0451809175780963
 
 NAD
Compartment: cytoplasm
Initial concentration: 1.50329030201531
 
 BPG
Compartment: cytoplasm
Initial concentration: 7.36873499865602E-4
 
 NADH
Compartment: cytoplasm
Initial concentration: 0.0867096979846952
 
 P3G
Compartment: cytoplasm
Initial concentration: 0.885688538360659
 
 P2G
Compartment: cytoplasm
Initial concentration: 0.127695817386632
 
 PEP
Compartment: cytoplasm
Initial concentration: 0.0632352144936527
 
 PYR
Compartment: cytoplasm
Initial concentration: 1.81531251192736
 
 AcAld
Compartment: cytoplasm
Initial concentration: 0.178140579850657
 
 GLCo
Compartment: cytoplasm
Initial concentration: 50.0
 
 CO2
Compartment: cytoplasm
Initial concentration: 1.0
 
 EtOH
Compartment: cytoplasm
Initial concentration: 50.0
 
 Glycerol
Compartment: cytoplasm
Initial concentration: 0.15
 
 Glycogen
Compartment: cytoplasm
Initial concentration: 0.0
 
 Trehalose
Compartment: cytoplasm
Initial concentration: 0.0
 
 Succinate
Compartment: cytoplasm
Initial concentration: 0.0
 
 mitochondrion Spatial dimensions: 3.0  Compartment size: 1.0
 
 PYRmito
Compartment: mitochondrion
Initial concentration: 0.0
 
 AcCoA
Compartment: mitochondrion
Initial concentration: 1.0
 
 CO2mito
Compartment: mitochondrion
Initial concentration: 1.0
 
Global Parameters (2)
 
   toggle_transport
Value: 1.0   (Units: dimensionless)
Constant
 
   WGD enzyme conc change
Value: 0.65   (Units: dimensionless)
Constant
 
HXT (3)
 
   Vmax_1
Value: 97.24   (Units: mmolepermin)
Constant
 
   Kglc_1
Value: 1.1918   (Units: mM)
Constant
 
   Ki_1
Value: 0.91   (Units: dimensionless)
Constant
 
HXK (6)
 
   Vmax_2
Value: 236.7   (Units: mMpermin)
Constant
 
   Kglc_2
Value: 0.08   (Units: mM)
Constant
 
   Katp_2
Value: 0.15   (Units: mM)
Constant
 
   Keq_2
Value: 2000.0   (Units: dimensionless)
Constant
 
   Kg6p_2
Value: 30.0   (Units: mM)
Constant
 
   Kadp_2
Value: 0.23   (Units: mM)
Constant
 
PGI (4)
 
   Vmax_3
Value: 1056.0   (Units: mMpermin)
Constant
 
   Kg6p_3
Value: 1.4   (Units: mM)
Constant
 
   Keq_3
Value: 0.29   (Units: dimensionless)
Constant
 
   Kf6p_3
Value: 0.3   (Units: mM)
Constant
 
PFK (14)
 
   Vmax_4
Value: 110.0   (Units: mMpermin)
Constant
 
   gR_4
Value: 5.12   (Units: dimensionless)
Constant
 
   Kf6p_4
Value: 0.1   (Units: mM)
Constant
 
   Katp_4
Value: 0.71   (Units: mM)
Constant
 
   L0_4
Value: 0.66   (Units: dimensionless)
Constant
 
   Ciatp_4
Value: 100.0   (Units: dimensionless)
Constant
 
   Kiatp_4
Value: 0.65   (Units: mM)
Constant
 
   Camp_4
Value: 0.0845   (Units: dimensionless)
Constant
 
   Kamp_4
Value: 0.0995   (Units: mM)
Constant
 
   Cf26_4
Value: 0.0174   (Units: dimensionless)
Constant
 
   Kf26_4
Value: 6.82E-4   (Units: mM)
Constant
 
   Cf16_4
Value: 0.397   (Units: dimensionless)
Constant
 
   Kf16_4
Value: 0.111   (Units: mM)
Constant
 
   Catp_4
Value: 3.0   (Units: dimensionless)
Constant
 
FBA (6)
 
   Vmax_5
Value: 94.69   (Units: mMpermin)
Constant
 
   Kf16bp_5
Value: 0.3   (Units: mM)
Constant
 
   Keq_5
Value: 0.069   (Units: mM)
Constant
 
   Kdhap_5
Value: 2.0   (Units: mM)
Constant
 
   Kgap_5
Value: 2.4   (Units: mM)
Constant
 
   Kigap_5
Value: 10.0   (Units: mM)
Constant
 
TPI (2)
 
   k1_6
Value: 450000.0   (Units: permin)
Constant
 
   k2_6
Value: 1.0E7   (Units: permin)
Constant
 
TDH (7)
 
