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Development of Constraint-Based System-Level Models of Microbial Metabolism

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Book cover Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 881))

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Abstract

Genome-scale models of metabolism are valuable tools for using genomic information to predict microbial phenotypes. System-level mathematical models of metabolic networks have been developed for a number of microbes and have been used to gain new insights into the biochemical conversions that occur within organisms and permit their survival and proliferation. Utilizing these models, computational biologists can (1) examine network structures, (2) predict metabolic capabilities and resolve unexplained experimental observations, (3) generate and test new hypotheses, (4) assess the nutritional requirements of the organism and approximate its environmental niche, (5) identify missing enzymatic functions in the annotated genome, and (6) engineer desired metabolic capabilities in model organisms. This chapter details the protocol for developing genome-scale models of metabolism in microbes as well as tips for accelerating the model building process.

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Acknowledgment

This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. This document was prepared as an account of work sponsored by an agency of the United States government. Neither the United States government nor Lawrence Livermore National Security, LLC, nor any of their employees makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States government or Lawrence Livermore National Security, LLC. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States government or Lawrence Livermore National Security, LLC, and shall not be used for advertising or product endorsement purposes. LLNL-BOOK-491430.

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  1. Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Ali Navid

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  1. Ali Navid
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  1. Physics & Life Sciences Directorate, Biosciences & Biotechnology Div., Lawrence Livermore National Laboratory, East Avenue 7000, Livermore, 94551, California, USA

    Ali Navid

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Navid, A. (2012). Development of Constraint-Based System-Level Models of Microbial Metabolism. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 881. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-827-6_18

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  • DOI: https://doi.org/10.1007/978-1-61779-827-6_18

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