Rex2013 - Genome scale metabolic model of D.shibae (iDsh827)

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.

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