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A Practical Protocol for Genome-Scale Metabolic Reconstructions

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Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Genome-scale metabolic reconstructions (GEMREs) are organism-specific knowledge bases. Such reconstructions are developed systematically through the integration of genome annotation, omic data sets, and biological knowledge available for the target species at the time of reconstruction. They can be further transformed into computational models enabling the quantitative prediction of phenotypic states in terms of fluxes through individual reactions. In addition, they can be used as unique computational scaffolds towards the integration and mechanistic contextualization of omic data. As a result, GEMREs are attracting great interest, and the scope of their applications keeps growing. However, the key reconstruction process is time-consuming, and it is extremely sensitive to the adherence to accepted quality standards and protocols. Therefore, high-quality reconstruction protocols reducing the time and effort involved in the reconstruction are desirable. This chapter provides a step-by-step protocol for genome-scale metabolic reconstruction accessible to nonexperts in the field. The protocol was applied to reconstruct the metabolic network of the aromatic hydrocarbon-degrading bacterium Pseudomonas putida F1 using the reconstruction of the related strain Pseudomonas putida KT2440 as template. The final model was further used to compare, from a mechanistic point of view, some of the metabolic capabilities of these two interesting environmental bacteria.

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Acknowledgments

This work was supported by the SYNPOL (FP7-KBBE 311815; http://www.synpol.org/) UE project.

Author information

Authors and Affiliations

  1. Department of Environmental Biology, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain

    Juan Nogales

Authors
  1. Juan Nogales
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Corresponding author

Correspondence to Juan Nogales .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

Supplementary Information

Supplementary Information

Supplementary file 1. Metabolic reconstruction of P. putida KT2440 (iJN746) in xml format.

Accessible through https://www.dropbox.com/s/7u8robuq63ikknx/iJN746_flux.xml

Supplementary file 2. Metabolic reconstruction of P. putida F1 (iJN739) in xml format.

Accessible through https://www.dropbox.com/s/w987b4p3ge6v31u/iJN739.xml

Supplementary Table 1. Excel sheet including iJN739 in xls format, details and examples of the addition of reactions during the protocol and details for BOF formulation.

Accessible through https://www.dropbox.com/s/wrfma7c8hh7pfaa/TableS1.xls

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© 2014 Springer-Verlag Berlin Heidelberg

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Nogales, J. (2014). A Practical Protocol for Genome-Scale Metabolic Reconstructions. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2014_12

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  • DOI: https://doi.org/10.1007/8623_2014_12

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-50433-8

  • Online ISBN: 978-3-662-50435-2

  • eBook Packages: Springer Protocols

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