Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities

Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on glycolysis and answered multiple research questions, but no commonly applicable model has been presented. This review systematically evaluates the literature to describe the current advances, limitations, and opportunities. Different kinetic models have unraveled key kinetic glycolytic mechanisms. Nevertheless, some uncertainties regarding model topology and parameter values still limit the application to specific cases. Progressive improvements in experimental measurement technologies as well as advances in computational tools create new opportunities to further extend the model scale. Notably, models need to be made more complex to consider the multiple layers of glycolytic regulation and external physiological variables regulating the bioprocess, opening new possibilities for extrapolation and validation. Finally, the onset of new data representative of individual cells will cause these models to evolve from depicting an average cell in an industrial fermenter, to characterizing the heterogeneity of the population, opening new and unseen possibilities for industrial fermentation improvement.

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Metabolic Changes Induced by Deletion of Transcriptional Regulator GCR2 in Xylose-Fermenting Saccharomyces cerevisiae

Microorganisms ◽

10.3390/microorganisms8101499 ◽

2020 ◽

Vol 8 (10) ◽

pp. 1499

Author(s):

Minhye Shin ◽

Soo Rin Kim

Keyword(s):

Saccharomyces Cerevisiae ◽

Carbon Source ◽

Pentose Phosphate Pathway ◽

Carbon Metabolism ◽

Transcriptional Regulator ◽

Central Carbon Metabolism ◽

Pentose Phosphate ◽

Metabolic Changes ◽

Regulatory Systems ◽

Central Carbon

Glucose repression has been extensively studied in Saccharomyces cerevisiae, including the regulatory systems responsible for efficient catabolism of glucose, the preferred carbon source. However, how these regulatory systems would alter central metabolism if new foreign pathways are introduced is unknown, and the regulatory networks between glycolysis and the pentose phosphate pathway, the two major pathways in central carbon metabolism, have not been systematically investigated. Here we disrupted gcr2, a key transcriptional regulator, in S. cerevisiae strain SR7 engineered to heterologously express the xylose-assimilating pathway, activating genes involved in glycolysis, and evaluated the global metabolic changes. gcr2 deletion reduced cellular growth in glucose but significantly increased growth when xylose was the sole carbon source. Global metabolite profiling revealed differential regulation of yeast metabolism in SR7-gcr2Δ, especially carbohydrate and nucleotide metabolism, depending on the carbon source. In glucose, the SR7-gcr2Δ mutant showed overall decreased abundance of metabolites, such as pyruvate and sedoheptulose-7-phosphate, associated with central carbon metabolism including glycolysis and the pentose phosphate pathway. However, SR7-gcr2Δ showed an increase in metabolites abundance (ribulose-5-phosphate, sedoheptulose-7-phosphate, and erythrose-4-phosphate) notably from the pentose phosphate pathway, as well as alteration in global metabolism when compared to SR7. These results provide insights into how the regulatory system GCR2 coordinates the transcription of glycolytic genes and associated metabolic pathways.

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Rewiring central carbon metabolism for tyrosol and salidroside production in Saccharomyces cerevisiae

Biotechnology and Bioengineering ◽

10.1002/bit.27370 ◽

2020 ◽

Vol 117 (8) ◽

pp. 2410-2419 ◽

Cited By ~ 5

Author(s):

Wei Guo ◽

Qiulan Huang ◽

Yuhui Feng ◽

Taicong Tan ◽

Suhao Niu ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Carbon Metabolism ◽

Central Carbon Metabolism ◽

Central Carbon

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Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

PLoS ONE ◽

10.1371/journal.pone.0172742 ◽

2017 ◽

Vol 12 (2) ◽

pp. e0172742 ◽

Cited By ~ 10

Author(s):

Fumio Matsuda ◽

Syohei Kinoshita ◽

Shunsuke Nishino ◽

Atsumi Tomita ◽

Hiroshi Shimizu

Keyword(s):

Saccharomyces Cerevisiae ◽

Carbon Metabolism ◽

Gene Deletion ◽

Single Gene ◽

Proteome Analysis ◽

Central Carbon Metabolism ◽

Central Carbon ◽

Single Gene Deletion

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Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression

