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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. Furthermore, 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:
ORCiD logo; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1337722
Alternate Identifier(s):
OSTI ID: 1282224
Grant/Contract Number:  
SC0008593; DOE-DE-SC0006719; SC0006719
Resource Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Name: PLoS ONE Journal Volume: 11 Journal Issue: 5; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science (PLoS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; phaeodactylum-tricornutum; functional-characterization; thalassiosira-pseudonana; biochemical-composition; extracellular-matrix; glycolytic pathway; signal peptides; marine diatoms; amino-acid; protein

Citation Formats

Levering, Jennifer, Broddrick, Jared, Dupont, Christopher L., Peers, Graham, Beeri, Karen, Mayers, Joshua, Gallina, Alessandra A., Allen, Andrew E., Palsson, Bernhard O., Zengler, Karsten, and Ianora, ed., Adrianna. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0155038.
Levering, Jennifer, Broddrick, Jared, Dupont, Christopher L., Peers, Graham, Beeri, Karen, Mayers, Joshua, Gallina, Alessandra A., Allen, Andrew E., Palsson, Bernhard O., Zengler, Karsten, & Ianora, ed., Adrianna. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. United States. doi:10.1371/journal.pone.0155038.
Levering, Jennifer, Broddrick, Jared, Dupont, Christopher L., Peers, Graham, Beeri, Karen, Mayers, Joshua, Gallina, Alessandra A., Allen, Andrew E., Palsson, Bernhard O., Zengler, Karsten, and Ianora, ed., Adrianna. Fri . "Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom". United States. doi:10.1371/journal.pone.0155038.
@article{osti_1337722,
title = {Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom},
author = {Levering, Jennifer and Broddrick, Jared and Dupont, Christopher L. and Peers, Graham and Beeri, Karen and Mayers, Joshua and Gallina, Alessandra A. and Allen, Andrew E. and Palsson, Bernhard O. and Zengler, Karsten and Ianora, ed., Adrianna},
abstractNote = {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. Furthermore, 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.},
doi = {10.1371/journal.pone.0155038},
journal = {PLoS ONE},
number = 5,
volume = 11,
place = {United States},
year = {2016},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1371/journal.pone.0155038

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Cited by: 15 works
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