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Title: Genome-scale model reveals metabolic basis of biomass partitioning in a model diatom

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.
ORCiD logo [1] ;  [2] ;  [3] ;  [4] ;  [3] ;  [5] ;  [1] ;  [6] ;  [1] ;  [1] ;  [7]
  1. Univ. of California San Diego, La Jolla, CA (United States). Dept. of Bioengineering
  2. Univ. of California San Diego, La Jolla, CA (United States). Div. of Biological Sciences; Dept. of Bioengineering
  3. J. Craig Venter Inst., La Jolla, CA (United States)
  4. Colorado State Univ., Fort Collins, CO (United States). Dept. of Biology
  5. Chalmers Univ. of Technology, Gothenburg (Sweden). Div. of Industrial Biotechnology, Dept. of Biology and Biotechnology
  6. Univ. of California San Diego, La Jolla, CA (United States). Integrative Oceanography Div., Scripps Inst. of Oceanography; J. Craig Venter Inst., La Jolla, CA (United States)
  7. Stazione Zoologicz Anton Dohrn, Naples (Italy)
Publication Date:
Grant/Contract Number:
SC0008593; SC0006719; DOE-DE-SC0006719
Published Article
Journal Name:
Additional Journal Information:
Journal Volume: 11; Journal Issue: 5; Journal ID: ISSN 1932-6203
Public Library of Science
Research Org:
Univ. of California, San Diego, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
59 BASIC BIOLOGICAL SCIENCES; phaeodactylum-tricornutum; functional-characterization; thalassiosira-pseudonana; biochemical-composition; extracellular-matrix; glycolytic pathway; signal peptides; marine diatoms; amino-acid; protein
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1282224