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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
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
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
journal title
PLANT JOURNAL
Plant J.
volume
70
issue
6
pages
1004 - 1014
Web of Science type
Article
Web of Science id
000305120400009
JCR category
PLANT SCIENCES
JCR impact factor
6.582 (2012)
JCR rank
7/193 (2012)
JCR quartile
1 (2012)
ISSN
0960-7412
DOI
10.1111/j.1365-313X.2012.04941.x
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2964814
handle
http://hdl.handle.net/1854/LU-2964814
date created
2012-07-30 11:43:20
date last changed
2012-08-06 16:59:38
@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},
  keyword      = {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},
}

Chicago
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.
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.
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.
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.