ArticleEnvironmental microbiology2020
High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities.
Article in Environmental microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 207 citations in OpenAlex.
- Growth-coupled microbial biosynthesis of the animal pigment xanthommatin.Nature biotechnology · 2026Article
- A fungal exudate-inspired substrate mixture elicits an emergent growth phenotype and metabolic responses inmSystems · 2026Article
- Functional redundancy driven by isocitrate dehydrogenase enhances metabolic robustness in Pseudomonas putida KT2440.Microbial cell factories · 2026Article
- Beyond the boundaries of microbial diversity in radioactive environments: novel microbial species isolated from a former silver-uranium mine's radon-saturated waters.BMC microbiology · 2026Article
- Biosynthesis of cerium and gadolinium nanoparticles by Pseudomonas putida KT2440 enables sustainable rare earth elements utilization.Scientific reports · 2026Article
- Multi-strain analysis ofmSystems · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Predicting Strain-Specific Metabolic Capabilities in the GenusComputational and structural biotechnology journal · 2026Article
- Describing and Designing Microbial Community Metabolic Models In Silico: A Comprehensive Protocol Utilizing FLYCOP.Methods in molecular biology (Clifton, N.J.) · 2026Article
- From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites.Microorganisms · 2025Review
- Development of an ethanol-based microbial platform for 3-hydroxypropionic acid production using engineered Pseudomonas putida KT2440.Journal of biological engineering · 2025Article
- Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coli.PLoS pathogens · 2025Article
- Multi-strain Analysis ofbioRxiv : the preprint server for biology · 2025Article
- Multiscale metabolic engineering in biological lignin valorization.Innovation (Cambridge (Mass.)) · 2025Review
- Differences in GenBank and RefSeq annotations may affect genomics data interpretation formSphere · 2025Article
- RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.Applied and environmental microbiology · 2025Article
- A blueprint for designing the next-generation of synthetic CNature communications · 2025Review
- Protein-Protein Complex Stability Controls Substrate Scope in a β-Ketoacyl-ACP Reductase Specific for Medium Chains.Angewandte Chemie (International ed. in English) · 2025Article
- Synthetic CmBio · 2025Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 5 institutions in 3 countries.
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Abstract
Genome-scale reconstructions of metabolism are computational species-specific knowledge bases able to compute systemic metabolic properties. We present a comprehensive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440 that greatly expands computable predictions of its metabolic states. The reconstruction represents a significant reactome expansion over available reconstructed bacterial metabolic networks. Specifically, iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knock-out library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin. Thus, this study provides a thoroughly updated metabolic reconstruction and new computable phenotypes for P. putida, which can be leveraged as a first step toward understanding the pan metabolic capabilities of Pseudomonas.
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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.