Podcast
Questions and Answers
What is the name of the model developed for Saccharomyces cerevisiae to integrate expression constraints and reaction thermodynamics?
What is the name of the model developed for Saccharomyces cerevisiae to integrate expression constraints and reaction thermodynamics?
- Eukaryotic Model
- yETFL (correct)
- ETFL
- S. cerevisiae Model
What does yETFL integrate with traditional genome-scale metabolic models?
What does yETFL integrate with traditional genome-scale metabolic models?
- Cell division
- DNA replication
- RNA and protein synthesis (correct)
- Metabolite transport
What is the main advantage of yETFL in predicting maximum growth rate and essential genes?
What is the main advantage of yETFL in predicting maximum growth rate and essential genes?
- Considerations for biomass composition (correct)
- Compartmentalized cellular expression system
- Integration of DNA and RNA synthesis
- Energetic costs of biological processes
What is the primary focus of the model yETFL?
What is the primary focus of the model yETFL?
What is one limitation of the ETFL model mentioned in the text?
What is one limitation of the ETFL model mentioned in the text?
What is the potential impact of the presented formulation of yETFL?
What is the potential impact of the presented formulation of yETFL?
How many unique metabolites are contained in the Yeast822 genome-scale model?
How many unique metabolites are contained in the Yeast822 genome-scale model?
How many reactions are associated with genes in Yeast822?
How many reactions are associated with genes in Yeast822?
What is the number of enzymes coupled to reactions in the yETFL model?
What is the number of enzymes coupled to reactions in the yETFL model?
How many transporters are associated with transport reactions in the yETFL model?
How many transporters are associated with transport reactions in the yETFL model?
Does yETFL account for operon structures?
Does yETFL account for operon structures?
How many types of models were developed to study the inclusion/exclusion of thermodynamic constraints and the type of resource allocation?
How many types of models were developed to study the inclusion/exclusion of thermodynamic constraints and the type of resource allocation?
What type of framework does yETFL use to model metabolism?
What type of framework does yETFL use to model metabolism?
What does yETFL predict in terms of biomass composition and transcription/translation machinery content?
What does yETFL predict in terms of biomass composition and transcription/translation machinery content?
How does yETFL differ from WM_S288C in expression modeling?
How does yETFL differ from WM_S288C in expression modeling?
What does yETFL predict about the shift in growth conditions?
What does yETFL predict about the shift in growth conditions?
What is the predicted maximum growth rate for E(T)FL.cb according to yETFL?
What is the predicted maximum growth rate for E(T)FL.cb according to yETFL?
What caused small discrepancies between experimental data and yETFL results?
What caused small discrepancies between experimental data and yETFL results?
What is the main challenge in engineering eukaryotic organisms for industrial biotechnology?
What is the main challenge in engineering eukaryotic organisms for industrial biotechnology?
Which method is introduced to overcome some of the issues with Flux Balance Analysis (FBA)?
Which method is introduced to overcome some of the issues with Flux Balance Analysis (FBA)?
What is the new approach called that includes the cellular expression system in addition to metabolic and catalytic constraints?
What is the new approach called that includes the cellular expression system in addition to metabolic and catalytic constraints?
What is the yETFL model specifically developed for?
What is the yETFL model specifically developed for?
What do the methodological advancements in ETFL provide avenues for?
What do the methodological advancements in ETFL provide avenues for?
What is the implication of the advancement in modeling eukaryotic organisms for industrial biotechnology?
What is the implication of the advancement in modeling eukaryotic organisms for industrial biotechnology?
What does yETFL use for feasible solution space and growth-dependent parameters?
What does yETFL use for feasible solution space and growth-dependent parameters?
Which model successfully predicts shifts in metabolic fluxes at high growth rates, capturing the Crabtree effect?
Which model successfully predicts shifts in metabolic fluxes at high growth rates, capturing the Crabtree effect?
What does yETFL predict more genes corresponding to compared to the FBA model?
What does yETFL predict more genes corresponding to compared to the FBA model?
What does the integration of thermodynamic constraints into FBA or EFL.cb models not change?
What does the integration of thermodynamic constraints into FBA or EFL.cb models not change?
Which models present earlier onset of Crabtree effect relative to E[T]FL.cb models?
Which models present earlier onset of Crabtree effect relative to E[T]FL.cb models?
What is affected by models with higher protein ratios?
What is affected by models with higher protein ratios?
Study Notes
Yeast Metabolic Model yETFL Predicts Gene Essentiality and Crabtree Effect
- yETFL uses highest reported ribosomal elongation rate for feasible solution space and growth-dependent parameters
- Regulatory system in S. cerevisiae drives metabolism towards optimality
- Gene essentiality analysis shows identical results for yETFL, EFL.cb, and FBA models for metabolic genes
- yETFL predicts more genes corresponding to RNA polymerases and ribosomes compared to FBA model
- Integration of thermodynamic constraints into FBA or EFL.cb does not change essentiality results
- Crabtree effect, or overflow metabolism, observed in S. cerevisiae at high growth rates
- yETFL successfully predicts shifts in metabolic fluxes at high growth rates, capturing the Crabtree effect
- yETFL considers limitations in catalytic capacity of enzymes and protein expression machinery
- Model shows good qualitative agreement with experimental data from aerobic, glucose-limited chemostat cultures
- E[T]FL.vb models present earlier onset of Crabtree effect relative to E[T]FL.cb models
- Models with higher protein ratios are less tightly constrained, affecting maximum growth rate and onset of Crabtree effect
- Slight deviation between model predictions and experimental observations in transition region for growth rates between 0.3 and 0.36 h−1
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Description
Test your knowledge about the yeast metabolic model yETFL and its predictions of gene essentiality and the Crabtree effect. This quiz covers topics such as ribosomal elongation rates, regulatory systems, gene essentiality analysis, thermodynamic constraints, and the integration of experimental data.
