Genome-scale modeling for metabolic engineering

Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii.

Ashbya gossypii is a filamentous fungus that naturally overproduces riboflavin, or vitamin B2. Advances in genetic and metabolic engineering of A. gossypii have permitted the switch from industrial chemical synthesis to the current biotechnological production of this vitamin. Additionally, A. gossypii is a model organism with one of the smallest eukaryote genomes being phylogenetically close to...

Metabolic modeling predicts endosymbiont genome reduction on a temporal scale

Metabolic modeling of endosymbiont genome reduction on a temporal scale

A fundamental challenge in Systems Biology is whether a cell-scale metabolic model can predict patterns of genome evolution by realistically accounting for associated biochemical constraints. Here, we study the order in which genes are lost in an in silico evolutionary process, leading from the metabolic network of Escherichia coli to that of the endosymbiont Buchnera aphidicola. We examine how...

Genome-scale metabolic networks.

During the last decade, models have been developed to characterize cellular metabolism at the level of an entire metabolic network. The main concept that underlies whole-network metabolic modeling is the identification and mathematical definition of constraints. Here, we review large-scale metabolic network modeling, in particular, stoichiometric- and constraint-based approaches. Although many ...

Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications

Background: A genome-scale metabolic network model (GEM) is a mathematical representation of an organism’s metabolism. Today, GEMs are popular tools for computationally simulating the biotechnological processes and for predicting biochemical properties of (engineered) strains.Objectives: In the present study, we have evaluated the predictive power of two ...