Reconstruction and analysis of central metabolism in microbes

Janaka N. Edirisinghe, José P. Faria, Nomi L. Harris, Benjamin H. Allen, Christopher S. Henry

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

2 Scopus citations

Abstract

Genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy due to the need for extensive gapfilling and the inference of periphery metabolic pathways based on lower-confidence annotations. The central carbon pathways and electron transport chains are among the most well-understood regions of microbial metabolism, and these pathways contribute significantly toward defining cellular behavior and growth conditions. Thus, it is often useful to construct a simplified core metabolic model (CMM) that is comprised of only the high-confidence central pathways. In this chapter, we discuss methods for producing core metabolic models (CMM) based on genome annotations. With its reduced scope compared to GEMs, CMM reconstruction focuses on accurate representation of the central metabolic pathways related to energy biosynthesis and accurate energy yield predictions. We demonstrate the reconstruction and analysis of CMMs using the DOE Systems Biology Knowledgebase (KBase). The complete workflow is available at http://kbase.us/core-models/.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages111-129
Number of pages19
DOIs
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1716
ISSN (Print)1064-3745

Keywords

  • Biochemical pathways
  • Central metabolism
  • Core metabolic models
  • Flux balance analysis
  • Metabolic model reconstruction
  • Model comparison

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