Advanced search
1 file | 446.93 KB

Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum

(2016) PLANT JOURNAL. 85(1). p.161-176
Author
Organization
Abstract
Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.
Keywords
WASTE-WATER, GLYCOLYTIC PATHWAY, PLASTIDS, ORIGIN, AMINO-ACID, OPTIMIZATION FRAMEWORK, computational model, intermediate metabolism, glycolysis, ancient eukaryotic metabolism, biofuels, KeyWords Plus:ORGANIC-CARBON SOURCES, MARINE DIATOM, PHOTOSYNTHESIS, Author Keywords:Phaeodactylum tricornutum, ESCHERICHIA-COLI

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 446.93 KB

Citation

Please use this url to cite or link to this publication:

Chicago
Kim, Joomi, Michele Fabris, Gino Baart, Min K Kim, Alain Goossens, Wim Vyverman, Paul G Falkowski, and Desmond S Lun. 2016. “Flux Balance Analysis of Primary Metabolism in the Diatom Phaeodactylum Tricornutum.” Plant Journal 85 (1): 161–176.
APA
Kim, Joomi, Fabris, M., Baart, G., Kim, M. K., Goossens, A., Vyverman, W., Falkowski, P. G., et al. (2016). Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. PLANT JOURNAL, 85(1), 161–176.
Vancouver
1.
Kim J, Fabris M, Baart G, Kim MK, Goossens A, Vyverman W, et al. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. PLANT JOURNAL. 2016;85(1):161–76.
MLA
Kim, Joomi, Michele Fabris, Gino Baart, et al. “Flux Balance Analysis of Primary Metabolism in the Diatom Phaeodactylum Tricornutum.” PLANT JOURNAL 85.1 (2016): 161–176. Print.
@article{7081792,
  abstract     = {Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.},
  author       = {Kim, Joomi and Fabris, Michele and Baart, Gino and Kim, Min K and Goossens, Alain and Vyverman, Wim and Falkowski, Paul G and Lun, Desmond S},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  language     = {eng},
  number       = {1},
  pages        = {161--176},
  title        = {Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum},
  url          = {http://dx.doi.org/10.1111/tpj.13081},
  volume       = {85},
  year         = {2016},
}

Altmetric
View in Altmetric
Web of Science
Times cited: