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Systematic Applications of Metabolomics in Metabolic Engineering
School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
Institute for Bioengineering & Bioscience, Georgia Institute of Technology, 315 Ferst Dr. NW, Atlanta, GA 30332, USA
* Author to whom correspondence should be addressed.
Received: 1 November 2012; in revised form: 29 November 2012 / Accepted: 10 December 2012 / Published: 14 December 2012
Abstract: The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules) to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.
Keywords: metabolomics; metabolic engineering; mass spectrometry; metabolic flux; metabolic profiling; principal components analysis; partial least squares regression; flux balance analysis; constraint-based models; kinetic ODE models
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MDPI and ACS Style
Dromms, R.A.; Styczynski, M.P. Systematic Applications of Metabolomics in Metabolic Engineering. Metabolites 2012, 2, 1090-1122.
Dromms RA, Styczynski MP. Systematic Applications of Metabolomics in Metabolic Engineering. Metabolites. 2012; 2(4):1090-1122.
Dromms, Robert A.; Styczynski, Mark P. 2012. "Systematic Applications of Metabolomics in Metabolic Engineering." Metabolites 2, no. 4: 1090-1122.