Smurfit Institute of Genetics, University of Dublin, Trinity College
Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
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.