A Practical Protocol for Genome-Scale Metabolic Reconstructions
Genome-scale metabolic reconstructions (GEMREs) are organism-specific knowledge bases. Such reconstructions are developed systematically through the integration of genome annotation, omic data sets, and biological knowledge available for the target species at the time of reconstruction. They can be further transformed into computational models enabling the quantitative prediction of phenotypic states in terms of fluxes through individual reactions. In addition, they can be used as unique computational scaffolds towards the integration and mechanistic contextualization of omic data. As a result, GEMREs are attracting great interest, and the scope of their applications keeps growing. However, the key reconstruction process is time-consuming, and it is extremely sensitive to the adherence to accepted quality standards and protocols. Therefore, high-quality reconstruction protocols reducing the time and effort involved in the reconstruction are desirable. This chapter provides a step-by-step protocol for genome-scale metabolic reconstruction accessible to nonexperts in the field. The protocol was applied to reconstruct the metabolic network of the aromatic hydrocarbon-degrading bacterium Pseudomonas putida F1 using the reconstruction of the related strain Pseudomonas putida KT2440 as template. The final model was further used to compare, from a mechanistic point of view, some of the metabolic capabilities of these two interesting environmental bacteria.
KeywordsConstraint-Based Reconstruction and Analysis Flux Balance Analysis Genome-scale model Pseudomonas Metabolic Reconstruction
This work was supported by the SYNPOL (FP7-KBBE 311815; http://www.synpol.org/) UE project.
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