ArticleMetabolic engineering2017
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes.
Article in Metabolic engineering, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 101 citations in OpenAlex.
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- MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models.Genome biology · 2025Article
- Unveiling new features of the human pathogenComputational and structural biotechnology journal · 2025Article
- BioModTool: from biomass composition data to structured biomass objective functions for genome-scale metabolic models.Bioinformatics advances · 2025Article
- Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches.NPJ systems biology and applications · 2024Article
- Genome-scale metabolic modelling of extremophiles and its applications in astrobiological environments.Environmental microbiology reports · 2024Review
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability.The ISME journal · 2023Article
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.PLoS computational biology · 2023Article
- Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution inmSystems · 2023Article
- Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms.Nature communications · 2023Article
- Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks.BMC microbiology · 2023Article
- Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities.Quantitative biology (Beijing, China) · 2023Review
- Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations.Computational and structural biotechnology journal · 2023Article
- Genome-scale reconstruction and metabolic modelling of the fast-growing thermophileMetabolic engineering communications · 2022Article
- COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions.PLoS computational biology · 2022Article
- Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.PLoS computational biology · 2022Article
- A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria.Frontiers in microbiology · 2022Article
- Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure.Journal of molecular evolution · 2021Article
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3 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthetic groups, is yet unclear. Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing universally essential cofactors for prokaryotic metabolism and also others that are specific for phylogenetic branches or metabolic modes. Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis. This work provides fundamental insights into the essentiality of organic cofactors and has implications for minimal cell studies as well as for modeling genotype-phenotype relations in prokaryotic metabolic networks.
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