ArticleNature communications2022
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed, 136 citations in OpenAlex.
- EINN: An enzyme-informed neural network guided by an enzyme-constrained genome-scale metabolic model.Synthetic and systems biotechnology · 2027Article
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- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Enzyme-constrained genome-scale model of Yarrowia lipolytica predicts growth-phase specific metabolic engineering targets.Applied microbiology and biotechnology · 2026Article
- A geometric deep learning framework for genome-wide prediction of enzyme turnover number.Genome biology · 2026Article
- Model-driven exploration of lactose and galactose metabolism via an oxidoreductive pathway in Sungouiella intermedia for cell factory applications.Microbial cell factories · 2026Article
- Digital twins for in vivo metabolic flux estimations in patients with brain cancer.Cell metabolism · 2026Article
- Systems biology of yeast metabolism.FEMS yeast research · 2026Review
- Bioinformatics Approaches in Noncoding RNAs Research.Experientia supplementum (2012) · 2026Review
- Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.Environmental microbiome · 2025Article
- Multi-omics reveals glucose repression of citric acid catabolism in Pichia kudriavzevii.Applied microbiology and biotechnology · 2025Article
- Unravelling the Complexity of Sarcopenia Through a Systems Biology Approach.International journal of molecular sciences · 2025Review
- The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions.ACS synthetic biology · 2025Review
- Metabolic engineering and adaptive laboratory evolution of Kluyveromyces Marxianus for lactic acid production.Microbial cell factories · 2025Article
- Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources.mSystems · 2025Article
- Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana.The New phytologist · 2025Article
- Coarse-Grained Modeling Elucidates Differential Metabolism ofACS synthetic biology · 2025Article
11 more citing papers are in PubMed but not listed here.
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10 authors at 6 institutions in 4 countries.
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No grant is acknowledged in the PubMed record.
Abstract
Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.
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