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Levering2016 - Phaeodactylum tricornutum metabolic model

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.

SUBMITTER: Rodrigo Santibanez

PROVIDER: MODEL2204200002 | BioModels | 2023-03-10

REPOSITORIES: BioModels

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			Action	DRS
	MODEL2204200002?filename=01_objective.tsv	Tabular
	MODEL2204200002?filename=02_fva.tsv	Tabular
	MODEL2204200002?filename=03_gene_deletion.tsv	Tabular
	MODEL2204200002?filename=04_reaction_deletion.tsv	Tabular
	MODEL2204200002?filename=Phaeodactylum%20tricornutum.xml	Xml

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Project description:Rex2013 - Genome scale metabolic model of D.shibae (iDsh827) The aerobic anoxygenic phototroph Dinoroseobacter shibae DFL12T is a representative of an important group of marine bacteria called the Roseobacter clade. To gain insight into the versatile metabolism of this clade, the authors have taken a constraint-based approach and created this genome-scale metabolic model (iDsh827). This model is the first one to account for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. This model is described in the article: Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. Rex R, Bill N, Schmidt-Hohagen K, Schomburg D. PLoS Comput Biol. 2013;9(10):e1003224. Abstract: The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae. This model is hosted on BioModels Database and identified by: MODEL1308180000 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Levering2016 - Phaeodactylum tricornutum metabolic model

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