A Saccharomyces cerevisiae strain with a minimal complement of glycolytic genes reveals strong redundancies in central metabolism
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE63884 | GEO | 2014/12/06
SECONDARY ACCESSION(S): PRJNA269329
REPOSITORIES: GEO
Similar Datasets
Project description:As a result of ancestral whole genome and small-scale duplication events, the genome of Saccharomyces cerevisiaeM-bM-^@M-^Ys, and of many eukaryotes, still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In ancestors of the Saccharomyces lineage, the duplication of glycolytic genes is purported to have played an important role leading to S. cerevisiae current lifestyle favoring fermentative metabolism even in the presence of oxygen and characterized by a high glycolytic capacity. In modern S. cerevisiae, the 12 glycolytic reactions leading to the biochemical conversion from glucose to ethanol are encoded by 27 paralogs. In order to experimentally explore the physiological role of this genetic redundancy, a yeast strain with a minimal set of 14 paralogs was constructed (MG strain). Remarkably, a combination of quantitative, systems approach and of semi-quantitative analysis in a wide array of growth environments revealed the absence of phenotypic response to the cumulative deletion of 13 glycolytic paralogs. This observation indicates that duplication of glycolytic genes is not a prerequisite for achieving the high glycolytic fluxes and fermentative capacities that are characteristic for S. cerevisiae and essential for many of its industrial applications and argues against gene dosage effects as a means for fixing minor glycolytic paralogs in the yeast genome. MG was carefully designed and constructed to provide a robust, prototrophic platform for quantitative studies, and is made available to the scientific community. The goals of the present study are to experimentally explore genetic redundancy in yeast glycolysis by cumulative deletion of minor paralogs and to provide a new experimental platform for fundamental yeast research by constructing a yeast strain with a functional M-bM-^@M-^Xminimal glycolysisM-bM-^@M-^Y. To this end, we deleted 13 minor paralogs, leaving only the 14 major paralogs for the S. cerevisiae glycolytic pathway. The cumulative impact of deleting all minor paralogs was investigated by two complementary approaches. A first, quantitative analysis focused on the impact on glycolytic flux under a number of controlled cultivation conditions that, in wild-type strains, result in different glycolytic fluxes. These quantitative growth studies were combined with transcriptome, enzyme-activity and intracellular metabolite assays to capture potential small phenotypic effects. A second, semi-quantitative characterization explored the phenotype of the M-bM-^@M-^Xminimal glycolysisM-bM-^@M-^Y strain under a wide array of experimental conditions to identify potential context-dependent phenotypes
2014-12-06 | E-GEOD-63884 | biostudies-arrayexpress
Project description:The ability of the yeast Saccharomyces cerevisiae to convert glucose, even in the presence of oxygen, via glycolysis and the fermentative pathway to ethanol has played an important role in its domestication. Despite the extensive knowledge on these pathways in S. cerevisiae, relatively little is known about these pathways in other industrially-relevant Saccharomyces yeast species. In this study we explore the diversity of the glycolytic and fermentative pathways within the Saccharomyces genus using S. cerevisiae, S. kudriavzevii and S. eubayanus as paradigms. Sequencing data revealed a highly conserved genetic makeup of the glycolytic and fermentative pathways in the three species in terms of number of paralogous genes. Although promoter regions were less conserved between the three species as compared to coding sequences, binding sites for Rap1, Gcr1 and Abf1, main transcriptional regulators of glycolytic and fermentative genes, were highly conserved. Transcriptome profiling of these three strains grown in aerobic batch cultivation in chemically defined medium with glucose as carbon source, revealed a remarkably similar expression of the glycolytic and fermentative genes across species, and the conserved classification of genes into major and minor paralogs. Furthermore, transplantation of the promoters of major paralogs of S. kudriavzevii and S. eubayanus into S. cerevisiae demonstrated not only the transferability of these promoters, but also the similarity of their strength and response to various environmental stimuli. The relatively low homology of S. kudriavzevii and S. eubayanus promoters to their S. cerevisiae relatives makes them very attractive alternatives for strain construction in S. cerevisiae, thereby expanding S. cerevisiae molecular toolbox.
