Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

Autor: Andrew E. Allen, Karen Beeri, Graham Peers, Christopher L. Dupont, Karsten Zengler, Jennifer Levering, Jared T. Broddrick, Joshua Mayers, Bernhard O. Palsson, Alessandra A. Gallina
Přispěvatelé: Ianora, Adrianna
Rok vydání: 2016
Předmět:
0301 basic medicine
Chloroplasts
Metabolic network
lcsh:Medicine
Plant Science
Endoplasmic Reticulum
Biochemistry
Genome
Models
Metabolites
Plastids
Biomass
lcsh:Science
Energy-Producing Organelles
Secretory Pathway
Multidisciplinary
biology
Genomics
Genome project
Plants
Plankton
Lipids
Protein subcellular localization prediction
Mitochondria
Cell Processes
Cellular Structures and Organelles
Cellular Types
Network Analysis
Research Article
Subcellular Fractions
Computer and Information Sciences
Algae
General Science & Technology
Plant Cell Biology
Thalassiosira pseudonana
Bioenergetics
Models
Biological
Metabolic engineering
Metabolic Networks
03 medical and health sciences
Plant Cells
Genetics
Animals
Phaeodactylum tricornutum
Plastid
Diatoms
lcsh:R
Organisms
Biology and Life Sciences
Computational Biology
Cell Biology
Genome Analysis
biology.organism_classification
Biological
Invertebrates
Genome Annotation
Metabolism
030104 developmental biology
Phytoplankton
lcsh:Q
Zdroj: PloS one, vol 11, iss 5
PLoS ONE, Vol 11, Iss 5, p e0155038 (2016)
PLoS ONE
Popis: 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.
Databáze: OpenAIRE
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