ArticleMolecular systems biology2023
Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation.
Article in Molecular systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Metabolic engineering ofSynthetic and systems biotechnology · 2026Article
- Decoding the Hot-Mitochondrion Paradox.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Integrating Vibrio natriegens for Photon Manipulation in Living Lighting Devices.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Mitigating protocatechuic acid toxicity in Vibrio natriegens enables poly-3-hydroxybutyrate production from an aromatic carbon source.Applied microbiology and biotechnology · 2026Article
- Genetic make-up and regulation of the L-lysine biosynthesis pathway inMicrobial cell (Graz, Austria) · 2026Article
- RBApy: extending resource allocation modeling to eukaryotes in complex environments.Bioinformatics advances · 2026Article
- Expanding genetic engineering capabilities in Vibrio natriegens with the Vnat Collection.Nucleic acids research · 2025Article
- Small-scale fed-batch cultivations of Vibrio natriegens: overcoming challenges for early process development.Bioprocess and biosystems engineering · 2025Article
- Dual roles of glycine betaine, dimethylglycine, and sarcosine as osmoprotectants and nutrient sources forApplied and environmental microbiology · 2025Article
- Vibrio natriegens: Application of a Fast-Growing Halophilic Bacterium.Advances in biochemical engineering/biotechnology · 2025Review
- Unraveling the impact of pH, sodium concentration, and medium osmolality on Vibrio natriegens in batch processes.BMC biotechnology · 2024Article
- Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle.ACS synthetic biology · 2024Review
- Expanding the capabilities of MuGENT for large-scale genetic engineering of the fastest-replicating species,Microbiology spectrum · 2024Article
- Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens.Communications biology · 2024Article
- Antibacterial and antibiofilm activity of halogenated phenylboronic acids againstFrontiers in cellular and infection microbiology · 2024Article
- DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.Briefings in bioinformatics · 2023Article
- Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation.Molecular systems biology · 2023Article
- Article
- Model validation and selection in metabolic flux analysis and flux balance analysis.Biotechnology progressReview
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10 authors.
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Abstract
Vibrio natriegens is a Gram-negative bacterium with an exceptional growth rate that has the potential to become a standard biotechnological host for laboratory and industrial bioproduction. Despite this burgeoning interest, the current lack of organism-specific qualitative and quantitative computational tools has hampered the community's ability to rationally engineer this bacterium. In this study, we present the first genome-scale metabolic model (GSMM) of V. natriegens. The GSMM (iLC858) was developed using an automated draft assembly and extensive manual curation and was validated by comparing predicted yields, central metabolic fluxes, viable carbon substrates, and essential genes with empirical data. Mass spectrometry-based proteomics data confirmed the translation of at least 76% of the enzyme-encoding genes predicted to be expressed by the model during aerobic growth in a minimal medium. iLC858 was subsequently used to carry out a metabolic comparison between the model organism Escherichia coli and V. natriegens, leading to an analysis of the model architecture of V. natriegens' respiratory and ATP-generating system and the discovery of a role for a sodium-dependent oxaloacetate decarboxylase pump. The proteomics data were further used to investigate additional halophilic adaptations of V. natriegens. Finally, iLC858 was utilized to create a Resource Balance Analysis model to study the allocation of carbon resources. Taken together, the models presented provide useful computational tools to guide metabolic engineering efforts in V. natriegens.
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