Use of genome-scale metabolic models for understanding microbial physiology
Journal article, 2010
The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their physiology. The availability of genome sequences and accumulation of high-throughput data allows gaining understanding of microbial physiology at the systems level, and genome-scale metabolic models represent a valuable framework for integrative analysis of metabolism of microorganisms. Genome-scale metabolic models are reconstructed based on a combination of genome sequence information and detailed biochemical information, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different stimuli. Here we discuss the requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals. We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into microbial physiology. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
escherichia-coli
Algorithm
transcriptional regulation
information-retrieval
Genome-scale metabolic model
Reconstruction
Microbial
flux-balance analysis
essential genes
yeast
intracellular environment
framework
amino-acids
optimization
physiology
cell-envelope
Author
Liming Liu
Chalmers, Chemical and Biological Engineering, Life Sciences
Rasmus Ågren
Chalmers, Chemical and Biological Engineering, Life Sciences
Sergio Velasco
Chalmers, Chemical and Biological Engineering, Life Sciences
Jens B Nielsen
Chalmers, Chemical and Biological Engineering, Life Sciences
FEBS Letters
0014-5793 (ISSN) 18733468 (eISSN)
Vol. 584 12 2556-2564Subject Categories
Industrial Biotechnology
Areas of Advance
Life Science Engineering (2010-2018)
DOI
10.1016/j.febslet.2010.04.052