A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models
Abstract Background Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can...
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | Biotechnology for Biofuels |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13068-017-0838-5 |
| _version_ | 1817971550487314432 |
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| author | Ljubisa Miskovic Susanne Alff-Tuomala Keng Cher Soh Dorothee Barth Laura Salusjärvi Juha-Pekka Pitkänen Laura Ruohonen Merja Penttilä Vassily Hatzimanikatis |
| author_facet | Ljubisa Miskovic Susanne Alff-Tuomala Keng Cher Soh Dorothee Barth Laura Salusjärvi Juha-Pekka Pitkänen Laura Ruohonen Merja Penttilä Vassily Hatzimanikatis |
| author_sort | Ljubisa Miskovic |
| collection | DOAJ |
| description | Abstract Background Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can help us to uncover new insights into cellular physiology and also to assist in the rational design of bioreactor or fermentation processes. Optimization and Risk Analysis of Complex Living Entities (ORACLE) framework for the construction of large-scale kinetic models can be used as guidance for formulating alternative metabolic engineering strategies. Results We used ORACLE in a metabolic engineering problem: improvement of the xylose uptake rate during mixed glucose–xylose consumption in a recombinant Saccharomyces cerevisiae strain. Using the data from bioreactor fermentations, we characterized network flux and concentration profiles representing possible physiological states of the analyzed strain. We then identified enzymes that could lead to improved flux through xylose transporters (XTR). For some of the identified enzymes, including hexokinase (HXK), we could not deduce if their control over XTR was positive or negative. We thus performed a follow-up experiment, and we found out that HXK2 deletion improves xylose uptake rate. The data from the performed experiments were then used to prune the kinetic models, and the predictions of the pruned population of kinetic models were in agreement with the experimental data collected on the HXK2-deficient S. cerevisiae strain. Conclusions We present a design–build–test cycle composed of modeling efforts and experiments with a glucose–xylose co-utilizing recombinant S. cerevisiae and its HXK2-deficient mutant that allowed us to uncover interdependencies between upper glycolysis and xylose uptake pathway. Through this cycle, we also obtained kinetic models with improved prediction capabilities. The present study demonstrates the potential of integrated “modeling and experiments” systems biology approaches that can be applied for diverse applications ranging from biotechnology to drug discovery. |
| first_indexed | 2024-04-13T20:48:23Z |
| format | Article |
| id | doaj.art-c9652f4332db4734b2878d12ad75ef70 |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-04-13T20:48:23Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-c9652f4332db4734b2878d12ad75ef702022-12-22T02:30:37ZengBMCBiotechnology for Biofuels1754-68342017-06-0110111910.1186/s13068-017-0838-5A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic modelsLjubisa Miskovic0Susanne Alff-Tuomala1Keng Cher Soh2Dorothee Barth3Laura Salusjärvi4Juha-Pekka Pitkänen5Laura Ruohonen6Merja Penttilä7Vassily Hatzimanikatis8Ecole Polytechnique Federale de Lausanne (EPFL)VTT Technical Research Centre of Finland LtdEcole Polytechnique Federale de Lausanne (EPFL)VTT Technical Research Centre of Finland LtdVTT Technical Research Centre of Finland LtdVTT Technical Research Centre of Finland LtdVTT Technical Research Centre of Finland LtdVTT Technical Research Centre of Finland LtdEcole Polytechnique Federale de Lausanne (EPFL)Abstract Background Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can help us to uncover new insights into cellular physiology and also to assist in the rational design of bioreactor or fermentation processes. Optimization and Risk Analysis of Complex Living Entities (ORACLE) framework for the construction of large-scale kinetic models can be used as guidance for formulating alternative metabolic engineering strategies. Results We used ORACLE in a metabolic engineering problem: improvement of the xylose uptake rate during mixed glucose–xylose consumption in a recombinant Saccharomyces cerevisiae strain. Using the data from bioreactor fermentations, we characterized network flux and concentration profiles representing possible physiological states of the analyzed strain. We then identified enzymes that could lead to improved flux through xylose transporters (XTR). For some of the identified enzymes, including hexokinase (HXK), we could not deduce if their control over XTR was positive or negative. We thus performed a follow-up experiment, and we found out that HXK2 deletion improves xylose uptake rate. The data from the performed experiments were then used to prune the kinetic models, and the predictions of the pruned population of kinetic models were in agreement with the experimental data collected on the HXK2-deficient S. cerevisiae strain. Conclusions We present a design–build–test cycle composed of modeling efforts and experiments with a glucose–xylose co-utilizing recombinant S. cerevisiae and its HXK2-deficient mutant that allowed us to uncover interdependencies between upper glycolysis and xylose uptake pathway. Through this cycle, we also obtained kinetic models with improved prediction capabilities. The present study demonstrates the potential of integrated “modeling and experiments” systems biology approaches that can be applied for diverse applications ranging from biotechnology to drug discovery.http://link.springer.com/article/10.1186/s13068-017-0838-5BioethanolMetabolic control analysisLarge-scale kinetic modelsHexokinaseHXK2 deletionXylose utilization |
| spellingShingle | Ljubisa Miskovic Susanne Alff-Tuomala Keng Cher Soh Dorothee Barth Laura Salusjärvi Juha-Pekka Pitkänen Laura Ruohonen Merja Penttilä Vassily Hatzimanikatis A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models Biotechnology for Biofuels Bioethanol Metabolic control analysis Large-scale kinetic models Hexokinase HXK2 deletion Xylose utilization |
| title | A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models |
| title_full | A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models |
| title_fullStr | A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models |
| title_full_unstemmed | A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models |
| title_short | A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models |
| title_sort | design build test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant s cerevisiae and improves predictive capabilities of large scale kinetic models |
| topic | Bioethanol Metabolic control analysis Large-scale kinetic models Hexokinase HXK2 deletion Xylose utilization |
| url | http://link.springer.com/article/10.1186/s13068-017-0838-5 |
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