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The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

Michele Fabris (UGent) , Michiel Matthijs (UGent) , Stephane Rombauts (UGent) , Wim Vyverman (UGent) , Alain Goossens (UGent) and Gino Baart (UGent)
(2012) PLANT JOURNAL. 70(6). p.1004-1014
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Abstract
Diatoms are one of the most successful groups of unicellular eukaryotic algae. Successive endosymbiotic events contributed to their flexible metabolism, making them competitive in variable aquatic habitats. Although the recently sequenced genomes of the model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana have provided the first insights into their metabolic organization, the current knowledge on diatom biochemistry remains fragmentary. By means of a genome-wide approach, we developed DiatomCyc, a detailed pathway/genome database of P. tricornutum. DiatomCyc contains 286 pathways with 1719 metabolic reactions and 1613 assigned enzymes, spanning both the central and parts of the secondary metabolism of P. tricornutum. Central metabolic pathways, such as those of carbohydrates, amino acids and fatty acids, were covered. Furthermore, our understanding of the carbohydrate model in P. tricornutum was extended. In particular we highlight the discovery of a functional EntnerDoudoroff pathway, an ancient alternative for the glycolytic EmbdenMeyerhofParnas pathway, and a putative phosphoketolase pathway, both uncommon in eukaryotes. DiatomCyc is accessible online (), and offers a range of software tools for the visualization and analysis of metabolic networks and omics data. We anticipate that DiatomCyc will be key to gaining further understanding of diatom metabolism and, ultimately, will feed metabolic engineering strategies for the industrial valorization of diatoms.
Keywords
ESCHERICHIA-COLI, FATTY-ACID-COMPOSITION, Entner-Doudoroff pathway, FUNCTIONAL-CHARACTERIZATION, metabolism, DiatomCyc, genome database, pathway, Phaeodactylum tricornutum, diatoms, ISOPRENOID BIOSYNTHESIS, COMPREHENSIVE DATABASE, EICOSAPENTAENOIC ACID, ADAPTIVE EVOLUTION, MARINE DIATOMS, GENOME, MICROALGAE

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MLA
Fabris, Michele, Michiel Matthijs, Stephane Rombauts, et al. “The Metabolic Blueprint of Phaeodactylum Tricornutum Reveals a Eukaryotic Entner-Doudoroff Glycolytic Pathway.” PLANT JOURNAL 70.6 (2012): 1004–1014. Print.
APA
Fabris, M., Matthijs, M., Rombauts, S., Vyverman, W., Goossens, A., & Baart, G. (2012). The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway. PLANT JOURNAL, 70(6), 1004–1014.
Chicago author-date
Fabris, Michele, Michiel Matthijs, Stephane Rombauts, Wim Vyverman, Alain Goossens, and Gino Baart. 2012. “The Metabolic Blueprint of Phaeodactylum Tricornutum Reveals a Eukaryotic Entner-Doudoroff Glycolytic Pathway.” Plant Journal 70 (6): 1004–1014.
Chicago author-date (all authors)
Fabris, Michele, Michiel Matthijs, Stephane Rombauts, Wim Vyverman, Alain Goossens, and Gino Baart. 2012. “The Metabolic Blueprint of Phaeodactylum Tricornutum Reveals a Eukaryotic Entner-Doudoroff Glycolytic Pathway.” Plant Journal 70 (6): 1004–1014.
Vancouver
1.
Fabris M, Matthijs M, Rombauts S, Vyverman W, Goossens A, Baart G. The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway. PLANT JOURNAL. 2012;70(6):1004–14.
IEEE
[1]
M. Fabris, M. Matthijs, S. Rombauts, W. Vyverman, A. Goossens, and G. Baart, “The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway,” PLANT JOURNAL, vol. 70, no. 6, pp. 1004–1014, 2012.
@article{2964814,
  abstract     = {Diatoms are one of the most successful groups of unicellular eukaryotic algae. Successive endosymbiotic events contributed to their flexible metabolism, making them competitive in variable aquatic habitats. Although the recently sequenced genomes of the model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana have provided the first insights into their metabolic organization, the current knowledge on diatom biochemistry remains fragmentary. By means of a genome-wide approach, we developed DiatomCyc, a detailed pathway/genome database of P. tricornutum. DiatomCyc contains 286 pathways with 1719 metabolic reactions and 1613 assigned enzymes, spanning both the central and parts of the secondary metabolism of P. tricornutum. Central metabolic pathways, such as those of carbohydrates, amino acids and fatty acids, were covered. Furthermore, our understanding of the carbohydrate model in P. tricornutum was extended. In particular we highlight the discovery of a functional EntnerDoudoroff pathway, an ancient alternative for the glycolytic EmbdenMeyerhofParnas pathway, and a putative phosphoketolase pathway, both uncommon in eukaryotes. DiatomCyc is accessible online (), and offers a range of software tools for the visualization and analysis of metabolic networks and omics data. We anticipate that DiatomCyc will be key to gaining further understanding of diatom metabolism and, ultimately, will feed metabolic engineering strategies for the industrial valorization of diatoms.},
  author       = {Fabris, Michele and Matthijs, Michiel and Rombauts, Stephane and Vyverman, Wim and Goossens, Alain and Baart, Gino},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keywords     = {ESCHERICHIA-COLI,FATTY-ACID-COMPOSITION,Entner-Doudoroff pathway,FUNCTIONAL-CHARACTERIZATION,metabolism,DiatomCyc,genome database,pathway,Phaeodactylum tricornutum,diatoms,ISOPRENOID BIOSYNTHESIS,COMPREHENSIVE DATABASE,EICOSAPENTAENOIC ACID,ADAPTIVE EVOLUTION,MARINE DIATOMS,GENOME,MICROALGAE},
  language     = {eng},
  number       = {6},
  pages        = {1004--1014},
  title        = {The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway},
  url          = {http://dx.doi.org/10.1111/j.1365-313X.2012.04941.x},
  volume       = {70},
  year         = {2012},
}

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