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

被引:25
作者
Rodenburg, Sander Y. A. [1 ,2 ]
Seidl, Michael F. [1 ]
De Ridder, Dick [2 ]
Govers, Francine [1 ]
机构
[1] Wageningen Univ, Lab Phytopathol, NL-6708 PB Wageningen, Netherlands
[2] Wageningen Univ, Bioinformat Grp, NL-6708 PB Wageningen, Netherlands
关键词
metabolic model; metabolism; oomycete; Phytophthora infestans; systems biology; CONSTRAINT-BASED MODELS; FATTY-ACID SYNTHESIS; APPRESSORIUM FORMATION; DRUG TARGETS; NETWORK; IDENTIFICATION; MITOCHONDRIAL; BIOSYNTHESIS; PREDICTION; SEQUENCE;
D O I
10.1111/mpp.12623
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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 invitro 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.
引用
收藏
页码:1403 / 1413
页数:11
相关论文
共 76 条
  • [1] Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis
    Abrahamian, Melania
    Ah-Fong, Audrey M. V.
    Davis, Carol
    Andreeva, Kalina
    Judelson, Howard S.
    [J]. PLOS PATHOGENS, 2016, 12 (12)
  • [2] The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
    Agren, Rasmus
    Liu, Liming
    Shoaie, Saeed
    Vongsangnak, Wanwipa
    Nookaew, Intawat
    Nielsen, Jens
    [J]. PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (03)
  • [3] Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT
    Agren, Rasmus
    Bordel, Sergio
    Mardinoglu, Adil
    Pornputtapong, Natapol
    Nookaew, Intawat
    Nielsen, Jens
    [J]. PLOS COMPUTATIONAL BIOLOGY, 2012, 8 (05)
  • [4] AHFONG AMV, 2017, BMC GENOMICS, V18
  • [5] Aung Hnin W, 2013, Ind Biotechnol (New Rochelle N Y), V9, P215
  • [6] Context-specific metabolic networks are consistent with experiments
    Becker, Scott A.
    Palsson, Bernhard O.
    [J]. PLOS COMPUTATIONAL BIOLOGY, 2008, 4 (05)
  • [7] Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution
    Belda, Eugeni
    Silva, Francisco J.
    Pereto, Juli
    Moya, Andres
    [J]. PLOS ONE, 2012, 7 (01):
  • [8] Constraint-based models predict metabolic and associated cellular functions
    Bordbar, Aarash
    Monk, Jonathan M.
    King, Zachary A.
    Palsson, Bernhard O.
    [J]. NATURE REVIEWS GENETICS, 2014, 15 (02) : 107 - 120
  • [9] Near-optimal probabilistic RNA-seq quantification (vol 34, pg 525, 2016)
    Bray, Nicolas L.
    Pimentel, Harold
    Melsted, Pall
    Pachter, Lior
    [J]. NATURE BIOTECHNOLOGY, 2016, 34 (08) : 888 - 888
  • [10] Carbohydrate-related enzymes of important Phytophthora plant pathogens
    Brouwer, Henk
    Coutinho, Pedro M.
    Henrissat, Bernard
    de Vries, Ronald P.
    [J]. FUNGAL GENETICS AND BIOLOGY, 2014, 72 : 192 - 200