Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
Journal Articles Biotechnology Journal Year : 2014

Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.

Tamás Fehér
  • Function : Correspondent author
Pablo Carbonell
Ioana Grigoras
Ekaterina Dariy
Alain Perret
Jean-Loup Faulon

Abstract

Metabolic engineering has succeeded in biosynthesis of numerous commodity or high value compounds. However, the choice of pathways and enzymes used for production was many times made ad hoc, or required expert knowledge of the specific biochemical reactions. In order to rationalize the process of engineering producer strains, we developed the computer-aided design (CAD) tool RetroPath that explores and enumerates metabolic pathways connecting the endogenous metabolites of a chassis cell to the target compound. To experimentally validate our tool, we constructed 12 top-ranked enzyme combinations producing the flavonoid pinocembrin, four of which displayed significant yields. Namely, our tool queried the enzymes found in metabolic databases based on their annotated and predicted activities. Next, it ranked pathways based on the predicted efficiency of the available enzymes, the toxicity of the intermediate metabolites and the calculated maximum product flux. To implement the top-ranking pathway, our procedure narrowed down a list of nine million possible enzyme combinations to 12, a number easily assembled and tested. One round of metabolic network optimization based on RetroPath output further increased pinocembrin titers 17-fold. In total, 12 out of the 13 enzymes tested in this work displayed a relative performance that was in accordance with its predicted score. These results validate the ranking function of our CAD tool, and open the way to its utilization in the biosynthesis of novel compounds.
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Dates and versions

hal-02639677 , version 1 (12-10-2023)

Identifiers

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Tamás Fehér, Anne-Gaëlle Planson, Pablo Carbonell, Alfred Fernández-Castané, Ioana Grigoras, et al.. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.. Biotechnology Journal, 2014, 9 (11), pp.1446-1457. ⟨10.1002/biot.201400055⟩. ⟨hal-02639677⟩
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