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MODEL2427021978_url.xml

ABSTRACT: Increased glycolytic flux as an outcome of whole-genome duplication in yeast. GC Conant and KH Wolfe, Mol Syst Biol 3:129,2007 This is the original model reproducing figure 3A of the article submitted by the authors. There exists a curated version with BIOMD0000000176 that reproduces figures 2A,3A and 3B from the publication. BIOMD0000000176 encompasses MODEL2426780967, MODEL2427021978, MODEL2427095802. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. 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.

SUBMITTER: Gavin Conant

PROVIDER: MODEL2427021978 | BioModels | 2005-01-01

REPOSITORIES: BioModels

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			Action	DRS
	MODEL2427021978?filename=MODEL2427021978-biopax2.owl	Owl
	MODEL2427021978?filename=MODEL2427021978-biopax3.owl	Owl
	MODEL2427021978?filename=MODEL2427021978.m	Other
	MODEL2427021978?filename=MODEL2427021978.pdf	Pdf
	MODEL2427021978?filename=MODEL2427021978.png	Other

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Publications

Increased glycolytic flux as an outcome of whole-genome duplication in yeast.

Conant Gavin C GC Wolfe Kenneth H KH

Molecular systems biology 20070731

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 fo ...[more]

PMID: 17667951

Similar Datasets

Project description: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 reproduced by changing the value of the parameters fV_xxx to 0.9 indiviually, with xxx signifying the different enzymes (HXT, HXK ...) Figure 3B from the publication can be reproduced by setting the parameter WGD_E to 0.75 and individually setting the parameters fV_xxx to 1.333. To reproduce figure 2A from the article change the parameter WGD_E in the range between 0.65 and 1.0. 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.

Project description: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.