Genome-Scale Reconstruction and Analysis of the Pseudomonasputida KT2440 Metabolic Network Facilitates Applications inBiotechnology

摘要

A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to its metabolic versatility, stress resistance, amenability to genetic modifications, and vast potential for environmental and industrial applications. To address both the elucidation of the metabolic wiring in P. putida and its uses in biocatalysis, in particular for the production of non-growth-related biochemicals, we developed and present here a genome-scale constraint-based model of the metabolism of P. putida KT2440. Network reconstruction and flux balance analysis (FBA) enabled definition of the structure of the metabolic network, identification of knowledge gaps, and pin-pointing of essential metabolic functions, facilitating thereby the refinement of gene annotations. FBA and flux variability analysis were used to analyze the properties, potential, and limits of the model. These analyses allowed identification, under various conditions, of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. The model was validated with data from continuous cell cultures,high-throughput phenotyping data, ¹³C-measurement of internal fluxdistributions, and specifically generated knock-out mutants. Auxotrophy wascorrectly predicted in 75% of the cases. These systematic analysesrevealed that the metabolic network structure is the main factor determining theaccuracy of predictions, whereas biomass composition has negligible influence.Finally, we drew on the model to devise metabolic engineering strategies toimprove production of polyhydroxyalkanoates, a class of biotechnologicallyuseful compounds whose synthesis is not coupled to cell survival. The solidlyvalidated model yields valuable insights into genotype–phenotyperelationships and provides a sound framework to explore this versatile bacteriumand to capitalize on its vast biotechnological potential.