ArticleNature communications2022
Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies.
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 59 papers.
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Who cites it
59 citing papers in PubMed, 109 citations in OpenAlex.
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- Dynamic, model-guided intensification of fuel ethanol production in yeast: proteome constraints, CRISPR rewiring, and high-gravity fermentations.Archives of microbiology · 2026Review
- Dynamic, model-guided intensification of fuel ethanol production in yeast: proteome constraints, CRISPR rewiring, and high-gravity fermentations.Archives of microbiology · 2026Review
- The proportional scaling of mRNA and ribosome concentrations controls eukaryotic cell growth.Nature cell biology · 2026Article
- Towards the construction of a virtual yeast.Nature · 2026Review
- Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics.bioRxiv : the preprint server for biology · 2026Article
- On the conditions for shifts in metabolic strategies.PLoS computational biology · 2026Review
- EnzymeTuning improves enzyme-constrained metabolic modeling and proteome abundance prediction through deep learning.Nature communications · 2026Article
- Whole-cell modeling predicts alternative proteome allocation strategies in the archaeon Methanococcus maripaludis.Scientific reports · 2026Article
- Stoichiometric analysis of microbial communities links function, structure, and biomass carrying capacity.The ISME journal · 2026Review
- Systems biology of yeast metabolism.FEMS yeast research · 2026Review
- Spatiotemporal control of mitoribosome-mediated metabolic reprogramming in cancer: implications for heterogeneity and therapeutic targeting.Frontiers in cell and developmental biology · 2026Review
- From Genome to Function: Metabolism-Wide Models of Lifecycle Stages of Parasites.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Overflow metabolism in bacterial, yeast, and mammalian cells: different names, same game.Molecular systems biology · 2025Review
- Glycolytic ATP production enables rapid mammalian cell growth.bioRxiv : the preprint server for biology · 2025Article
- Article
- A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations.PLoS computational biology · 2025Article
- A Trade-off between Force and Flow May Lead to Reduced Entropy Production Rate during Faster Microbial Growth.The journal of physical chemistry. B · 2025Article
- Coarse-Grained Modeling Elucidates Differential Metabolism ofACS synthetic biology · 2025Article
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 5 countries.
Funding
Abstract
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation-known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.