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

Fabris, M; Matthijs, M; Rombauts, S; Vyverman, W; Goossens, A; Baart, GJE

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

Fabris, M

Matthijs, M Rombauts, S Vyverman, W Goossens, A Baart, GJE

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Publication Type:: Journal Article
Citation:: Plant Journal, 2012, 70 (6), pp. 1004 - 1014
Issue Date:: 2012-06-01

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Field	Value	Language
dc.contributor.author	Fabris, M https://orcid.org/0000-0003-2910-2089	en_US
dc.contributor.author	Matthijs, M	en_US
dc.contributor.author	Rombauts, S	en_US
dc.contributor.author	Vyverman, W	en_US
dc.contributor.author	Goossens, A	en_US
dc.contributor.author	Baart, GJE	en_US
dc.date.issued	2012-06-01	en_US
dc.identifier.citation	Plant Journal, 2012, 70 (6), pp. 1004 - 1014	en_US
dc.identifier.issn	0960-7412	en_US
dc.identifier.uri	http://hdl.handle.net/10453/43559
dc.description.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 Entner-Doudoroff pathway, an ancient alternative for the glycolytic Embden-Meyerhof-Parnas 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. © 2012 Blackwell Publishing Ltd.	en_US
dc.relation.ispartof	Plant Journal	en_US
dc.relation.isbasedon	10.1111/j.1365-313X.2012.04941.x	en_US
dc.subject.classification	Plant Biology & Botany	en_US
dc.subject.mesh	Diatoms	en_US
dc.subject.mesh	Glycolysis	en_US
dc.subject.mesh	Genome	en_US
dc.subject.mesh	Internet	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Databases, Genetic	en_US
dc.subject.mesh	Carbohydrate Metabolism	en_US
dc.subject.mesh	Metabolomics	en_US
dc.subject.mesh	Data Mining	en_US
dc.title	The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway	en_US
dc.type	Journal Article
utslib.citation.volume	6	en_US
utslib.citation.volume	70	en_US
utslib.for	0607 Plant Biology	en_US
utslib.for	0601 Biochemistry and Cell Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	closed_access
pubs.issue	6	en_US
pubs.publication-status	Published	en_US
pubs.volume	70	en_US

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 Entner-Doudoroff pathway, an ancient alternative for the glycolytic Embden-Meyerhof-Parnas 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. © 2012 Blackwell Publishing Ltd.

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http://hdl.handle.net/10453/43559