In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.
There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.
Department of Chemical Engineering and Applied Chemistry, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada. krishna.mahadevan@utoronto.ca
Radhakrishnan
R
Mahadevan
Bernhard Ø
BØ
Palsson
Derek R
DR
Lovley
D003198:Computer Simulation; D004777:Environment; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D016680:Genome, Bacterial; D045302:Geobacter / Q000235:genetics* / Q000378:metabolism*; D008954:Models, Biological