title: Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.
abstract: Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Jennifer
authors.identifier: 0000-0001-8491-9337
authors.initials: J
authors.lastname: Levering
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.|Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Jared
authors.initials: J
authors.lastname: Broddrick
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Graham
authors.initials: G
authors.lastname: Peers
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Karen
authors.initials: K
authors.lastname: Beeri
authors.affiliation: Division of Industrial Biotechnology, Department of Biology and Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Joshua
authors.initials: J
authors.lastname: Mayers
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Alessandra A
authors.initials: AA
authors.lastname: Gallina
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.|Integrative Oceanography Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Karsten
authors.initials: K
authors.lastname: Zengler
mesh_terms: D018533:Biomass; D017377:Diatoms / Q000235:genetics*; D016678:Genome; D008928:Mitochondria / Q000378:metabolism; D008954:Models, Biological; D018087:Plastids / Q000378:metabolism; D013347:Subcellular Fractions / Q000201:enzymology