2018-07-21 | GSE117404 | GEO
Project description:Prolonged cultivation of Saccharomyces cerevisiae in aerobic, glucose-limited chemostat cultures (dilution rate, 0·10 hâ1) resulted in a progressive decrease of the residual glucose concentration (from 20 to 8 mg lâ1 after 200 generations). This increase in the affinity for glucose was accompanied by a fivefold decrease of fermentative capacity, and changes in cellular morphology. These phenotypic changes were retained when single-cell isolates from prolonged cultures were used to inoculate fresh chemostat cultures, indicating that genetic changes were involved. Kinetic analysis of glucose transport in an âevolvedâ strain revealed a decreased Km, while Vmax was slightly increased relative to the parental strain. Apparently, fermentative capacity in the evolved strain was not controlled by glucose uptake. Instead, enzyme assays in cell extracts of the evolved strain revealed strongly decreased capacities of enzymes in the lower part of glycolysis. This decrease was corroborated by genome-wide transcriptome analysis using DNA microarrays. In aerobic batch cultures on 20 g glucose lâ1, the specific growth rate of the evolved strain was lower than that of the parental strain (0·28 and 0·37 hâ1, respectively). Instead of the characteristic instantaneous production of ethanol that is observed when aerobic, glucose-limited cultures of wild-type S. cerevisiae are exposed to excess glucose, the evolved strain exhibited a delay of 90 min before aerobic ethanol formation set in. This study demonstrates that the effects of selection in glucose-limited chemostat cultures extend beyond glucose-transport kinetics. Although extensive physiological analysis offered insight into the underlying cellular processes, the evolutionary âdriving forceâ for several of the observed changes remains to be elucidated Experiment Overall Design: A crucial feature of bakers' yeast is its capacity to produce CO2, referred to as fermentative capacity (van Hoek et al., 1998). After prolonged glucose-limited cultivation of S. cerevisiae, in addition to an increased affinity for glucose, we observed a dramatic decrease in fermentative capacity. Consequently, the aim of the present study was to perform an integral analysis of the long-term adaptation of S. cerevisiae during prolonged glucose-limited, aerobic cultivation in chemostat cultures, with special emphasis on the regulation of glucose transport and glycolytic capacity. To this end, we applied an integrated approach that combined transcriptome analysis, measurement of fermentative capacity and activities of glucose transport and glycolytic enzymes, and characterization of cellular morphology.
2008-06-16 | E-GEOD-8898 | biostudies-arrayexpress
Project description:Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes. In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains. aCGH analysis of parental and hybrid strains.
2015-03-30 | E-GEOD-48117 | biostudies-arrayexpress
Project description:Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes. In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains.
2015-03-30 | GSE48117 | GEO
Project description:To understand the gene expression in Saccharomyces cerevisiae under fermentative and respiraotry conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of S. cerevisiae wild type, sef1 deletion, and hyperactive SEF1-VP16 mutants under the YPD and YPGly conditions.
2024-03-25 | GSE262043 | GEO
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.
2024-09-02 | BIOMD0000000176 | BioModels
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.
2024-09-02 | BIOMD0000000177 | BioModels
Project description:When the yeast Saccharomyces cerevisiae is subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from being purely respiratory to mixed respiratory and fermentative. This shift is characterized by ethanol production, a phenomenon known as the Crabtree effect due to its analogy with lactate overflow in cancer cells. It is well known that at high glycolytic fluxes there is glucose repression of respiratory pathways resulting in a decrease in the respiratory capacity. Despite many years of detailed studies on this subject, it is not known whether the onset of the Crabtree effect (or overflow metabolism) is due to a limited respiratory capacity or caused by glucose-mediated repression of respiration. We addressed this issue by increasing respiration in S. cerevisiae by introducing a heterologous alternative oxidase, and observed reduced aerobic ethanol formation. In contrast, increasing non-respiratory NADH oxidation by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, while NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic NADH dehydrogenases in S. cerevisiae. These results indicate that NADH oxidase localizes in the cytosol, while alternative oxidase is directed to the mitochondria. The onset of aerobic ethanol formation is demonstrated to be a consequence of an imbalance in mitochondrial redox balancing. In addition to answering fundamental physiological questions, our findings are relevant for all biomass derived applications of S. cerevisiae. Experiment Overall Design: Heterologous gene expression in chemostats using Affymetrix Yeast Genome 2.0 arrays. Total RNA extraction and sample preparation, hybridization was done according to the manufacturer's protocol.
2008-06-14 | E-GEOD-6277 | biostudies-arrayexpress
Project description:Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit.
2012-03-01 | GSE35541 | GEO