Journal of Bacteriology ◽

10.1128/jb.183.4.1441-1451.2001 ◽

2001 ◽

Vol 183 (4) ◽

pp. 1441-1451 ◽

Cited By ~ 243

Author(s):

Andreas Karoly Gombert ◽

Margarida Moreira dos Santos ◽

Bjarke Christensen ◽

Jens Nielsen

Keyword(s):

Saccharomyces Cerevisiae ◽

Growth Rate ◽

Specific Growth Rate ◽

Batch Culture ◽

Network Structure ◽

Carbon Metabolism ◽

Specific Growth ◽

Central Carbon Metabolism ◽

Published Data ◽

Central Carbon

ABSTRACT The network structure and the metabolic fluxes in central carbon metabolism were characterized in aerobically grown cells ofSaccharomyces cerevisiae. The cells were grown under both high and low glucose concentrations, i.e., either in a chemostat at steady state with a specific growth rate of 0.1 h−1 or in a batch culture with a specific growth rate of 0.37 h−1. Experiments were carried out using [1-13C]glucose as the limiting substrate, and the resulting summed fractional labelings of intracellular metabolites were measured by gas chromatography coupled to mass spectrometry. The data were used as inputs to a flux estimation routine that involved appropriate mathematical modelling of the central carbon metabolism ofS. cerevisiae. The results showed that the analysis is very robust, and it was possible to quantify the fluxes in the central carbon metabolism under both growth conditions. In the batch culture, 16.2 of every 100 molecules of glucose consumed by the cells entered the pentose-phosphate pathway, whereas the same relative flux was 44.2 per 100 molecules in the chemostat. The tricarboxylic acid cycle does not operate as a cycle in batch-growing cells, in contrast to the chemostat condition. Quantitative evidence was also found for threonine aldolase and malic enzyme activities, in accordance with published data. Disruption of the MIG1 gene did not cause changes in the metabolic network structure or in the flux pattern.

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Metabolic Impact of Redox Cofactor Perturbations on the Formation of Aroma Compounds in Saccharomyces cerevisiae

Applied and Environmental Microbiology ◽

10.1128/aem.02429-15 ◽

2015 ◽

Vol 82 (1) ◽

pp. 174-183 ◽

Cited By ~ 22

Author(s):

Audrey Bloem ◽

Isabelle Sanchez ◽

Sylvie Dequin ◽

Carole Camarasa

Keyword(s):

Saccharomyces Cerevisiae ◽

Volatile Compounds ◽

Carbon Metabolism ◽

Isoamyl Alcohol ◽

Redox Status ◽

Central Carbon Metabolism ◽

Ethyl Esters ◽

Content Type ◽

Central Carbon ◽

The Impact

ABSTRACTRedox homeostasis is a fundamental requirement for the maintenance of metabolism, energy generation, and growth inSaccharomyces cerevisiae. The redox cofactors NADH and NADPH are among the most highly connected metabolites in metabolic networks. Changes in their concentrations may induce widespread changes in metabolism. Redox imbalances were achieved with a dedicated biological tool overexpressing native NADH-dependent or engineered NADPH-dependent 2,3-butanediol dehydrogenase, in the presence of acetoin. We report that targeted perturbation of the balance of cofactors (NAD+/NADH or, to a lesser extent, NADP+/NADPH) significantly affected the production of volatile compounds. In most cases, variations in the redox state of yeasts modified the formation of all compounds from the same biochemical pathway (isobutanol, isoamyl alcohol, and their derivatives) or chemical class (ethyl esters), irrespective of the cofactors. These coordinated responses were found to be closely linked to the impact of redox status on the availability of intermediates of central carbon metabolism. This was the case for α-keto acids and acetyl coenzyme A (acetyl-CoA), which are precursors for the synthesis of many volatile compounds. We also demonstrated that changes in the availability of NADH selectively affected the synthesis of some volatile molecules (e.g., methionol, phenylethanol, and propanoic acid), reflecting the specific cofactor requirements of the dehydrogenases involved in their formation. Our findings indicate that both the availability of precursors from central carbon metabolism and the accessibility of reduced cofactors contribute to cell redox status modulation of volatile compound formation.

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