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Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective

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  • Graham Rockwell
  • Nicholas J Guido
  • George M Church

Abstract

Advances in computational metabolic optimization are required to realize the full potential of new in vivo metabolic engineering technologies by bridging the gap between computational design and strain development. We present Redirector, a new Flux Balance Analysis-based framework for identifying engineering targets to optimize metabolite production in complex pathways. Previous optimization frameworks have modeled metabolic alterations as directly controlling fluxes by setting particular flux bounds. Redirector develops a more biologically relevant approach, modeling metabolic alterations as changes in the balance of metabolic objectives in the system. This framework iteratively selects enzyme targets, adds the associated reaction fluxes to the metabolic objective, thereby incentivizing flux towards the production of a metabolite of interest. These adjustments to the objective act in competition with cellular growth and represent up-regulation and down-regulation of enzyme mediated reactions. Using the iAF1260 E. coli metabolic network model for optimization of fatty acid production as a test case, Redirector generates designs with as many as 39 simultaneous and 111 unique engineering targets. These designs discover proven in vivo targets, novel supporting pathways and relevant interdependencies, many of which cannot be predicted by other methods. Redirector is available as open and free software, scalable to computational resources, and powerful enough to find all known enzyme targets for fatty acid production. Author Summary: A deeper understanding of biological processes, along with methods in synthetic biology, is driving the frontier of metabolic engineering. In particular, a better representation of cell metabolism will enable the engineering of bacterial strains that can act as factories for valuable biochemical products, from medicines to biofuels. Models which predict the behavior of these complex biological systems enable better engineering design as well as a more comprehensive understanding of fundamental biological principles. Here we develop a new method, called Redirector, for modeling metabolic alterations, and their relationship to cell growth. This method optimizes genetic engineering changes to achieve metabolite production using a new representation of the metabolic impact of genetic manipulation, which is more biologically realistic than existing models. We discover proven and novel engineering targets to improve fatty acid production, correctly predicting how different combinations of genes build upon one another. This work demonstrates that Redirector is a powerful method for designing cell factories and improving our understanding of metabolic systems.

Suggested Citation

  • Graham Rockwell & Nicholas J Guido & George M Church, 2013. "Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective," PLOS Computational Biology, Public Library of Science, vol. 9(1), pages 1-15, January.
    • Handle: RePEc:plo:pcbi00:1002882
    DOI: 10.1371/journal.pcbi.1002882
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    References listed on IDEAS

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    5. Nicholas J. Guido & Xiao Wang & David Adalsteinsson & David McMillen & Jeff Hasty & Charles R. Cantor & Timothy C. Elston & J. J. Collins, 2006. "A bottom-up approach to gene regulation," Nature, Nature, vol. 439(7078), pages 856-860, February.
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    1. Andrea Patané & Giorgio Jansen & Piero Conca & Giovanni Carapezza & Jole Costanza & Giuseppe Nicosia, 2019. "Multi-objective optimization of genome-scale metabolic models: the case of ethanol production," Annals of Operations Research, Springer, vol. 276(1), pages 211-227, May.

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