ArticleBMC systems biology2008
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
Article in BMC systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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111 citing papers in PubMed.
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- 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
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.World journal of microbiology & biotechnology · 2025Review
- Investigating Lipid and Energy Dyshomeostasis Induced by Per- and Polyfluoroalkyl Substances (PFAS) Congeners in Mouse Model Using Systems Biology Approaches.Metabolites · 2025Article
- Artificial symbiont replacement in a vertically transmitted plant symbiosis reveals a role for microbe-microbe interactions in enforcing specificity.The ISME journal · 2025Article
- A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers.PLoS computational biology · 2025Article
- Nutrient Requirements Shape the Preferential Habitat of Allorhizobium vitis VAR03-1, a Commensal Bacterium, in the Rhizosphere of Arabidopsis thaliana.Plant & cell physiology · 2024Article
- Strategy for Optimizing Vitamin B12 Production inMetabolites · 2024Article
- Physiology, fast and slow: bacterial response to variable resource stoichiometry and dilution rate.mSystems · 2024Article
- Review
- Pseudomonas putida as a platform for medium-chain length α,ω-diol production: Opportunities and challenges.Microbial biotechnology · 2024Article
- Article
- FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization.Microbial cell factories · 2024Article
- Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12.BMC genomics · 2024Article
- Computational analysis into the potential of azo dyes as a feedstock for actinorhodin biosynthesis in Pseudomonas putida.PloS one · 2024Article
51 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundPseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. Since the publication of P. putida KT2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. However, global understanding of the capabilities of P. putida KT2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-throughput data. The constraint-based reconstruction and analysis (COBRA) approach has been successfully used to build and analyze in silico genome-scale metabolic reconstructions.
resultsWe present a genome-scale reconstruction of P. putida KT2440's metabolism, iJN746, which was constructed based on genomic, biochemical, and physiological information. This manually-curated reconstruction accounts for 746 genes, 950 reactions, and 911 metabolites. iJN746 captures biotechnologically relevant pathways, including polyhydroxyalkanoate synthesis and catabolic pathways of aromatic compounds (e.g., toluene, benzoate, phenylacetate, nicotinate), not described in other metabolic reconstructions or biochemical databases. The predictive potential of iJN746 was validated using experimental data including growth performance and gene deletion studies. Furthermore, in silico growth on toluene was found to be oxygen-limited, suggesting the existence of oxygen-efficient pathways not yet annotated in P. putida's genome. Moreover, we evaluated the production efficiency of polyhydroxyalkanoates from various carbon sources and found fatty acids as the most prominent candidates, as expected.
conclusionHere we presented the first genome-scale reconstruction of P. putida, a biotechnologically interesting all-surrounder. Taken together, this work illustrates the utility of iJN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production.
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