ArticleMolecular systems biology2021
Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Niche Construction: A Rational Engineering Strategy for Regulating Microbial Assembly to Enhance Flavor and Bioactivity of Fermented Foods.Comprehensive reviews in food science and food safety · 2026Review
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- Whole-cell modeling predicts alternative proteome allocation strategies in the archaeon Methanococcus maripaludis.Scientific reports · 2026Article
- Integrative Thermodynamic Strategies in Microbial Metabolism.International journal of molecular sciences · 2025Article
- Alkaline pH-Driven Metabolic Plasticity of Lactococcus lactis FM03.Environmental microbiology · 2025Article
- Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources.mSystems · 2025Article
- Reconstruction of a Genome-Scale Metabolic Model forInternational journal of molecular sciences · 2025Article
- A framework for understanding collective microbiome metabolism.Nature microbiology · 2024Review
- Biopurification using non-growing microorganisms to improve plant protein ingredients.NPJ science of food · 2024Article
- Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0.Nature protocols · 2024Review
- Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides.PLoS computational biology · 2023Article
- Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems.Computational and structural biotechnology journal · 2023Review
- A Computational Toolbox to Investigate the Metabolic Potential and Resource Allocation in Fission Yeast.mSystems · 2022Article
- Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.Nature communications · 2022Article
- Manganese Modulates Metabolic Activity and Redox Homeostasis in Translationally BlockedMicrobiology spectrum · 2022Article
- SALARECON connects the Atlantic salmon genome to growth and feed efficiency.PLoS computational biology · 2022Article
- Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.Nature communications · 2022Article
- Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast.Life science alliance · 2022Article
- Review
- Understanding FBA Solutions under Multiple Nutrient Limitations.Metabolites · 2021Article
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9 authors.
Funding
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Abstract
Cells adapt to different conditions via gene expression that tunes metabolism for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade-offs. Resource allocation under proteome constraints has explained regulatory strategies in bacteria. It is unclear, however, to what extent these constraints can predict evolutionary changes, especially for microorganisms that evolved under nutrient-rich conditions, i.e., multiple available nitrogen sources, such as Lactococcus lactis. Here, we present a proteome-constrained genome-scale metabolic model of L. lactis (pcLactis) to interpret growth on multiple nutrients. Through integration of proteomics and flux data, in glucose-limited chemostats, the model predicted glucose and arginine uptake as dominant constraints at low growth rates. Indeed, glucose and arginine catabolism were found upregulated in evolved mutants. At high growth rates, pcLactis correctly predicted the observed shutdown of arginine catabolism because limited proteome availability favored lactate for ATP production. Thus, our model-based analysis is able to identify and explain the proteome constraints that limit growth rate in nutrient-rich environments and thus form targets of fitness improvement.
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