A Study of Genomics and Metabolic Reconstructions with Pseudomonas from Biotechnology

Biotechnology

The best-studied pollutant-degrading bacterium, Pseudomonas putida, is used in industrial biotechnology to manufacture fine compounds. Some in silico evaluations of P. putida KT2440's metabolic and biotechnological capacities have been reported since the genome was published. However, a comprehensive knowledge of P. putida KT2440's capabilities necessitates the development of a metabolic model that allows the integration of traditional experimental data with genomic and high-throughput data. In silico genome-scale metabolic reconstructions have been successfully built and analysed using the constraint-based reconstruction and analysis (COBRA) method. The employment of microorganisms in the efficient manufacture of chemicals and the eradication of toxic waste is a cornerstone of biotechnology. Due to its metabolic plasticity, stress resilience, amenability to genetic alterations, and great potential for environmental and industrial applications, Pseudomonas putida is an exemplar of such bacteria. We built and describe here a genome-scale constraint-based model of P. putida KT2440 metabolism to address both the elucidation of the metabolic wiring in P. putida and its applications in biocatalysis, particularly for the synthesis of non-growth related biochemicals. Network reconstruction and flux balance analysis (FBA) allowed the topology of the metabolic network to be defined, knowledge gaps to be identified, and critical metabolic functions to be pinpointed, allowing for the refining of gene annotations.

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