   C_7
Value: 1.0   (Units: dimensionless)
Constant
 
   Vmaxf_7
Value: 1152.0   (Units: mMpermin)
Constant
 
   Kgap_7
Value: 0.21   (Units: mM)
Constant
 
   Knad_7
Value: 0.09   (Units: mM)
Constant
 
   Vmaxr_7
Value: 6719.0   (Units: mMpermin)
Constant
 
   Kbpg_7
Value: 0.0098   (Units: mM)
Constant
 
   Knadh_7
Value: 0.06   (Units: mM)
Constant
 
PGK (6)
 
   Vmax_8
Value: 1288.0   (Units: mMpermin)
Constant
 
   Keq_8
Value: 3200.0   (Units: dimensionless)
Constant
 
   Kp3g_8
Value: 0.53   (Units: mM)
Constant
 
   Katp_8
Value: 0.3   (Units: mM)
Constant
 
   Kbpg_8
Value: 0.0030   (Units: mM)
Constant
 
   Kadp_8
Value: 0.2   (Units: mM)
Constant
 
PGM (4)
 
   Vmax_9
Value: 2585.0   (Units: mMpermin)
Constant
 
   Kp3g_9
Value: 1.2   (Units: mM)
Constant
 
   Keq_9
Value: 0.19   (Units: dimensionless)
Constant
 
   Kp2g_9
Value: 0.08   (Units: mM)
Constant
 
ENO (4)
 
   Vmax_10
Value: 201.6   (Units: mMpermin)
Constant
 
   Kp2g_10
Value: 0.04   (Units: mM)
Constant
 
   Keq_10
Value: 6.7   (Units: dimensionless)
Constant
 
   Kpep_10
Value: 0.5   (Units: mM)
Constant
 
PYK (6)
 
   Vmax_11
Value: 1000.0   (Units: mMpermin)
Constant
 
   Kpep_11
Value: 0.14   (Units: mM)
Constant
 
   Kadp_11
Value: 0.53   (Units: mM)
Constant
 
   Keq_11
Value: 6500.0   (Units: dimensionless)
Constant
 
   Kpyr_11
Value: 21.0   (Units: mM)
Constant
 
   Katp_11
Value: 1.5   (Units: mM)
Constant
 
PDC (3)
 
   Vmax_12
Value: 857.8   (Units: mMpermin)
Constant
 
   Kpyr_12
Value: 4.33   (Units: mM)
Constant
 
   nH_12
Value: 1.9   (Units: dimensionless)
Constant
 
ADH (10)
 
   Vmax_13
Value: 209.5   (Units: mMpermin)
Constant
 
   Ketoh_13
Value: 17.0   (Units: mM)
Constant
 
   Kinad_13
Value: 0.92   (Units: mM)
Constant
 
   Keq_13
Value: 6.9E-5   (Units: dimensionless)
Constant
 
   Knad_13
Value: 0.17   (Units: mM)
Constant
 
   Knadh_13
Value: 0.11   (Units: mM)
Constant
 
   Kinadh_13
Value: 0.031   (Units: mM)
Constant
 
   Kacald_13
Value: 1.11   (Units: mM)
Constant
 
   Kiacald_13
Value: 1.1   (Units: mM)
Constant
 
   Kietoh_13
Value: 90.0   (Units: mM)
Constant
 
ATPase (1)
 
   Katpase_14
Value: 39.5   (Units: permin)
Constant
 
adenylate_kinase (2)
 
   k1_15
Value: 45.0   (Units: permMpermin)
Constant
 
   k2_15
Value: 100.0   (Units: permMpermin)
Constant
 
glycerol-3-phosphate_dehydrogenase (6)
 
   Vmax_16
Value: 47.11   (Units: mMpermin)
Constant
 
   Kdhap_16
Value: 0.4   (Units: mM)
Constant
 
   Knadh_16
Value: 0.023   (Units: mM)
Constant
 
   Keq_16
Value: 4300.0   (Units: dimensionless)
Constant
 
   Kglycerol_16
Value: 1.0   (Units: mM)
Constant
 
   Knad_16
Value: 0.93   (Units: mM)
Constant
 
glycogenbranch (1)
 
   KGLYCOGEN_17
Value: 6.0   (Units: mMpermin)
Constant
 
trehalose_synthesis (1)
 
   Ktrehalose_18
Value: 2.4   (Units: mMpermin)
Constant
 
succinate_synthesis (1)
 
   k_19
Value: 21.4   (Units: permin)
Constant
 
pyruvate_shuttling (2)
 
   k1
Value: 1.0   (Units: permin)
Constant
 
   k2
Value: 1.0   (Units: permin)
Constant
 
pyruvate dehydrogenase (6)
 
   Vmax_PDH
Value: 379.2   (Units: mMpermin)
Constant
 
   tot_NAD_in_mito
Value: 8.01   (Units: mM)
Constant
 
   K_PYR
Value: 70.0   (Units: mM)
Constant
 
   K_NAD
Value: 160.0   (Units: mM)
Constant
 
   Ki_NADH
Value: 50.0   (Units: mM)
Constant
 
   Ki_PYR
Value: 20.0   (Units: mM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000177

Curator's comment: (updated: 06 Aug 2008 10:20:57 BST)

reconstruction of fig. 2C from the corrigendum to the publication using SBMLodeSolver (20080507).

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