Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

TitleCharacterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.
Publication TypeJournal Article
Year of Publication2016
AuthorsBrunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HGarcia, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TSoon
JournalCell Syst
PubMed Date05/2016
ISSN2405-4712
Abstract

Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks.

Alternate JournalCell Syst
PubMed ID27211860
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