Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 535999
Title Genome-wide characterization of Phytophthora infestans metabolism : a systems biology approach
Author(s) Rodenburg, Y.A.; Seidl, M.F.; Ridder, D. de; Govers, F.
Source Molecular Plant Pathology 19 (2018)6. - ISSN 1464-6722 - p. 1403 - 1413.
DOI https://doi.org/10.1111/mpp.12623
Department(s) Bioinformatics
Laboratory of Phytopathology
EPS
Publication type Refereed Article in a scientific journal
Publication year 2018
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.
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