Applications of metabolic modeling to drive bioprocess development for the production of value-added chemicals |
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Authors: | Radhakrishnan Mahadevan Anthony P Burgard Iman Famili Steve Van Dien Christophe H Schilling |
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Institution: | (1) Genomatica, Inc., 5405 Morehouse Drive, Suite 210, 92130 San Diego, CA, USA |
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Abstract: | Increasing numbers of value added chemicals are being produced using microbial fermentation strategies. Computational modeling
and simulation of microbial metabolism is rapidly becoming an enabling technology that is driving a new paradigm to accelerate
the bioprocess development cycle. In particular, constraint-based modeling and the development of genome-scale models of industrial
microbes are finding increasing utility across many phases of the bioprocess development workflow. Herein, we review and discuss
the requirements and trends in the industrial application of this technology as we build toward integrated computational/experimental
platforms for bioprocess engineering. Specifically we cover the following topics: (1) genome-scale models as genetically and
biochemically consistent representations of metabolic networks; (2) the ability of these models to predict, assess, and interpret
metabolic physiology and flux states of metabolism; (3) the model-guided integrative analysis of high throughput ‘omics’ data;
(4) the reconciliation and analysis of on- and off-line fermentation data as well as flux tracing data; (5) model-aided strain
design strategies and the integration of calculated biotransformation routes; and (6) control and optimization of the fermentation
processes. Collectively, constraint-based modeling strategies are impacting the iterative characterization of metabolic flux
states throughout the bioprocess development cycle, while also driving metabolic engineering strategies and fermentation optimization. |
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Keywords: | bioprocess development constraint-based modeling metabolic engineering SimPheny? |
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