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Metabolic Network Reconstruction and Modeling pp 177–196Cite as

Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1716))

Abstract

Intraspecific genomic exchanges happen frequently between bacteria living in the same natural environment and can also be performed artificially in the laboratory for basic research or genetic/metabolic engineering purposes. In silico metabolic reconstruction and simulation of the metabolism of the hybrid strains that result from these processes can be used to predict the phenotypic outcome of such genomic rearrangements; this can be especially helpful as a designing tool in the purview of synthetic biology. However, reconstructing the metabolism of a bacterium with a hybrid genome through in silico approaches is not a trivial task, as it requires taking into account the complex relationships existing between metabolic genes and how they change (or remain unchanged) when new genes are placed in a different genomic context. Furthermore, in order to “mix” the metabolic models of different bacterial strains one needs at least two different metabolic models to begin with, and reconstructing a genome-scale model from the ground up is a challenging task itself, requiring an intensive manual effort and a great deal of information. In this chapter, we propose two general protocols to address the aforementioned issues of: (1) quickly generating strain-specific metabolic models, given the relevant genomic sequence and an already existing, high-quality metabolic model of a different strain belonging to the same species, and (2) reconstructing the metabolic model of a hybrid strain containing genomic elements from two different parental strains.

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Author information

Authors and Affiliations

  1. Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Florence, Italy

    Alessio Mengoni & Marco Fondi

  2. LENS, European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, Italy

    Tiziano Vignolini

Authors
  1. Tiziano Vignolini
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  2. Alessio Mengoni
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  3. Marco Fondi
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Corresponding author

Correspondence to Marco Fondi .

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Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

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Vignolini, T., Mengoni, A., Fondi, M. (2018). Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_8

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7527-3

  • Online ISBN: 978-1-4939-7528-0

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