ArticleMolecular systems biology2021
Genome-scale metabolic modeling reveals key features of a minimal gene set.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- The return of metabolism: biochemistry and physiology of glycolysis.Biological reviews of the Cambridge Philosophical Society · 2026Review
- A kinetic mathematical model of comprehensive iron metabolism in a respiring yeast cell: a basic-pathways approach to solving a large system dynamically.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2026Article
- Genome engineering on size reduction and complexity simplification: A review.Journal of advanced research · 2024Review
- Review
- Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience.Biomolecules · 2023Article
- Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures.Metabolites · 2023Review
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria.Frontiers in microbiology · 2023Article
- Article
- Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties ofMicroorganisms · 2022Review
- Computational approaches to understanding Clostridioides difficile metabolism and virulence.Current opinion in microbiology · 2022Review
- Article
- In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology.Microbial biotechnology · 2022Article
- SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A.Protein science : a publication of the Protein Society · 2022Article
- Genome-scale metabolic modeling reveals key features of a minimal gene set.Molecular systems biology · 2021Article
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Authors and funding
12 authors.
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Abstract
Mesoplasma florum, a fast-growing near-minimal organism, is a compelling model to explore rational genome designs. Using sequence and structural homology, the set of metabolic functions its genome encodes was identified, allowing the reconstruction of a metabolic network representing ˜ 30% of its protein-coding genes. Growth medium simplification enabled substrate uptake and product secretion rate quantification which, along with experimental biomass composition, were integrated as species-specific constraints to produce the functional iJL208 genome-scale model (GEM) of metabolism. Genome-wide expression and essentiality datasets as well as growth data on various carbohydrates were used to validate and refine iJL208. Discrepancies between model predictions and observations were mechanistically explained using protein structures and network analysis. iJL208 was also used to propose an in silico reduced genome. Comparing this prediction to the minimal cell JCVI-syn3.0 and its parent JCVI-syn1.0 revealed key features of a minimal gene set. iJL208 is a stepping-stone toward model-driven whole-genome engineering.
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