Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach

Y.A. Rodenburg, M.F. Seidl, D. de Ridder, F. Govers*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

Abstract

Genome-scale metabolic models (GEMs) provide a functional view of the complex network of biochemical reactions in the living cell. Initially mainly applied to reconstruct the metabolism of model organisms, the availability of increasingly sophisticated reconstruction methods and more extensive biochemical databases now make it possible to reconstruct GEMs for less well-characterized organisms, and have the potential to unravel the
metabolism in pathogen–host systems. Here, we present a GEM for the oomycete plant pathogen Phytophthora infestans as a first step towards an integrative model with its host. We predict the biochemical reactions in different cellular compartments and investigate the gene–protein–reaction associations in this model to obtain an impression of the biochemical capabilities of
P. infestans . Furthermore, we generate life stage-specific models to place the transcriptomic changes of the genes encoding metabolic enzymes into a functional context. In sporangia and zoospores, there is an overall down-regulation, most strikingly reflected in the fatty acid biosynthesis pathway. To investigate the robustness of the GEM, we simulate gene deletions to predict which enzymes are essential for in vitro growth. This model is an
essential first step towards an understanding of P. infestans and its interactions with plants as a system, which will help to formulate new hypotheses on infection mechanisms and disease prevention.
Original languageEnglish
Pages (from-to)1403-1413
JournalMolecular Plant Pathology
Volume19
Issue number6
Early online date30 Jan 2018
DOIs
Publication statusPublished - Jun 2018

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