Reconstruction and validation of the genome scale in silico model of Pseudomonas putida KT2440

Abstract

In this study, an in silico model for the saprophytic soil bacterium Pseudomonas putida KT2440 is constructed for the purpose of bettering understanding the strain for rational engineering of enhanced phenotypes in a number of biotechnological applications. Pseudomonas putida has been considered as the model organism for soil bacterium due to its versatility in stressful environments and has been identified for applications in a number of applications, including bioremediation, biocatalysts, and the production of a number of bioproducts such as bioplastics. With the construction of an in silico model, the design of engineered strains is simplified and greatly reduces the number of experimental hours in identifying targets for perturbation. By using metabolic flux analysis, changes in flux distributions from genetic and environmental alterations can be studied, for example, amplification or deletion of genes. With results of these analyses, in vivo experimental tests can be performed to verify the accuracy of the model as well as identify new information that can be incorporated into the model to improve accuracy. Thus with the completion of this genome scale model, strategies for strain improvement in the various biotechnological applications for the P. putida can be optimally designed.