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Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design

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Synthetic Metabolic Pathways

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1671))

Abstract

Engineering biological systems that are capable of overproducing products of interest is the ultimate goal of any biotechnology application. To this end, stoichiometric (or steady state) and kinetic models are increasingly becoming available for a variety of organisms including prokaryotes, eukaryotes, and microbial communities. This ever-accelerating pace of such model reconstructions has also spurred the development of optimization-based strain design techniques. This chapter highlights a number of such frameworks developed in recent years in order to generate testable hypotheses (in terms of genetic interventions), thus addressing the challenges in metabolic engineering. In particular, three major methods are covered in detail including two methods for designing strains (i.e., one stoichiometric model-based and the other by integrating kinetic information into a stoichiometric model) and one method for analyzing microbial communities.

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Acknowledgement

This work was supported by the University of Nebraska-Lincoln faculty start-up grant 21-1106-4308 to R.S.

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  1. Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA

    Mohammad Mazharul Islam & Rajib Saha

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  1. Mohammad Mazharul Islam
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  2. Rajib Saha
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Correspondence to Rajib Saha .

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  1. The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark

    Michael Krogh Jensen

  2. Joint BioEnergy Institute, Emeryville, California, USA

    Jay D. Keasling

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Islam, M.M., Saha, R. (2018). Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design. In: Jensen, M.K., Keasling, J.D. (eds) Synthetic Metabolic Pathways. Methods in Molecular Biology, vol 1671. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7295-1_5

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  • DOI: https://doi.org/10.1007/978-1-4939-7295-1_5

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