title: Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum.
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.
authors.affiliation: Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.
authors.forename: Joomi
authors.initials: J
authors.lastname: Kim
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), Faculty of Science University of Technology, Sydney, New South Wales, Australia.|Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium.|Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium.
authors.forename: Michele
authors.initials: M
authors.lastname: Fabris
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium.|Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium.|Centre of Microbial and Plant Genetics Lab for Genetics and Genomics and Leuven Institute for Beer Research, Leuven University, Gaston Geenslaan 1, B-3001, Leuven, Belgium.
authors.forename: Gino
authors.initials: G
authors.lastname: Baart
authors.affiliation: Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA.
authors.forename: Min K
authors.initials: MK
authors.lastname: Kim
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium.
authors.forename: Alain
authors.initials: A
authors.lastname: Goossens
authors.affiliation: Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Vyverman
authors.affiliation: Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Falkowski
authors.affiliation: Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA.|Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA.|School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, South Australia, Australia.
authors.forename: Desmond S
authors.initials: DS
authors.lastname: Lun
mesh_terms: D056804:Biofuels; D019295:Computational Biology; D003198:Computer Simulation; D016208:Databases, Factual; D017377:Diatoms / Q000254:growth & development / Q000378:metabolism*; D016678:Genome / Q000235:genetics*; D006019:Glycolysis; D053858:Metabolic Networks and Pathways; D058086:Microalgae; D008928:Mitochondria / Q000378:metabolism; D008954:Models, Biological; D010788:Photosynthesis; D013045:Species Specificity
chemical_list: D056804:Biofuels
keywords: Phaeodactylum tricornutum; ancient eukaryotic metabolism; biofuels; computational model; glycolysis; intermediate metabolism